Abstract
Agrobiodiversity is the variety and variability of animals, plants and microorganisms that are used directly or indirectly for food and agriculture, including crops, livestock, forestry and fisheries. It also includes the diversity of non-harvested species that support production (soil microorganisms, predators, pollinators) and those in the wider environment that support agroecosystems. Now, the agrobiodiversity is threatened by changing patterns of land use (urbanization, deforestation), agricultural modernization (monocultures and abandoning of traditional, biodiversity-based practices), westernization of diets and their supply chains. After analysing the target species, strategies adopted to conserve and promote agrobiodiversity are in situ and ex situ conservation along with habitat conservation, management and promotion of agrobiodiversity through sustainable uses. Recently, molecular techniques are facilitating the identification and evaluation of interspecific diversity and evolutionary history, restoration of potential species which may be vulnerable in the near future and conservation of closely related species for the possibility of exploring useful bioactive molecules present in them. These molecular approaches include both non-PCR- and PCR-based techniques. PCR-based techniques have been widely applied in conservation and restoration of agrobiodiversity through molecular characterization, assessing genetic diversity, DNA barcoding, phylogenetics, QTL mapping, MAS, genome sequencing, pangenome construction, etc. Besides these, target genes were discovered for quantitative traits using association mapping and genome-wide prediction studies. Different biotechnological tools have also been employed for genomic manipulation through important gene cloning and genetic modification and genome editing tools in important crop germplasm to conserve, manage and restore from wild population to avoid its depletion. These DNA technologies can be a viable option to develop genetically modified crops with enhanced resistance and improved yields to fight against climate change, droughts and chronic food shortages. National Plant Germplasm System (NPGS) and GenBank repositories are developed to maintain agricultural biodiversity and ensure the preservation of the genetic resources and reduce the genetic vulnerability. Thus, a wide array of DNA approaches available may be used to exploit and harness the diversity in wild crop resource of agriculture for achieving higher genetic gains for food and nutritional security.
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References
Abdel-Haleem H, Carter TE, Purcell LC et al (2012) Mapping of quantitative trait loci for canopy-wilting trait in soybean (Glycine max L. Merr). Theor Appl Genet 125(5):837–846
Abdel-Haleem H, Carter TE, Rufty TW et al (2014) Quantitative trait loci controlling aluminum tolerance in soybean: candidate gene and single nucleotide polymorphism marker discovery. Mol Breed 33(4):851–862
Abdurakhmonov IY, Kohel RJ, Yu JZ et al (2008) Molecular diversity and association mapping of fiber quality traits in exotic Gossypium herbaceum L. germplasm. Genomics 92(6):478–487
Achleitner A, Tinker N, Zechner E et al (2008) Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits. Theor Appl Genet 117(7):1041–1053
Acquadro A, Portis E, Albertini E et al (2005) M-AFLP-based protocol for microsatellite loci isolation in Cynara cardunculus L. (Asteraceae). Mol Ecol Notes 5:272–274
Agrama HA, Moussa ME (1996) Mapping QTLs in breeding for drought tolerance in maize (Zea mays L.). Euphytica 91:89–97
Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341–356
Ajibade SR, Weeden NF, Chite SM (2000) Inter-simple sequence repeat analysis of genetic relationships in the genus Vigna. Euphytica 111:47–55
Albertini E, Porceddu A, Marconi G et al (2003) Microsatellite-AFLP for genetic mapping of complex polyploids. Genomics 46:824–832
Al-Dous EK, George B, Al-Mahmoud ME et al (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29(6):521–527
Amar MH, Biswas MK, Zhang Z et al (2011) Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of citrus germplasm collection. Sci Hortic 128:220–227
Anand D, Prabhu KV, Singh AK (2012) Analysis of molecular diversity and fingerprinting of commercially grown Indian rice hybrids. J Plant Biochem Biotechnol 21:173–179
Andersson M, Turesson H, Nicolia A et al (2017) Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Rep 36:117–128
Anzalone AV, Randolph PB, Davis JR et al (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576(7785):149–157
Aranzana MJ, Kim S, Zhao K et al (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1(5):e60
Arens P, Odinot P, Van Heusden AW et al (1995) GATA and GACA repeats are not evenly distributed throughout the tomato genome. Genomics 38:84–90
Argout X, Salse J, Aury JM et al (2011) The genome of Theobroma cacao. Nat Genet 43(2):101–108
Arora RK, Nayar ER (1984) Wild relatives of crop plants in India. NBPGR Sci Mongr 9:90
Arora RK, Mehra KL, Hardas MW (1975) The Indian gene centre: prospects for exploration and collection of herbage grasses. Forage Res 1(1):11–22
Asad MA, Bai B, Lan C et al (2014) Identification of QTL for adult-plant resistance to powdery mildew in Chinese wheat landrace Pingyuan 50. Crop J 2:308–314
Ashikari M, Sakakibara H, Lin S et al (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745
Ashkenazi V, Chani E, Lavi U et al (2001) Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genomics 44:50–62
Asoro FG, Newell MA, Beavis WD et al (2013) Genomic, marker-assisted, and pedigree-blup selection methods for b-glucan concentration in elite oat. Crop Sci 53:1894–1906
Awad M, Fahmy RM, Mosa KA et al (2017) Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Comput Biol Chem 71:20–31
Badji A, Otim M, Machida L et al (2018) Maize combined insect resistance genomic regions and their co-localization with cell wall constituents revealed by tissue-specific QTL meta-analyses. Front Plant Sci 9:895
Bao JS, Corke H, Sun M (2006) Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theor Appl Genet 113(7):1185–1196
Bar-Hen A, Charcosset A, Bourgoin M et al (1995) Relationship between genetic-markers and morphological traits in a maize inbred line collection. Euphytica 84:145–154
Barrero JM, Cavanagh C, Verbyla KL et al (2015) Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL. Genome Biol 16:93
Becher SA, Steinmetz K, Weising K et al (2000) Microsatellites for cultivar identification in pelargonium. Theor Appl Genet 101:643–651
Beckman JS, Soller M (1990) Toward a unified approach to gene mapping of eukaryotes based on sequence tagged microsatellite sites. Bio/Technology 8:930–932
Beer SC, Siripoonwiwat W, O’donoughue LS et al (1997) Associations between molecular markers and quantitative traits in an oat germplasm pool: can we infer linkages? J Agric Genom 3:1–16
Bennetzen JL, Schmutz J, Wang H et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6):555–561
Bernardo R, Yu J (2007) Prospects for genome-wide selection for quantitative traits in maize. Crop Sci 47:1082–1090
Bertier LD, Ron M, Huo H et al (2018) High-resolution analysis of the efficiency, heritability, and editing outcomes of CRISPR-Cas9 induced modifications of NCED4 in lettuce (Lactuca sativa). G3 8:1513–1521
Bharat SS, Li S, Li J et al (2020) Base editing in plants: current status and challenges. Crop J 8:384–395
Bhatia D, Wing RA, Yu Y et al (2018) Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. Euphytica 214:41
Biswas MK, Xu Q, Deng XX (2011) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci Hortic 124:254–261
Bonneau J, Taylor J, Parent B et al (2013) Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat. Theor Appl Genet 126:747–761
Botwright Acuña TL, Rebetzke GJ, He X et al (2014) Mapping quantitative trait loci associated with root penetration ability of wheat in contrasting environments. Mol Breed 34(2):631–642
Bouchez A, Causse M, Gallais A et al (2002) Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics 162(4):1945–1959
Bredemeijer GMM, Arens P, Wouters D et al (1998) The use of semi-automated fluorescent microsatellite analysis for tomato cultivar identification. Theor Appl Genet 97:584–590
Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
Brozynska M, Furtado A, Henry RJ (2014) Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding. PLoS One 9:e110387
Bryan GJ, Collins AJ, Stephenson P et al (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94:557–563
Budak H, Shearman RC, Parmaksiz I et al (2004) Comparative analysis of seeded and vegetative biotype buffalo grasses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs. Theor Appl Genet 109:280–288
Burton AL, Johnson JM, Foerster JM et al (2014) QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.). Theor Appl Genet 127:2293–2311
Busti A, Caceres ME, Calderini O et al (2004) RFLP markers for cultivars identification in tall fescue (Festuca arundinacea Schreb.) Genet. Resour Crop Evol 51:443–448
Caceres ME, Pupilli F, Piano E et al (2000) RFLP markers are an effective tool for the identification of creeping bentgrass (Agrostis stolonifera L.) cultivars. Genet Resour Crop Evol 47:455–459
Caetano-Anollis G (1994) MAAP - a versatile and universal tool for genome analysis. Plant Mol Biol 25:1011–1026
Caetano-Anollis G, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology 9:553–557
Cai Y, Chen L, Liu X et al (2018) CRISPR/Cas9-mediated targeted mutagenesis of GmFT2a delays flowering time in soybean. Plant Biotechnol J 16:176–185
Cannarozzi G, Plaza-Wuthrich S, Esfeld K et al (2014) Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 15(1):581–600
Cantos C, Francisco P, Trijatmiko KR et al (2014) Identification of “safe harbor” loci in indica rice genome by harnessing the property of zinc finger nucleases to induce DNA damage and repair. Front Plant Sci 5:302
Caramante M, Corrado G, Monti LM et al (2011) Simple sequence repeats are able to trace tomato cultivars in tomato food chains. Food Control 22:549–554
Cerrudo D, Cao S, Yuan Y et al (2018) Genomic selection outperforms marker assisted selection for grain yield and physiological traits in a maize doubled haploid population across water treatments. Front Plant Sci 9:366
Chaib J, Lecomte L, Buret M et al (2006) Stabilityover genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato. Theor Appl Genet 112:934–944
Chalhoub B, Denoeud F, Liu S et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345(6199):950–953
Chan AP, Crabtree J, Zhao Q et al (2010) Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 28(9):951–956
Chankaew S, Isemura T, Naito K et al (2014) QTL mapping for salt tolerance and domestication-related traits in Vigna marina subspp. oblonga, a halophytic species. Theor Appl Genet 127(3):691–702
Charters YM, Wilkinson MJ (2000) The use of self-pollinated progenies as ‘in-groups’ for the genetic characterization of cocoa germplasm. Theor Appl Genet 100:160–166
Charters YM, Robertson A, Wilkinson MJ et al (1996) PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5’-anchored simple sequence repeat (SSR) primers. Theor Appl Genet 92:442–447
Chaudhary J, Deshmukh R, Sonah H (2019) Mutagenesis approaches and their role in crop improvement. Plants 8(11):467
Cheema KK, Navtej SB, Mangat GS et al (2008) Development of high yielding IR64 × Oryza rufipogon (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers. Euphytica 160:401–409
Chen H, Wang S, Zhang Q (2002) New gene for bacterial blight resistance in rice located on chromosome 12 identified from Minghui 63, an elite restorer line. Phytopathology 92(7):750–754
Chen HM, Liu CA, Kuo CG et al (2007) Development of a molecular marker for a bruchid (Callosobruchus chinensis L.) resistance gene in mung bean. Euphytica 157(1–2):113–122
Chen S, Yao H, Han J et al (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5:e8613
Chen Z, Wang B, Dong XL et al (2014) An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population. BMC Genomics 15(1):433
Chen X, Lu X, Shu N et al (2017) Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system. Sci Rep 7(1):44304
Chwedorzewska KJ, Bednarek PT, Puchalski J (2002) Studies on changes in specific rye genome regions due to seed aging and regeneration. Cell Mol Biol Lett 7:569–576
Cobos MJ, Winter P, Kharrat M et al (2009) Genetic analysis of agronomic traits in a wide cross of chick pea. Field Crop Res 111(1-2):130–136
Collard BCY, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27:86–93
Concibido VC, La Vallee B, Mclaird P et al (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106:575–582
Convention on Biological Diversity (1992). https://www.cbd.int/doc/legal/cbd-en.pdf
Cretazzo E, Meneghetti S, De Andre’s MT et al (2010) Clone differentiation and varietal identification by means of SSR, AFLP, SAMPL and M-AFLP in order to assess the clonal selection of grapevine: the case study of Manto Negro, Callet and Moll, autochthonous cultivars of Majorca. Ann Appl Biol 157:213–227
Crossa J, Pérez-Rodríguez P, Cuevas J et al (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22:961–975
D’Hont A, Denoeud F, Aury JM et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217
Demirsoy L, Demir T, Demirsoy H et al (2008) Identification of some sweet cherry cultivars grown in Amasya by RAPD markers. Acta Hortic 795:147–152
Denoeud F, Carretero-Paulet L, Dereeper A et al (2014) The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345(6201):1181–1184
Deokar A, Sagi M, Daba K et al (2019) QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea. Plant Biotechnol J 17:275–288
Descalsota GIL, Swamy BPM, Zaw H et al (2018) Genome-wide association mapping in a rice MAGIC plus population detects QTL and genes useful for biofortification. Front Plant Sci 9:1347
Desta ZA, Ortiz R (2014) Genomic selection: genome-wide prediction in plant improvement. Trends Plant Sci 19:592–601
Dje Y, Tahi GC, Zoro BIA et al (2006) Optimization of ISSR marker for African edible-seeded cucurbitaceae species genetic diversity analysis. Afr J Biotechnol 5:83–87
Dje Y, Tahi CG, Zoro BI et al (2010) Use of ISSR markers to assess genetic diversity of African edible seeded Citrullus lanatus landraces. Sci Hortic 124:159–164
Djukanovic V, Smith J, Lowe K et al (2013) Male-sterile maize plants produced by targeted mutagenesis of the cytochrome P450-like gene (MS26) using a re-designed I-CreI homing endonuclease. Plant J 76:888–899
Dohm JC, Minoche AE, Holtgrawe D et al (2014) The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505(7484):546–549
Dong QH, Cao X, Guang Y et al (2010) Discovery and characterization of SNPs in Vitis vinifera and genetic assessment of some grapevine cultivars. Sci Hortic 125:233–238
Dong W, Liu J, Yu J et al (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 7:e35071
Du X, Liu S, Sun J et al (2018) Dissection of complicate genetic architecture and breeding perspective of cotton seed traits by genome-wide association study. BMC Genomics 19:451
Dubreuil P, Warburton ML, Chastanet M et al (2006) More on the introduction of temperate maize into Europe: large-scale bulk SSR genotyping and new historical elements. Maydica 51:281–291
Dussle C, Quint M, Xu M et al (2002) Conversion of AFLP fragments tightly linked to SCMV resistance genes Scmv1 and Scmv2 into simple PCR-based markers. Theor Appl Genet 105(8):1190–1205
Ersoz ES, Yu J, Buckler ES (2007) Applications of linkage disequilibrium and association mapping in crop plants. In: Genomics-assisted crop improvement. Springer, pp 97–119
Eyzaguirre P, Linares OF (2004) Home gardens and agrobiodiversity. Smithsonian Books, Washington, DC
Fang J, Zhu X, Wang C et al (2016) Applications of DNA technologies in agriculture. Curr Genom 17:379–386
FAO (1996) Report on the state of the World’s plant genetic resources for food and agriculture, prepared for the international technical conference on plant genetic resources, Leipzig, Germany, 17-23 June 1996. FAO, Rome
FAO (1997) The state of the world’s plant genetic resources for food and agriculture. FAO, Rome. www.fao.org/ag/AGP/AGPS/PGRFA/pdf/swrfull.pdf
FAO (1999a) Agricultural biodiversity. In: Multifunctional Character of Agriculture and Land Conference, Background Paper 1. Maastricht, Netherlands. FAO, Rome
FAO (1999b) Women: users, preservers and managers of agrobiodiversity. FAO, Rome. www.fao.org/FOCUS/E/Women/Biodiv-e.htm
FAO (2002) Gene flow from GM to non-GM populations in the crop, forestry, animal and fishery sectors. In: Background Document to Conference 7 of the FAO Biotechnology Forum (31 May to 5 July 2002). FAO, Rome. www.fao.org/biotech/C7doc.htm
FAO (2006) Status the role of biotechnology in exploring and protecting agricultural genetic resources by John Ruane and Andrea Sonnino. Italy, Rome. http://www.fao.org/3/a0399e/A0399E00.htm
Ferreira ME (2005) Molecular analysis of gene banks for sustainable conservation and increased use of crop genetic resources. In: Ruane J, Sonnino A (eds) The role of biotechnology in exploring and protecting agricultural genetic resources. FAO, Rome
Fister AS, Landherr L, Maximova SN et al (2018) Transient expression of CRISPR/cas9 machinery targeting TCNPR3 enhances defense response in Theobroma cacao. Front Plant Sci 9:268
Flavell AJ, Knox MR, Pearce SR et al (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–650
Francia E, Barabaschi D, Tondelli A et al (2007) Fine mapping of a HvCBF gene cluster at the frost resistance locus Fr-H2 in barley. Theor Appl Genet 115:1083–1091
Frary A, Nesbitt TC, Frary A et al (2000) fw22: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88
Fukuoka S, Okuno K (2001) QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice. Theor Appl Genet 103:185–190
Gadaleta A, Giancaspro A, Blechl AE et al (2008) A transgenic durum wheat line that is free of marker genes and expresses 1DY10. J Cereal Sci 48:439–445
Gao R, Feyissa BA, Croft M et al (2018) Gene editing by CRISPR/Cas9 in the obligatory outcrossing Medicago sativa. Planta 247:1043–1050
Gao J, Wang S, Zhou Z et al (2019) Linkage mapping and GWAS reveal candidate genes conferring thermotolerance of seed-set in maize. J Exp Bot 70:4849–4864
George MLC, Prasanna BM, Rathore RS et al (2003) Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor Appl Genet 107:544–551
Ghareyazie B, Huang N, Second G et al (1995) Classification of rice germplasm, I Analysis using ALP and PCR-based RFLP. Theor Appl Genet 91:218–227
Gidoni D, Rom M, Kunik T et al (2006) Strawberry cultivar identification using randomly amplified polymorphic DNA (RAPD) markers. Plant Breed 113(4):339–342
Gilbert JE, Lewis RV, Wilkinson MJ et al (1999) Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theor Appl Genet 98:1125–1131
Goff SA, Ricke D, Lan T et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296(5565):92–100
Golicz AA, Bayer PE, Barker GC et al (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390
Gomez SM, Boopathi NM, Kumar SS et al (2010) Molecular mapping and location of QTLs for drought-resistance traits in indica rice (Oryza sativa L.) lines adapted to target environments. Acta Physiol Plant 32:355–364
Gonzalez VM, Benjak A, Henaff EM et al (2010) Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy. BMC Plant Biol 10(1):246
Gordon SP, Contreras-Moreira B, Woods DP et al (2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat Commun 8:2184
Grenier C, Cao TV, Ospina Y et al (2015) Accuracy of genomic selection in a rice synthetic population developed for recurrent selection breeding. PLoS One 10:e0136594
Groombridge B (1992) Global biodiversity: status of the Earth’s living resources. A report compiled by the world conservation monitoring Centre. Chapman and Hall, London
Guo YP, Saukel J, Mittermayr R et al (2005) AFLP analyses demonstrate genetic divergence, hybridization, and multiple polyploidization in the evolution of Achillea (Asteraceae-Anthemideae). New Phytol 166:273–289
Guo S, Zhang J, Sun H et al (2013a) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45(1):51–58
Guo Z, Tucker DM, Wang D et al (2013b) Accuracy of across-environment genome-wide prediction in maize nested association mapping populations. G3 3:263–272
Gupta M, Chyi YS, Romero-Severson JR et al (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple sequence repeats. Theor Appl Genet 89:998–1006
Gupta PK, Langridge P, Mir RR (2010) Marker-assisted wheat breeding: present status and future possibilities. Mol Breed 26(2):145–161
Gupta PK, Kulwal PL, Jaiswal V (2014) Association mapping in crop plants: opportunities and challenges. Adv Genet 85:110–139
Ha BK, Vuong TD, Velusamy V et al (2013) Genetic mapping of quantitative trait loci conditioning salt tolerance in wild soybean (Glycine soja) PI 483463. Euphytica 193(1):79–88
Hamwieh A, Imtiaz M, Malhotra RS (2013) Multi-environment QTL analyses for drought-related traits in a recombinant inbred population of chickpea (Cicer arietinum L.). Theor Appl Genet 126(4):1025–1038
Han L, Chen J, Mace ES et al (2015) Fine mapping of qGW1, a major QTL for grain weight in sorghum. Theor Appl Genet 128:1813–1821
Harjes CE, Rocheford TR, Bai L et al (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330–333
Hasan MM, Rafii MY, Ismail MR et al (2015) Marker-assisted backcrossing: a useful method for rice improvement. Biotechnol Biotechnol Equip 29(2):237–254
Haun W, Coffman A, Clasen BM et al (2014) Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnol J 12:934–940
Haverkort AJ, Struik PC, Visser RGF et al (2009) Applied biotechnology to combat late blight in potato caused by Phytophthora infestans. Potato Res 52:249–264
Hayashi K (1992) PCR-SSCP: a method for detection of mutations. Genet Anal Tech Appl 9:73–79
He Y, Wu D, Wei D et al (2017) GWAS, QTL mapping and gene expression analyses in Brassica napus reveal genetic control of branching morphogenesis. Sci Rep 7:15971
Heath DD, Iwama GK, Devlin RH (1993) PCR primed with VNTR core sequences yields species specific patterns and hypervariable probes. Nucleic Acids Res 21:5782–5785
Herrmann D, Barre P, Santoni S et al (2010) Association of a CONSTANS-LIKE gene to flowering and height in autotetraploid alfalfa. Theor Appl Genet 121:865–876
Hess GT, Tycko J, Yao D et al (2017) Methods and applications of CRISPR-mediated base editing in eukaryotic genomes. Mol Cell 68:26–43
Heywood VH (1995) Global biodiversity assessment. UNEP. Cambridge University Press, Cambridge
Hirakawa H, Shirasawa K, Miyatake K et al (2014) Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res 21(6):649–660
Hirsch CN, Foerster JM, Johnson JM et al (2014) Insights into the maize pan-genome and pantranscriptome. Plant Cell 26:121–135
Hossain F, Muthusamy V, Pandey N et al (2018) Marker-assisted introgression of opaque2 allele for rapid conversion of elite hybrids into quality protein maize. J Genet 97(1):287–298
Hou S et al (2018) Genome-wide association studies reveal genetic variation and candidate genes of drought stress-related traits in cotton (Gossypium hirsutum L). Front Plant Sci 9:1276
Hu Y, Wang L, Xie X et al (2010) Genetic diversity of wild populations of Rheum tanguticum endemic to China as revealed by ISSR analysis. Biochem Syst Ecol 38:264–274
Hua K, Tao X, Zhu JK (2019) Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnol J 17:499–504
Huang XQ, Coster H, Ganal MW et al (2003) Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor Appl Genet 106:1379–1389
Huang S, Li R, Zhang Z et al (2009a) The genome of the cucumber, Cucumis sativus L. Nat Genet 41(12):1275–1281
Huang X, Feng Q, Qian Q et al (2009b) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076
Huang X, Wei X, Sang T et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967
Hurgobin B, Edwards D (2017) SNP discovery using a pangenome: has the single reference approach become obsolete? Biology 6:21
Hurgobin B, Golicz AA, Bayer PE et al (2018) Homeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnol J 16:1265–1271
Hyeong JJ, Walid F, Wilfre DV et al (2012) RNAi suppression of lignin biosynthesis in sugarcane reduces recalcitrance for biofuel production from lignocellulosic biomass. Plant Biotechnol J 10:1067–1076
Ibrahim IK, Zhang L, Niyitanga S et al (2020) Principles and approaches of association mapping in plant breeding. Trop Plant Biol 13:212–224
Iglesias-Garcia R, Prats E, Fondevilla S et al (2015) Quantitative trait loci associated to drought adaptation in pea (Pisum sativum L.). Plant Mol Biol Rep 33(6):1768–1778
Ito Y, Nishizawa-Yokoi A, Endo M et al (2015) CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem Biophys Res Commun 467:76–82
Jacobsen SE (2012) What is wrong with the sustainability of Quinoa production in Southern Bolivia - a reply to Winkel et al. (2012). J Agron Crop Sci 198:320–323
Jaganathan D, Ramasamy K, Sellamuthu G et al (2018) CRISPR for crop improvement: an update review. Front Plant Sci 9:985
Jaganathan D, Bohra A, Thudi M et al (2020) Fine mapping and gene cloning in the post-NGS era: advances and prospects. Theor Appl Genet 133:1791–1810
Janga MR, Campbell LM, Rathore KS (2017) CRISPR/Cas9-mediated targeted mutagenesis in upland cotton (Gossypium hirsutum L.). Plant Mol Biol 94:349–360
Jankowicz-Cieslak J, Tai TH et al (2017) Biotechnologies for plant mutation breeding. Springer International Publishing, Cham, p 340. ISBN 978-3-319-45021-6
Jannati M, Fotouhi R, Pourjan A et al (2009) Genetic diversity analysis of Iranian citrus varieties using microsatellite (SSR) based markers. J Hortic For 1:120–125
Jarvis DI, Hodgkin T (2008) The maintenance of crop genetic diversity on farm: supporting the convention on biological diversity’s programme of work on agricultural biodiversity. Biodiversity 9:23–38
Jeong N, Suh SJ, Kim MH et al (2012) Ln is a key regulator of leaflet shape and number of seeds per pod in soybean. Plant Cell 24:4807–4818
Jia H, Wang N (2014) Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One 9:e93806
Jia G, Huang X, Zhi H et al (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961
Jiang GL (2013) Molecular markers and marker-assisted breeding in plants. Plant Breed Lab Fields 22:45–83
Jiang D, Ye QL, Wang FS et al (2010) The mining of citrus EST-SNP and its application in cultivar discrimination. Agric Sci China 9:179–190
Johnson RC (2008) Gene banks pay big dividends to agriculture, the environment, and human welfare. PLoS Biol 6(6):e148
Jones RB, Rakotoarisaona JJ (2007) Supporting the development of sustainable seed systems for non-hybrid crops. Acta Hortic 752:77–82
Jones ES, Dupal MP, Kolliker R et al (2001) Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405–415
Joshi BK, Shrestha BB (2017) Notes on plant and crop classification. In: Joshi BK, Kc HB, Acharya AK (eds) Proceedings of 2nd National Workshop: Conservation and Utilization of Agricultural Plant Genetic Resources in Nepal., 22-23 May 2017, Dhulikhel. NAGRC, FDD, DoA and MoAD, Kathmandu, pp 17–20
Joshi SP, Gupta VS, Aggarwal RK et al (2000) Genetic diversity and phylogenetic relationship as revealed by inter-simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100:1311–1320
Joshi BK, Ghimire KH, Gauchan D et al (2017) Agrobiodiversity: conservation strategies, methods and action plans. In: Joshi BK, Gauchan D (eds) Rebuilding Local Seed System of Native Crops in Earthquake Affected Areas of Nepa. Proceedings of a National Sharingshop 18 Dec 2017, Kathmandu, Nepal. ISBN: 9789937034289
Joshi BK, Gauchan D, Bhandari B et al (2020) Good practices for agrobiodiversity management. NAGRC, LI-BIRD and Bioversity International, Kathmandu
Juarez MJA, Ramirez-Malagon R, Gil-Vega KC et al (2009) AFLP analysis of genetic variability in three reproductive forms of Agave tequilana. Rev Fitotec Mex 32:171–175
Kagalem S, Koh C, Nixon J et al (2014) The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure. Nat Commun 5:3706
Kalendar R, Grob T, Regina M et al (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711
Kang YJ, Kim SK, Kim MY et al (2014) Genome sequence of mung bean and insights into evolution within Vigna species. Nat Commun 5:5443
Kang BC, Yun JY, Kim ST et al (2018) Precision genome engineering through adenine base editing in plants. Nat Plant 4:427–431
Kantety RV, Zeng XP, Bennetzen JL et al (1995) Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification. Mol Breed 1:365–373
Kantor A, McClements ME, MacLaren RE (2020) CRISPR-Cas9 DNA base-editing and prime-editing. Int J Mol Sci 21(17):6240
Kapusi E, Corcuera-Gomez M, Melnik S et al (2017) Heritable genomic fragment deletions and small indels in the putative engase gene induced by CRISPR/Cas9 in barley. Front Plant Sci 8:540
Karaagac E, Yilma S, Cuesta-Marcos A et al (2014) Molecular analysis of potatoes from the pacific Northwest Tri-State cultivar development program and selection of markers for practical DNA fingerprinting applications. Am J Cardiol 91:195–203
Kaur N, Alok A, Kaur SN et al (2018) CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Rasthali genome. Funct Integr Genom 18:89–99
Keller B, Manzanares C, Jara C et al (2015) Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.). Theor Appl Genet 128:813–826
Kim S, Park M, Yeom SI et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46(3):270–278
Kim D, Alptekin B, Budak H (2018) CRISPR/Cas9 genome editing in wheat. Funct Integr Genom 18:31–41
Klap C, Yeshayahou E, Bolger AM et al (2017) Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function. Plant Biotecnol J 15:634–647
Klein A, Houtin H, Rond C et al (2014) QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance. Theor Appl Genet 127(6):1319–1330
Klimek-Chodacka M, Oleszkiewicz T, Lowder LG et al (2018) Efficient CRISPR/Cas9-based genome editing in carrot cells. Plant Cell Rep 37:575–586
Kolliker R, Jones ES, Jahufer MZZ et al (2001) Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.). Euphytica 121:305–315
Korir NK, Han J, Shangguan L et al (2012) Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 33(2):111–125
Kraakman ATW, Martinez F, Mussiraliev B et al (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed 17:41–58
Krishnan NM, Pattnaik S, Jain P et al (2012) A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. BMC Genomics 13(1):464
Kulwal P, Kumar N, Gaur A et al (2005) Mapping of a major QTL for pre-harvest sprouting tolerance on chromosome 3A in bread wheat. Theor Appl Genet 111:1052–1059
Kumar A, Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci 6:127–134
Kumawat S, Rana N, Bansal R et al (2019) Expanding avenue of fast neutron mediated mutagenesis for crop improvement. Plants 8(6):164
Kump KL, Bradbury PJ, Wisser RJ et al (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168
Kunert A, Naz AA, Dedeck O et al (2007) AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (Triticum turgidum ssp. dicoccoides × T. tauschii) as a source of favourable alleles for milling and baking quality traits. Theor Appl Genet 115:683–695
Kunihisa M, Fukino N, Matsumoto S (2005) CAPS markers improved by cluster-specific amplification for identification of octoploid strawberry (Fragaria × ananassa Duch.) cultivars, and their disomic inheritance. Theor Appl Genet 110:1410–1418
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461
Li JZ, Huang XQ, Heinrichs F et al (2006) Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley. Genomics 49:454–466
Li YY, Shen JX, Wang TH et al (2007) Construction of a linkage map using SRAP, SSR and AFLP markers in Brassica napus L. Sci Agric Sin 40:1118–1126
Li Q, Liu QC, Zhai H et al (2008a) Genetic diversity in main parents of sweet potato in China as revealed by ISSR markers. Acta Agron Sin 34(6):972–977
Li YL, Dong Y, Niu S et al (2008b) Identification of agronomically favourable quantitative trait loci alleles from a dent corn inbred Dan232 using advanced backcross QTL analysis and comparison with the F2:3 populations in popcorn. Mol Breed 21:1–14
Li X, Wang Z, Gao S et al (2008c) Analysis of QTL for resistance to head smut (Sporisorium reiliana) in maize. Field Crop Res 106:148–155
Li X, Wei Y, Moore K et al (2011) Association mapping of biomass yield and stem composition in a tetraploid alfalfa breeding population. Plant Genom 4(1):24–35
Li YH, Zhou GY, Ma JX et al (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol 32:1045–1052
Li L, Lin F, Wang W et al (2016) Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean. Theor Appl Genet 129:2379–2386
Li J, Sun Y, Du J et al (2017a) Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. Mol Plant 10:526–529
Li J, Zhang H, Si X et al (2017b) Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene. J Genet Genom 44:465–468
Li C, Hao M, Wang W et al (2018) An efficient CRISPR/cas9 platform for rapidly generating simultaneous mutagenesis of multiple gene homoeologs in allotetraploid oilseed rape. Front Plant Sci 9:442
Liang F, Deng Q, Wang Y et al (2004) Molecular marker assisted selection for yield-enhancing genes in the progeny of “9311× O. rufipogon” using SSR. Euphytica 139(2):159–165
Liller CB, Walla A, Boer MP et al (2017) Fine mapping of a major QTL for awn length in barley using a multiparent mapping population. Theor Appl Genet 130:269–281
Lin ZX, Zhang XL, Nie YC et al (2003) Construction of a genetic linkage map for cotton based on SRAP. Chin Sci Bull 48:2063–2067
Lin K, Zhang N, Severing EI et al (2014) Beyond genomic variation-comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics 15:250
Lipper L, Anderson CL, Dalton TJ, Keleman A (2010) Conclusions and policy implications. In: Lipper L, Anderson CL, Dalton TJ (eds) Seed trade in rural markets: implications for crop diversity and agricultural development. United National Food and Agricultural Organization (FAO), Rome, Italy, pp 209–222
Liu LW, Zhao LP, Gong YQ et al (2008a) DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD, ISSR and SRAP markers. Sci Hortic 116:240–247
Liu L, Mu P, Li X et al (2008b) Localization of QTL for basal root thickness in japonica rice and effect of marker-assisted selection for a major QTL. Euphytica 164:729–737
Liu S, Liu Y, Yang X et al (2014a) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930
Liu MJ, Zhao J, Cai QL et al (2014b) The complex jujube genome provides insights into fruit tree biology. Nat Commun 5:5315
Liu R, Gong J, Xiao X et al (2018) GWAS analysis and QTL identification of fiber quality traits and yield components in upland cotton using enriched high density SNP markers. Front Plant Sci 9:1067
Lou J, Chen L, Yue G et al (2009) QTL mapping of grain quality traits in rice. J Cereal Sci 50:145–151
Lu J, Knox MR, Ambrose MJ et al (1996) Comparative analysis of genetic diversity in pea assessed by RFLP- and PCR-based methods. Theor Appl Genet 93:1103–1111
Lu XJ, Liu LW, Gong YQ et al (2009) Cultivar identification and genetic diversity analysis of broccoli and its related species with RAPD and ISSR markers. Sci Hortic 122:645–648
Lu Y, Zhang S, Shah T et al (2010) Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. PNAS 107(45):19585–19590
Luo Y, Sangha JS, Wang S et al (2012) Marker-assisted breeding of Xa4, Xa21 and Xa27 in the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight. Mol Breed 30(4):1601–1610
Lv C, Song Y, Gao L et al (2014) Integration of QTL detection and marker assisted selection for improving resistance to Fusarium head blight and important agronomic traits in wheat. Crop J 2(1):70–78
Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63
Malik S, Rahman M, Malik TA (2015) Genetic mapping of potential QTLs associated with drought tolerance in wheat. J Anim Plant Sci 25(4):1032–1040
Malosetti M, van der Linden CG, Vosman B et al (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175:879–889
Mannur DM, Babbar A, Thudi M et al (2019) Super Annigeri 1 and improved JG 74: two Fusarium wilt resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.). Mol Breed 39:2
Martin JP, Sanchez-Yelamo MD (2000) Genetic relationships among species of the genus Diplotaxis (Brassicaceae) using inter-simple sequence repeat markers. Theor Appl Genet 101:1234–1241
Martineau B (2001) First fruit. The creation of the flavr tomato and the birth of biotech foods. MC Graw-Hill Press, p 269
Massman JM, Jung HJG, Bernardo R (2013) Genome-wide selection vs. marker-assisted recurrent selection to improve grain yield and stover-quality traits for cellulosic ethanol in maize. Crop Sci 53:58–66
Maulana F, Ayalew H, Anderson JD et al (2018) Genome-wide association mapping of seedling heat tolerance in winter wheat. Front Plant Sci 9:1772
McGregor CE, Lambert CA, Greyling MM et al (2000) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L) germplasm. Euphytica 113:135–144
McGregor CE, van Treuren R, Hoekstra R et al (2002) Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation. Theor Appl Genet 104:146–156
Meilleur BA, Hodgkin T (2004) In situ conservation of crop wild relatives: status and trends. Biodivers Conserv 13:663–684
Meng Y, Hou Y, Wang H et al (2017) Targeted mutagenesis by CRISPR/Cas9 system in the model legume Medicago truncatula. Plant Cell Rep 36:371–374
Merchuk-Ovnat L, Barak V, Fahima T et al (2016) Ancestral QTL alleles from wild emmer wheat improve drought resistance and productivity in modern wheat cultivars. Front Plant Sci 8:703
Mi X, Swenson NG, Valencia R et al (2012) The contribution of rare species to community phylogenetic diversity across a global network of forest plots. Am Nat 180:E17–E30
Ming R, Hou S, Feng Y et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452(7190):991–996
Montenegro JD, Golicz AA, Bayer PE et al (2017) The pangenome of hexaploid bread wheat. Plant J 90:1007–1013
Morgante M, Vogel J (1994) Compound microsatellite primers for the detection of genetic polymorphisms. U.S. Patent Application No. 08/326456
Morris GP, Ramu P, Deshpande SP et al (2012) Population genomic and genomewide association studies of agroclimatic traits in sorghum. PNAS 110:453–458
Mukeshimana G, Butare L, Cregan PB et al (2014) Quantitative trait loci associated with drought tolerance in common bean. Crop Sci 54(3):923–938
Mulualem T, Bekero Z (2016) Advances in quantitative trait loci, mapping and importance of marker assisted selection in plant breeding research. Int J Plant Breed Genet 10(2):58–68
Munos S, Ronc N, Botton E et al (2011) Increase in tomato locule number is controlled by two single-nucleotide nucleotide polymorphisms located near Wuschel. Plant Physiol 156:2244–2254
Murtaza N (2006) Cotton genetic diversity study by AFLP markers. Electron J Biotechnol 9(4). https://doi.org/10.2225/vol9-issue4-fulltext-9
Myburg A, Grattapaglia D, Tuskan G et al (2011) The Eucalyptus grandis Genome Project: genome and transcriptome resources for comparative analysis of woody plant biology. IUFRO Tree Biotechnology Conference 2011: From Genomes to Integration and Delivery. Arraial d’Ajuda, Bahia, Brazil, 26 June - 2 July 2011. BMC Proc 5(7):120
NAAS (1998) Conservation, management and use of agrobiodiversity. Policy paper 4. National Academy of Agricultural Sciences, New Delhi, p 7
Nair SK, Prasanna BM, Garg A et al (2005) Identification and validation of QTLs conferring resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in maize. Theor Appl Genet 110:1384–1392
Nair SK, Babu R, Magorokosho C et al (2015) Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines. Theor Appl Genet 128:1839–1854
Nakajima I, Ban Y, Azuma A et al (2017) CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS One 12:e0177966
Nalluri N, Karri VR (2020) Recent advances in genetic manipulation of crops: promising approach to address the global food and industrial applications. Plant Sci Today 7(1):70–92
Nandi S, Subudhi P, Senadhira D et al (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol Gen Genet 255:1–8
Naz AA, Kunert A, Lind V et al (2008) AB-QTL analysis in winter wheat: II. Genetic analysis of seedling and field resistance against leaf rust in a wheat advanced backcross population. Theor Appl Genet 116:1095–1104
Negi MS, Sabharwal V, Wilson N et al (2006) Comparative analysis of the efficiency of SAMPL and AFLP in assessing genetic relationships among Withania somnifera genotypes. Curr Sci 91:464–471
Negri V (2005) Agro-biodiversity conservation in Europe: ethical issues. J Agric Environ Ethics 18:3–25
Nie G, Huang T, Ma X et al (2019) Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers. Peer J 7(4):e7742
Novakova A, Simackova K, Barta J (2009) Potato variety identification by molecular markers based on retrotransposon analyses. Czech J Genet Plant Breed 45:1–10
Nwakanma DC, Pillay M, Okoli BE et al (2003) Sectional relationships in the genus Musa L. inferred from the PCR-RFLP of organelle DNA sequences. Theor Appl Genet 107:850–856
Odipio J, Alicai T, Ingelbrecht I et al (2017) Efficient CRISPR/Cas9 genome editing of phytoene desaturase in cassava. Front Plant Sci 8:1780
Oliveira E, Vilela de Resende MD, Santos V et al (2012) Genome-wide selection in Cassava. Euphytica 187:263–276
Onogi A, Ideta O, Inoshita Y et al (2015) Exploring the areas of applicability of whole-genome prediction methods for Asian rice (Oryza sativa L.). Theor Appl Genet 128:41–53
Oraguzie NC, Rikkerink EHA, Gardiner SE et al (2007) Association mapping in plants. Springer, Tokyo; New York, NY., p 277
Osakabe Y, Osakabe K (2015) Genome editing with engineered nucleases in plants. Plant Cell Physiol 56(3):389–400
Osei MK, Prempeh R, Adjebeng-Danquah J et al (2018) Marker-assisted selection (MAS): a fast-track tool in tomato breeding. In: Recent advances in tomato breeding and production. Intech Open
Osman SA, Ramadan WA (2019) DNA barcoding of different Triticum species. Bull Nat Res Centre 43:1–13
Paliwal R, Roder MS, Kumar U et al (2012) QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.). Theor Appl Genet 125:561–575
Pan C, Ye L, Qin L et al (2016) CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 6:24765
Papa R (2005) Gene flow and introgression between domesticated crops and their wild relatives. In: Ruane J, Sonnino A (eds) The role of biotechnology in exploring and protecting agricultural genetic resources. FAO, Rome
Papa R, Gepts P (2003) Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor Appl Genet 106:239–250
Park KJ, Sa KJ, Kim BW et al (2014) Genetic mapping and QTL analysis for yield and agronomic traits with an F2: 3 population derived from a waxy corn× sweet corn cross. Genes Genom 36:179–189
Pasam RK, Sharma R, Malosetti M et al (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16
Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556
Patishtan J, Hartley TN, Fonseca de Carvalho R et al (2018) Genome-wide association studies to identify rice salt-tolerance markers. Plant Cell Environ 41:970–982
Peng Z, Lu Y, Li L et al (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45(4):456–461
Pierre CS, Burgueno J, Crossa J et al (2016) Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones. Sci Rep 6:1–11
Pilliai SV, Sunderasan S, Sheela MN (2002) Biotechnology in cassava germplasm conservation and breeding in India. In: Proceedings of the 7th Regional Cassava Workshop: Cassava Research and Development in Asia: Exploring New Opportunities for an Ancient Crop. October 28 to November 1, Bangkok, Thailand, pp 140–149
Poland J, Endelman J, Dawson J et al (2012) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genom 5:103–113
Polashock J, Zelzion E, Fajardo D et al (2014) The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC Plant Biol 14(1):165–181
Poulton C, Dorward A, Kydd J (2010) The future of small farms: new directions for services, institutions, and intermediation. World Dev 38(10):1413–1428
Powell W, Morgante M, Andre C et al (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238
Pradeep RM, Sarla N, Siddiq EA (2002) Inter simple sequence repeat ISSR polymorphism and its application in plant breeding. Euphytica 128:9–17
Presterl T, Ouzunova M, Schmidt W et al (2007) Quantitative trait loci for early plant vigour of maize grown in chilly environments. Theor Appl Genet 114:1059–1070
Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112
Pushpavalli R, Krishnamurthy L, Thudi M et al (2015) Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2× JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines. BMC Plant Biol 15(1):124
Qian W, Ge S, Hong DY (2001) Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor Appl Genet 102:440–449
Qiu JL (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32:947–951
Qualset CO, Damania AB, Zanatta ACA et al (1997) Locally based crop plant conservation. In: Maxted N, Ford-Lloyd BV, Hawkes JG (eds) Plant genetic conservation: the in situ approach. Chapman and Hall, London, pp 160–175
Ranjan R, Yadav R (2019) Targeting nitrogen use efficiency for sustained production of cereal crops. J Plant Nutr 42(9):1086–1113
Ravel C, Praud S, Murigneux A et al (2006) Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genomics 49:1131–1139
Rawal R, Kumar V, Rani A et al (2020) Genetic elimination of off-flavour generating lipoxygenase-2 gene of soybean through marker assisted backcrossing and its effect on seed longevity. Plant Breed Biotechnol 8(2):163–173
Ren B, Yan F, Kuang Y et al (2018) Improved base editor for efficiently inducing genetic variations in rice with CRISPR/Cas9-guided hyperactive hAID mutant. Mol Plant 11:623–626
Resende RT, de Resende MDV, Azevedo CF et al (2018) Genome-wide association and regional heritability mapping of plant architecture, lodging and productivity in Phaseolus vulgaris. G3 8:2841–2854
Riesner DG, Steger U, Wiese M et al (1992) Temperature-gradient electrophoresis for the detection of polymorphic DNA and for quantitative polymerase chain reaction. Electrophoresis 13:632–636
Roder MS, Wendehake K, Korzun V et al (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73
Roder MS, Huang XQ et al (2008) Fine mapping of the region on wheat chromosome 7D controlling grain weight. Funct Integr Genom 8:79–86
Rommens CM, Yan H, Swords K et al (2008) Low acrylamide French fries and potato chips. Plant Biotechnol J 6:843–853
Ron M, Kajala K, Pauluzzi G et al (2014) Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol 166:455–469
Rostoks N, Ramsay L, MacKenzie K et al (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. PNAS 103(49):18656–18661
Rousset M, Bonnin I, Remoue C et al (2011) Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). Theor Appl Genet 123(6):907–926
Rutkoski JE, Poland JA, Singh RP et al (2014) Genomic selection for quantitative adult plant stem rust resistance in wheat. Plant Genom 7:1–10
Saade S, Maurer A, Shahid M et al (2016) Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Sci Rep 6:32586
Saghai-Maroof MA, Biyashev RM, Yang GP et al (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations and population dynamics. PNAS 91:5466–5470
Saıdou AA, Mariac C, Luong V et al (2009) Association studies identify natural variation at PHYC linked to flowering time and morphological variation in pearl millet. Genetics 182:899–910
Saini P, Saini P, Kaur JJ et al (2020) Molecular approaches for harvesting natural diversity for crop improvement. In: Salgotra R, Zargar S (eds) Rediscovery of genetic and genomic resources for future food security. Springer, Singapore
Salimath SS, de Oliveira AC, Godwin ID et al (1995) Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers. Genomics 38:757–763
Salvi S, Sponza G, Morgante M et al (2007) Conserved noncoding genomic sequences associated with a flowering time quantitative trait locus in maize. PNAS 104:11376–11381
Sanchez de la Hoz MP, Davila JA, Loarce Y et al (1996) Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley. Genomics 39:112–117
Santra D, Chen X, Santra M et al (2008) Identification and mapping QTL for high-temperature adult-plant resistance to stripe rust in winter wheat (Triticum aestivum L.) cultivar Stephens. Theor Appl Genet 117:793–802
Schatz MC, Maron LG, Stein JC et al (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 15:506
Schmalenbach I, March TJ, Bringezu T et al (2011) High-resolution genotyping of wild barley introgression lines and fine-mapping of the threshability locus thresh-1 using the Illumina Golden-Gate assay. G3 1:187–196
Schmidhuber J, Tubiello F (2007) Global food security under climate change. PNAS 104(50):19703–19708
Schmierer DA, Kandemir N, Kudrna DA et al (2004) Molecular marker-assisted selection for enhanced yield in malting barley. Mol Breed 14(4):463–473
Schmutz J, Cannon SB, Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463(7278):178–183
Schmutz J, McClean PE, Mamidi S et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46(7):707–713
Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity and dynamics. Science 326(5956):1112–1115
Shabanimofrad M, Yusop MR, Ashkani S et al (2015) Marker-assisted selection for rice brown plant hopper (Nilaparvata lugens) resistance using linked SSR markers. Turkish J Biol 39(5):666–673
Shapcott A, Forster PI, Guymer GP et al (2015) Mapping biodiversity and setting conservation priorities for SE Queensland’s rainforests using DNA barcoding. PLoS One 10:e0122164
Shimatani Z, Kashojiya S, Takayama M et al (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat Biotechnol 35:441–443
Shukla KV, Doyon Y, Miller JC et al (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441
Shulaev V, Sargent DJ, Crowhurst RN et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43(2):109–116
Sierro N, Battey JN, Ouadi S et al (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5:3833
Singh BD, Singh AK (2015) Marker-assisted plant breeding: principles and practices. Springer, New Delhi
Singh R, Ong-Abdullah M, Low ET et al (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500(7462):335–339
Singh J, Datta P, Kakade M et al (2017) Evaluation of potential DNA barcoding loci from plastid genome: intraspecies discrimination in rice (Oryza species). Int J Curr Micro Appl Sci 6(5):2746–2756
Sivaraj N, Sunil N, Kumar R et al (2018) Agrobiodiversity status in India: status and concern. In: Kumar B, Singh R (eds) Sustainable agriculture for food security concepts and approaches. Biotech Book, New Dehli, pp 121–137. ISBN: 978-81-7622-411-6
Skot L, Humphreys J, Humphreys MO et al (2007) Association of candidate genes with l owering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics 177:535–547
Spindel J, Wright M, Chen C et al (2013) Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 126:2699–2716
Spindel J, Begum H, Akdemir D et al (2015) Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 11:e1004982
Spindel JE, Begum H, Akdemir D et al (2016) Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity 116:395–408
Spindel JE, Dahlberg J, Colgan M et al (2018) Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought. BMC Genomics 19:679
Spooner DM, Nunez J, Trujillo G et al (2007) Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. PNAS 104:19398–19403
Stevens R, Buret M, Duffe P et al (2007) Candidate genes and quantitative trait loci affecting fruit ascorbic acid content in three tomato populations. Plant Physiol 143:1943–1953
Stich B, Melchinger AE, Piepho HP et al (2006) A new test for family-based association mapping with inbred lines from plant breeding programs. Theor Appl Genet 113:1121–1130
Stich B, Piepho H, Schulz B et al (2008) Multi-trait association mapping in sugar beet (Beta vulgaris L.). Theor Appl Genet 117(6):947–954
Stracke S, Haseneyer G, Veyrieras JB et al (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118:259–273
Su J, Li L, Zhang C et al (2018) Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton. Theor Appl Genet 131:1299–1314
Sukumaran S, Yu J (2014) Association mapping of genetic resources: achievements and future perspectives. In: Genomics of plant genetic resources. Springer, Dordrecht, pp 207–235
Sun L, Rodriguez GR, Clevenger JP et al (2015) Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape. J Exp Bot 66:6471–6482
Sun Y, Jiao G, Liu Z et al (2017) Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Front Plant Sci 8:298
Sun Z, Li H, Zhang Y et al (2018) Identification of SNPs and candidate genes associated with salt tolerance at the seedling stage in cotton (Gossypium hirsutum L). Front Plant Sci 9:1011
Sutton T, Baumann U, Hayes J et al (2007) Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318:1446–1449
Tan Y, Sun M, Xing Y et al (2001) Mapping quantitative trait loci for milling quality, protein content and colour characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theor Appl Genet 103:1037–1045
Tanaka M, Takahata Y, Nakayama H et al (2010) Development of cleaved amplified polymorphic sequence (CAPS)-based markers for identification of sweet potato cultivars. Sci Hortic 123:436–442
Tang F, Yang S, Liu J et al (2016) Rj4, a gene controlling nodulation specificity in soybeans, encodes a thaumatin-like protein but not the one previously reported. Plant Physiol 170:26–32
Tang X, Sretenovic S, Ren Q et al (2020) Plant prime editors enable precise gene editing in rice cells. Mol Plant 13(5):667–670
Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203
Tao Y, Mace ES, Tai S et al (2017) Whole-genome analysis of candidate genes associated with seed size and weight in Sorghum bicolor reveals signatures of artificial selection and insights into parallel domestication in cereal crops. Front Plant Sci 8:1237
Tao Y, Zhao X, Mace E et al (2019) Exploring and exploiting pan-genomics for crop improvement. Mol Plant 12:156–169
Tar’An B, Michaels TE, Pauls KP (2001) Mapping genetic factors affecting the reaction to Xanthomonas axonopodis pv. phaseoli in Phaseolus vulgaris L. under field conditions. Genomics 44(6):1046–1056
Taramino G, Sauer M, Stauffer JL et al (2007) The maize (Zea mays L) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shoot-borne root initiation. Plant J 50:649–659
Taylor MS, Tornqvist CE, Zhao X et al (2018) Genome-wide association study in pseudo-F2 populations of switch grass identifies genetic loci affecting heading and anthesis dates. Front Plant Sci 9:1250
Tettelin H, Masignani V, Cieslewicz MJ et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. PNAS 102:13950–13955
Thalapati S, Batchu AK, Neelamraju S et al (2012) Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice. Funct Integr Genom 12:277–289
The 3000 Rice Genomes Project (2014) The 3000 rice genome project. Giga Sci 3:7
The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–1039
The French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467
The International Peach Genome Initiative (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487–494
The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475(7355):189–195
The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641
Tian HL, Xue JH, Wen J et al (2008) Genetic diversity and relationships of lotus (Nelumbo) cultivars based on allozyme and ISSR markers. Sci Hortic 116:421–429
Tian Y, Zhang H, Xu P et al (2015) Genetic mapping of a QTL controlling leaf width and grain number in rice. Euphytica 202:1–11
Tian S, Jiang L, Gao Q et al (2017) Efficient CRISPR/Cas9-based gene knockout in watermelon. Plant Cell Rep 36:399–406
Tian D, Guo X, Zhang Z et al (2019) Improving blast resistance of the rice restorer line, Hui 316, by introducing Pi9 or Pi2 with marker-assisted selection. Biotechnol Biotechnol Equip 33(1):1195–1203
Tilman D (1999) Global environmental impacts of agricultural expansion: the need for sustainable and efficient practices. PNAS 96:5995–6000
Tracy WF, Whitt SR, Buckler ES (2006) Recurrent mutation and genome evolution: example of Sugary1 and the origin of sweet maize. Crop Sci 46:S49–S54
Trick M, Adamski NM, Mugford SG et al (2012) Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 12:14
Tsai CC, Chen YKH, Chen CH et al (2013) Cultivar identification and genetic relationship of mango (Mangifera indica) in Taiwan using 37 SSR markers. Sci Hortic 164:196–201
Tseng YT, Lo HF, Hwang SY (2002) Genotyping and assessment of genetic relationships in elite polycross breeding cultivars of sweet potato in Taiwan based on SAMPL polymorphisms. Bot Bull Acad Sin 43:99–105
Tuskan GA, Difazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596–1604
Uga Y, Sugimoto K, Ogawa S et al (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45:1097–1102
Van Bakel H, Stout JM, Cote AG et al (2011) The draft genome and transcriptome of Cannabis sativa. Genome Biol 12:102
Varshney RK, Chen W, Li Y et al (2011) Draft genome sequence of pigeon pea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30(1):83–90
Varshney RK, Song C, Saxena RK et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31(3):240–248
Varshney RK, Thudi M, Nayak SN et al (2014) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor Appl Genet 127:445–462
Veillet F, Perrot L, Chauvin L et al (2019) Transgene-free genome editing in tomato and potato plants using Agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor. Int J Mol Sci 20(2):402
Verma KVVK, Behera TK, Munshi AD et al (2007) Genetic diversity of ash gourd [Benincasa hispida (Thunb.) Cogn.] inbred lines based on RAPD and ISSR markers and their hybrid performance. Sci Hortic 113:231–237
de Vicente MC, Guzman FA, Engels J et al (2005) Genetic characterization and its use in decision-making for the conservation of crop germplasm. In: Ruane J, Sonnino A (eds) The role of biotechnology in exploring and protecting agricultural genetic resources. FAO, Rome
Vijayalakshmi K, Fritz AK, Paulsen GM et al (2010) Modeling and mapping QTL for senescence-related traits in winter wheat under high temperature. Mol Breed 26:163–175
Virk PS, Ford-Lloyd BV, Jackson MT et al (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304
Vitte C, Ishii T, Lamy F et al (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Genet Genomics 272:504–511
Vlk D, Repkova J (2017) Application of next-generation sequencing in plant breeding. Czech J Genet Plant Breed 53:89–96
Von Zitzewitz J, Cuesta-Marcos A, Condon F et al (2011) The genetics of winterhardiness in barley: perspectives from genome-wide association mapping. Plant Genom 4(1):76–91
Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Wada N, Ueta R, Osakabe Y et al (2020) Precision genome editing in plants: state of-the-art in CRISPR/Cas9-based genome engineering. BMC Plant Biol 20:234
Wambugu PW, Brozynska M, Furtado A et al (2015) Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep 5:13957
Wang G, Mahalingan R, Knap HT (1998) CA and GA anchored simple sequence repeats (ASSRs) generated polymorphism in soybean, Glycine max (L.) Merr. Theor Appl Genet 96:1086–1096
Wang H, Nussbaum-Wagler T, Li B et al (2005) The origin of the naked grains of maize. Nature 436:714–719
Wang J, McClean P, Lee R et al (2008) Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor Appl Genet 116(6):777–787
Wang JP, Dobrowolski MP, Cogan NOI et al (2009) Assignment of individual genotype to specific forage cultivars of perennial ryegrass based on SSR markers. Crop Sci 49:49–58
Wang M, Sukumaran S, Barkley N et al (2011) Population structure and marker-trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection. Theor Appl Genet 123(8):1307–1317
Wang AY, Li Y, Zhang CQ (2012) QTL mapping for stay-green in maize (Zea mays). Can J Plant Sci 92:249–256
Wang L, Chen L, Li R et al (2017) Reduced drought tolerance by CRISPR/Cas9-mediated SlMAPK3 mutagenesis in tomato plants. J Agric Food Chem 65:8674–8682
Wang WS, Mauleon R, Hu ZQ et al (2018a) Genomic variation in 3010 diverse accessions of Asian cultivated rice. Nature 557:43–49
Wang W, Pan Q, He F et al (2018b) Transgenerational CRISPR-Cas9 activity facilitates multiplex gene editing in allopolyploid wheat. CRISPR J 1(1):65–74
Wang Y, Wang J, Zhao X et al (2020) Overexpression of the transcription factor gene Osstap1 increases salt tolerance in rice. Rice 13(1):50
Watanabe K, Oda-Yamamizo C, Sage-Ono K et al (2018) Alteration of flower colour in Ipomoea nil through CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase 4. Transgenic Res 27:25–38
Weber AL, Briggs WH, Rucker J (2008) The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping. Genetics 180:1221–1232
Weeks JT, Ye J, Rommens CM (2008) Development of an in planta method for transformation of alfalfa (Medicago sativa). Transgenic Res 17:587–597
Wei XM, Jackson PA, McIntyre CL et al (2006) Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theor Appl Genet 114:155–164
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Whankaew S, Sraphet S, Thaikert R (2011) M-AFLP based development of microsatellite markers for the characterization of cassava (Manihot esculenta Crantz). Genet Mol Res 11(2):1319–1326
White MB, Carvalho M, Derse D et al (1992) Detecting single base substitutions as notes heteroduplex polymorphisms. Genomics 12:301–306
Williams JG, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Williams MNV, Pande N, Nair M et al (1991) Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA. Theor Appl Genet 82:489–498
Wilson EO (1992) The diversity of life. Penguin, London
Wilson LM, Whitt SR, Rocheford TR et al (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733
Witcombe JR, Joshi A, Joshi KD et al (1996) Farmer participatory crop improvement. I: varietal selection and breeding methods and their impact on biodiversity. Exp Agric 32:445–460
Witsenboer H, Michelmore RW, Vogel J (1997) Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.). Genomics 40:923–936
Wolff K, Zietkiewicz E, Hofstra H (1995) Identification of Chrysanthemum cultivars and stability of DNA fingerprint patterns. Theor Appl Genet 91:439–447
Wu J, Wang Z, Shi Z et al (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23(2):396–408
Wu GA, Prochnik S, Jenkins J (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32(7):656–662
Wu J, Zhang M, Zhang X et al (2017) Development of InDel markers for the restorer gene Rf1 and assessment of their utility for marker-assisted selection in cotton. Euphytica 213(11):251
Wurschum T, Maurer H, Kraft T et al (2011) Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet 123(7):1121–1131
Xie RJ, Zhou J, Wang GY et al (2011) Cultivar identification and genetic diversity of Chinese bayberry (Myrica rubra) accessions based on fluorescent SSR markers. Plant Mol Biol Rep 29:554–562
Xie JZ, Wang LL, Wang Y et al (2017) Fine mapping of powdery mildew resistance gene PmTm4 in wheat using comparative genomics. J Integr Agric 16:540–550
Xiong FQ, Tang RH, Chen ZL et al (2009) SCoT: a novel gene targeted marker technique based on the translation start codon. Mol Plant Breed 7:635–638
Xu Q, Chen LL, Ruan X et al (2013a) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45(1):59–66
Xu X, Zeng L, Tao Y et al (2013b) Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing. PNAS 110:13469–13474
Xu Y, Zhang XQ, Harasymow S et al (2018) Molecular marker-assisted backcrossing breeding: an example to transfer a thermostable β-amylase gene from wild barley. Mol Breed 38(5):63
Xu Z, Hua J, Wang F et al (2020) Marker-assisted selection of qMrdd8 to improve maize resistance to rough dwarf disease. Breed Sci 70:183–192
Yadawad A, Gadpale A, Hanchinal RR (2017) Pyramiding of leaf rust resistance genes in bread wheat variety DWR 162 through marker assisted backcrossing. Ind J Genet Plant Breed 77:251–257
Yan J, Cirincione A, Adamson B (2020) Prime editing: precision genome editing by reverse transcription. Mol Cell 77(2):210–212
Yang W, de Oliveira AC, Godwin I et al (1996) Comparison of DNA marker technologies in characterizing plant genome diversity: variability in Chinese sorghums. Crop Sci 36:1669–1676
Yang H, Sweetingham MW, Cowling WA et al (2001) DNA fingerprinting based on microsatellite-anchored fragment length polymorphisms, and isolation of sequence-specific PCR markers in lupin (Lupinus angustifolius L.). Mol Breed 7:203–209
Yang X, Caro M, Hutton SF et al (2014) Fine mapping of the tomato yellow leaf curl virus resistance gene on chromosome 11 of tomato. Mol Breed 34:749–760
Yang X, Xia X, Zeng Y et al (2018) Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing. PLoS One 13:e0196690
Yao H, Song J, Liu C et al (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5:e13102
Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79–92
Yu L, Lorenz A, Rutkoski J et al (2011) Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet 123(8):1257–1268
Yu H, Qiu Z, Xu Q et al (2017) Fine mapping of low tiller 1, a gene controlling tillering and panicle branching in rice. Plant Growth Regul 83:93–104
Zaefizadeh M, Goliev R (2009) Diversity and relationships among durum wheat landraces (subconvars) by SRAP and phenotypic marker polymorphism. Res J Biol Sci 4:960–966
Zhang X, Yuan Y (2019) Genome-wide association mapping and genomic prediction analyses reveal the genetic architecture of grain yield and flowering time under drought and heat stress conditions in maize. Front Plant Sci 9:1919
Zhang YX, Sun J, Zhang XR et al (2011) Analysis on genetic diversity and genetic basis of the main sesame cultivars released in China. Agric Sci China 10:509–518
Zhang Q, Chen W, Sun L et al (2012) The genome of Prunus mume. Nat Commun 3:1318
Zhang J, Ku L, Han Z et al (2014) The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.). J Exp Bot 65:5063–5076
Zhang F, LeBlanc C, Irish VF et al (2017) Rapid and efficient CRISPR/Cas9 gene editing in citrus using the YAO promoter. Plant Cell Rep 36:1883–1887
Zhang Z, Hua L, Gupta A et al (2019) Development of an Agrobacterium-delivered CRISPR/Cas9 system for wheat genome editing. Plant Biotechnol J 17:1623–1635
Zhang W, Sun Y, Liu J et al (2021) DNA barcoding of Oryza: conventional, specific, and super barcodes. Plant Mol Biol 105:215–228
Zhao J, Paulo M, Jamar D et al (2007) Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa. Genomics 50(10):963–973
Zhao Q, Feng Q, Lu HY et al (2018) Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet 50:278–284
Zhou J, Peng Z, Long J et al (2015) Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice. Plant J 82:632–643
Zhou Z, Tan H, Li Q et al (2018) CRISPR/Cas9-mediated efficient targeted mutagenesis of RAS in Salvia miltiorrhiza. Phytochemistry 148:63–70
Zietkiewicz E, Rafalski A, Labuda D et al (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183
Zong Y, Wang Y, Li C et al (2017) Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Biotechnol 35:438–440
Zou J, Jiang C, Cao Z et al (2010) Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mapping. Genomics 53(11):908–916
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Dhakad, A.K., Mohanapuria, P., Ranjan, R., Vaishnav, V., Yadav, S.K. (2022). Molecular Approaches in Conservation and Restoration of Agrobiodiversity. In: Kumar, P., Tomar, R.S., Bhat, J.A., Dobriyal, M., Rani, M. (eds) Agro-biodiversity and Agri-ecosystem Management. Springer, Singapore. https://doi.org/10.1007/978-981-19-0928-3_10
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