Abstract
Chickpea is an important cool-season grain legume. High-quality seed has the potential to attract premium prices. Hence, the breeding for desirable quality traits, including seed size and weight, is important. A set of 27 chickpea genotypes comprising 14 small and 13 large seeded, representing desi and Kabuli types, were used in the present study. A total of 43 SSR markers which were earlier reported to be associated with 100-seed weight and yield-contributing traits following QTL mapping in unrelated genetic background were used for validation purpose. Out of 43 SSR primers, 33 showed polymorphism amplifying 135 alleles. Neighbor joining-based analysis separated small- and large-seeded genotypes into two broad groups. These markers could distinguish small-seeded chickpea from that of large-seeded ones as well as desi types from that of Kabuli types, thereby validating all these QTL-linked markers in different genetic backgrounds. Fifteen of these primers also amplified 20 unique alleles in 13 chickpea genotypes and can be useful in molecular characterization and identification of specific genotype which has now become mandatory under Protection of Plant Varieties and Farmers Rights’ Act of India.
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References
Abbo S, Molina C, Jungmann R, Grusak M, Berkovitch Z, Reifen R (2005) Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.). Theor Appl Genet 111:185–195
Ahmad Z, Nisar M, Mumtaz A, Ghafoor A, Ali S (2014) SSR Markers linked to seed size and seed weight in local and exotic chickpea germplasm reported from Pakistan. Pak J Bot 46:2113–2120
Bajaj D, Saxena M, Kujur A, Das S, Badoni S, Tripathi S et al (2015) Genome wide conserved non coding microsatellite (CNMS) marker based integrative genetical genomics for quantitative dissection of seed weight in chickpea. J Exp Bot 66:1271–1290
Bajaj D, Upadhyaya H, Khan Y, Das S, Badoni S, Shree T et al (2015) A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Nat Sci Rep 5:9264
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Cho S, Kumar J, Shultz J, Anupama K, Tefera F, Muehlbauer F (2002) Mapping genes for double podding and other morphological traits in chickpea. Euphytica 125:285–292
Choudhary S, Kaur J, Chhuneja P, Sandhu J, Singh I, Singh S, Sirari A (2012) Assessment of genetic diversity in Kabuli chickpea (Cicer arietinum L.) genotypes in relation to seed size using SSR markers. J Food Legum 26:70–73
Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591–608
Cobos M, Rubio J, Fernandez-Romero M, Garza R, Moreno M, Millan T, Gil J (2007) Genetic analysis of seed size, yield and days to flowering in a chickpea recombinant inbred line population derived from a Kabuli × Desi cross. Ann Appl Biol 151:33–42
Cobos M, Winter P, Kharrat M, Cubero J, Gil J, Millan T, Rubio J (2009) Genetic analysis of agronomic traits in a wide cross of chickpea. Field Crop Res 111:130–136
Dellaporta S, Wood J, Hick J (1983) A plant DNA minipreparation. Plant Mol Biol Rep 13:19–21
Gaur PM, Jukanti AK, Varshney RK (2012) Impact of genomic technologies on chickpea breeding strategies. Agronomy 2:199–221
Gowda S, Radhika P, Mhase L, Jamadagni B, Gupta V, Kadoo N (2011) Mapping of QTLs governing agronomic and yield traits in chickpea. J Appl Genet 52:9–21
Hajibarat Z, Saidi A, Hajibarat Z, Talebi R (2014) Genetic diversity and population structure analysis of landrace and improved chickpea (Cicer arietinum L.) genotypes using morphological and microsatellite markers. Environ Exp Biol 12:161–166
Hossain S, Ford R, McNeil D, Pittock C, Panozzo J (2010) Inheritance of seed size in Cicer arietinum L. and identification of QTL based on 100 seed weight and seed size index. Aust J Crop Sci 4:126–135
Jadhav AA, Rayate SJ, Mhase LB, Thudi M, Chitikineni A, Harer PN, Jadhav AS, Varshney RK, Kulwal PL (2015) Marker-trait association study for protein content in chickpea (Cicer arietinum L.). J Genet 94:279–286
Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW et al (2013) A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J 74:715–729
Jamalabadi J, Saidi A, Karami E, Kharkesh M, Talebi R (2013) Molecular mapping and characterization of genes governing time to flowering, seed weight and plant height in an intraspecific genetic linkage map of chickpea (Cicer arietinum L.). Biochem Genet 51:387–397
Khatodia S, Bhatotia K, Passricha N, Khurana SMP, Tuteja N (2016) The CRISPR/Cas genome-editing tool: application in improvement of crops. Front Plant Sci. doi:10.3389/fpls.2016.00506
Kulwal PL, Mhase LB (2016) Protein content exhibits a significant positive correlation with seed weight in chickpea germplasm collection. Plant Genet Resour C. doi:10.1017/S147926211500060X
Kulwal PL, Mahendar T, Varshney RK (2012) Genomics interventions in crop breeding for sustainable agriculture. In: Meyers RA (ed) Encyclopedia of sustainability science and technology, Springer, New York. doi:10.1007/978-1-4419-0851-3
Kulwal PL, Mahendar T, Mhase LB, Varshney RK (2016) Association analysis identifies important QTL for seed weight in chickpea. Iore J Genet 1(1):1–7
Kumar S, Singh O (1995) Inheritance of seed size in chickpea. J Genet Breed 49:9104
Kumar V, Jain M (2015) The CRISPR–Cas system for plant genome editing: advances and opportunities. J Exp Bot 66:47–57
Kumar Y, Kwon SJ, Coyne CJ, Hu J, Grusak MA, Kisha TJ, McGee RJ, Sarker A (2014) Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum L.) germplasm. Genet Resour Crop Evol 61:965–977
Kujur A, Bajaj D, Saxena M, Tripathi S, Upadhyaya H, Gowda C et al (2013) Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Res 20:355–374
Kujur A, Bajaj D, Saxena M, Tripathi S, Upadhyaya H et al (2014) An efficient and cost-effective approach for genic microsatellite marker-based large scale trait association mapping: identification of candidate genes for seed weight in chickpea. Mol Breed 34:241–265
Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129
Nayak S, Zhu H, Varghese N, Datta S, Choi H et al (2010) Integration of novel SSR and gene based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theor Appl Genet 120:1415–1441
Protection of Plant Varieties and Farmers’ Rights Authority (PPV & FRA), Government of India (2007) Guidelines for the conduct of test for Distinctiveness, Uniformity and Stability on chickpea (Cicer arietinum L.) SG/06/2007
Saeed A, Hovsepyan H, Darvishzadeh R, Imtiaz M, Panguluri SK, Nazaryan R (2011) Genetic diversity of Iranian accessions, improved lines of chickpea (Cicer arietinum L.) and their wild relatives by using simple sequence repeats. Plant Mol Biol Rep 29:848–858
Sethy N, Shokeen B, Edwards K, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112:1416–1428
Thudi M, Bohra A, Nayak S, Varghese N, Shah T, Varma R et al (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE 6:1–12
Upadhyaya H, Dwivedi S, Baum M, Varshney R, Udupa S, Gowda C, Hoisington D, Singh S (2008) Genetic structure, diversity and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol 8:106
Upadhyaya HD, Furman BJ, Dwivedi SL, Udupa SM, Gowda CLL, Baum M, Crouch JH, Buhariwalla HK, Singh S (2006) Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea. Plant Genet Res 4:13–19
Upadhyaya H, Kumar S, Gowda C, Singh S (2006) Two major genes for seed size in chickpea (Cicer arietinum L.). Euphytica 147:311–315
Vadez V, Krishnamurthy L, Thudi M, Anuradha C, Colmer T, Turner N et al (2012) Assessment of ICCV-2 × JG-62 chickpea progenies shows sensitivity of reproduction to salt stress and reveals QTL for seed yield and yield components. Mol Breed 30:9–21
Vadivelu KK, Ramakrishna V (1983) Effect of seed size on quality attributes and yield of seeds in Bengal gram (Cicer arietinum L.). Seed Res 11:177–181
Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J et al (2013) Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. Plant Genome. doi:10.3835/plantgenome2013.07.0022
Varshney RK, Mohan SM, Gaur PM, Chamarthi SK, Singh VK, Srinivasan S et al (2014) Marker-assisted backcrossing to introgress resistance to fusarium wilt race 1 and ascochyta blight in C214, an elite cultivar of chickpea. Plant Genome. doi:10.3835/plantgenome2013.10.0035
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246
Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L et al (2014) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor Appl Genet 127:445–462
Varshney R, Tuberosa R (2007) Genomics-assisted crop improvement: an overview. In: Varshney RK, Tuberosa R (eds) Genomic assisted crop improvement: genomics approaches and platforms, vol I. Springer, New York, pp 1–12
Winter P, Pfaff T, Udupa S, Huttel B, Sharma P, Sahi S et al (1999) Characterization and mapping of sequence tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet 262:90–101
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PLK, LBM and ASJ designed the study, VVB performed laboratory work, and PLK wrote the article.
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Borse, V.V., Kulwal, P.L., Mhase, L.B. et al. Validation of Seed Weight-Associated SSR Markers and Their Usefulness in Distinguishing Chickpea Genotypes According to Seed Size. Agric Res 6, 130–138 (2017). https://doi.org/10.1007/s40003-017-0256-8
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DOI: https://doi.org/10.1007/s40003-017-0256-8