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Assessing genetic diversity, allelic richness and genetic relationship among races in ICRISAT foxtail millet core collection

Published online by Cambridge University Press:  30 October 2012

M. Vetriventhan
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru502 324, Andhra Pradesh, India
H. D. Upadhyaya*
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru502 324, Andhra Pradesh, India
C. R. Anandakumar
Affiliation:
Agricultural College and Research Institute, Tamil Nadu Agricultural University (TNAU), Madurai625 104, Tamil Nadu, India
S. Senthilvel
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru502 324, Andhra Pradesh, India
H. K. Parzies
Affiliation:
University of Hohenheim, Institute of Plant Breeding, Seed Science and Population Genetics, Fruwirthstr. 21, D-70599Stuttart, Germany
A. Bharathi
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru502 324, Andhra Pradesh, India
R. K. Varshney
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru502 324, Andhra Pradesh, India
C. L. L. Gowda
Affiliation:
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru502 324, Andhra Pradesh, India
*
*Corresponding author. E-mail: [email protected]

Abstract

Foxtail millet (Setaria italica (L.) P. Beauv.) is an ideal crop for changing climate and food habits of peoples due to its short duration, high photosynthetic efficiency, nutritional richness and fair resistance to pest and diseases. However, foxtail millet yields are low mainly due to the lack of effort for its improvement and the lack of proper utilization of existing genetic variability. To enhance the use of diverse germplasm in breeding programmes, a core collection in foxtail millet consisting of 155 accessions was established. Core collection accessions were fingerprinted using 84 markers (81 simple sequence repeats (SSRs) and three Expressed Sequence Tag (EST)-SSRs). Our results showed the presence of greater molecular diversity in the foxtail millet core collection. The 84 markers detected a total of 1356 alleles with an average of 16.14 alleles (4–35) per locus. Of these, 368 were rare alleles, 906 common alleles and 82 the most frequent alleles. Sixty-one unique alleles that were specific to a particular accession and useful for germplasm identification were also detected. In this study, the genetic diversity of foxtail millet was fairly correlated well with racial classification, and the race Indica showed a greater genetic distance from the races Maxima and Moharia. The pairwise estimate of dissimilarity was >0.50 except in 123 out of 11,935 pairs which indicated a greater genetic variability. Two hundred and fifty pairs of genetically most diverse accessions were identified. This large molecular variation observed in the core collection could be utilized effectively by breeders or researchers for the selection of diverse parents for breeding cultivars and the development of mapping populations.

Type
Research Article
Copyright
Copyright © NIAB 2012

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References

Abdurakhmonov, IY, Kohel, RJ, Yu, JZ, Pepper, AE, Abdullaev, AA, Kushanov, FN, Salakhutdinov, IB, Buriev, ZT, Saha, S, Scheffler, BE, Jenkins, JN and Abdukarimov, A (2008) Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92: 478487.CrossRefGoogle ScholarPubMed
Agrama, HA and Eizenga, GC (2008) Molecular diversity and genome wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives. Euphytica 160: 339355.Google Scholar
Agrama, HA, Eizenga, GC and Yan, W (2007) Association mapping of yield and its components in rice cultivars. Molecular Breeding 19: 341356.CrossRefGoogle Scholar
Agrama, HA, Yan, WG, Lee, F, Fjellstrom, R, Chen, MS, Jia, M and McClung, A (2009) Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Science 49: 13361346.Google Scholar
Ahanchede, A, Hamon, SP and Darmency, H (2004) Why no tetraploid cultivar of foxtail millet? Genetic Resources and Crop Evolution 51: 227230.Google Scholar
Ali, ML, Rajewski, JF, Baenziger, PS, Gill, KS, Kskridge, KM and Dweikat, I (2008) Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers. Molecular Breeding 21: 497509.CrossRefGoogle Scholar
Austin, DF (2006) Foxtail millets (Setaria: Poaceae) – abandoned food in two hemispheres. Economic Botany 60: 143158.CrossRefGoogle Scholar
Bennetzen, JL, Schmutz, J, Wang, H, Percifield, R, Hawkins, J, Pontaroli, AC, Estep, M, Feng, L, Vaughn, JN, Grimwood, J, Jenkins, J, Barry, K, Lindquist, E, Hellsten, U, Deshpande, S, Wang, X, Wu, X, Mitros, T, Triplett, J, Yang, X, Chu-Yu, Ye, Mauro-Herrera, M, Wang, L, Li, P, Sharma, M, Sharma, R, Ronald, PC, Panaud, O, Kellogg, EA, Brutnell, TP, Doust, AN, Tuskan, GA, Rokhsar, D and Devos, KM (2012) Reference genome sequence of the model plant Setaria. Nature Biotechnology doi:101038/nbt2196.Google Scholar
Blair, MW, Díaz, LM, Buendía, HF and Duque, MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theoretical and Applied Genetics 119: 955972.Google Scholar
Borba, TCO, Brondani, RPV, Breseghello, F, Coelho, ASG, Mendonça, JA, Rangel, PHN and Brondani, C (2010) Association mapping for yield and grain quality traits in rice (Oryza sativa L.). Genetics and Molecular Biology 33: 515524.Google Scholar
Dida, MM, Srinivasachary, , Ramakrishnan, S, Bennetzen, JL, Gale, MD and Devos, KM (2007) The genetic map of finger millet, Eleusine coracana. Theoretical and Applied Genetics 114: 321332.Google Scholar
Frankel, OH (1984) Genetic perspective of germplasm conservation. In: (eds) Genetic Manipulations: Impact of Man and Society. Cambridge: Cambridge University Press, pp. 161170.Google Scholar
Gepts, P (1995) Genetic markers and core collections. In: (eds) Core Collections of Plant Genetic Resources. Chichester: John Wiley and Sons, pp. 127146.Google Scholar
Hao, CY, Zhang, XY, Wang, LF, Dong, YS, Shang, XW and Jia, JZ (2006) Genetic diversity and core collection evaluations in common wheat germplasm from the North western Spring wheat regions in China. Molecular Breeding 17: 6977.CrossRefGoogle Scholar
Henderson, ST and Peters, TD (1992) Instability of simple sequence DNA in Saccharomyces cerevisiae. Molecular and Cell Biology 12: 27492757.Google ScholarPubMed
Hokanson, SC, Szewc-McFadden, AK, Lamboy, WF and McFerson, JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity, and relationships in a Malus × domestica Borkh. core subset collection. Theoretical and Applied Genetics 97: 671683.Google Scholar
Jia, XP, Shi, YS, Song, YC, Wang, GY, Wang, TY and Li, Y (2007) Development of EST-SSR in foxtail millet (Setaria italica). Genetic Resources and Crop Evolution 54: 233236.CrossRefGoogle Scholar
Jia, X, Zhang, Z, Liu, Y, Zhang, C, Shi, Y, Song, Y, Wang, T and Li, Y (2009) Development and genetic mapping of SSR markers in foxtail millet (Setaria italica (L.) P. Beauv.). Theoretical and Applied Genetics 118: 821829.Google Scholar
Jin, L, Lu, Y, Xiao, P, Sun, M, Corke, H and Bao, J (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theoretical and Applied Genetics 121: 475487.CrossRefGoogle ScholarPubMed
Jun, TH, Van, K, Kim, MY, Lee, SH and Walker, DR (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162: 179191.CrossRefGoogle Scholar
Kalia, RK, Rai, MK, Kalia, S, Singh, R and Dhawan, AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177: 309334.Google Scholar
Kihara, H and Kishimoto, E (1942) Bastradezwischen Setaria italica und S. viridis (in Japanese with German summary). The Botanical Magazine Tokyo 56: 6267.CrossRefGoogle Scholar
Koppolu, R, Upadhyaya, HD, Dwivedi, SL, Hoisington, DA and Vershney, RK (2010) Genetic relationships among seven sections of genus Arachis studied by using SSR markers. BMC Plant Biology 10: 15.Google Scholar
Kottapalli, KR, Burow, MD, Burow, G, Burke, J and Puppala, N (2007) Molecular characterization of the U.S. peanut mini core collection using microsatellite markers. Crop Science 47: 17181727.Google Scholar
Li, H, Meng, WJ and Liu, TM (1935) Problems in the breeding of millet [Setaria italica (L.) Beauv.]. Journal of the American Society of Agronomy 27: 426438.CrossRefGoogle Scholar
Li, HW, Li, CH and Pao, WK (1945) Cytological and genetical studies of the interspecific cross of cultivated foxtail millet, Setaria italica (L.) Beauv., and the green foxtail millet, S. viridis L. Journal of the American Society of Agronomy 37: 3254.Google Scholar
Lin, HS, Liao, GI, Chiang, CY, Kuoh, CS and Chang, SB (2012) Genetic diversity in the foxtail millet (Setaria italica) germplasm as determined by agronomic traits and microsatellite markers. Australian Journal of Crop Science 6: 342349.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 21282129.CrossRefGoogle Scholar
Liu, F, Sun, G, Salomon, B and Bothmer, RV (2002) Characterization of genetic diversity in core collection accessions of wild barley, Hordeum vulgare ssp. spontaneum. Hereditas 136: 6773.CrossRefGoogle ScholarPubMed
Liu, Z, Bai, G, Zhang, D, Znu, C, Xia, X, Cheng, Z and Shi, Z (2011) Genetic diversity and population structure of elite foxtail millet (Setaria italica (L.) P. Beauv.) germplasm in China. Crop Science 51: 16551663.CrossRefGoogle Scholar
Lu, H, Zhang, J, Liu, KB, Wu, N, Li, Y, Zhou, K, Ye, M, Zhang, T, Zhang, H, Yang, X, Shen, L, Xu, D and Li, Q (2009) Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago. Proceedings of the National Academy of Sciences of the United States of America 106: 73677372.Google Scholar
Mace, ES, Buhariwalla, HK and Crouch, JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Molecular Biology Reporter 21: 459a459h.Google Scholar
Matus, IA and Hayes, PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45: 10951106.Google Scholar
Mondini, L, Noorani, A and Pagnotta, MA (2009) Assessing plant genetic diversity by molecular tools. Diversity I: 1935.Google Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70: 33213323.CrossRefGoogle ScholarPubMed
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288295.Google Scholar
Peleg, Z, Fahima, T, Abbo, S, Krugman, T and Saranga, Y (2008 a) Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers. Genome 51: 187195.CrossRefGoogle ScholarPubMed
Peleg, Z, Saranga, Y, Krugman, T, Abbo, S, Nevo, E and Fahima, T (2008 b) Allelic diversity associated with aridity gradient in wild emmer wheat populations. Plant Cell and Environment 31: 3949.Google Scholar
Perrier, X and Jacquemoud-Collet, JP (2006) Darwin software. Available athttp://darwin.cirad.fr/darwin.Google Scholar
Pervaiz, ZH, Rabbani, MA, Pearce, SR and Malik, SA (2009) Determination of genetic variability of Asian rice (Oryza sativa L.) varieties using microsatellite markers. African Journal of Biotechnology 8: 56415651.Google Scholar
Prasada Rao, KE, de Wet, JMJ, Brink, DK and Mengesha, MH (1987) Intraspecific variation and systematics of cultivated Setaria italica, foxtail millet (Poaceae). Economic Botany 41: 108116.Google Scholar
Senior, ML, Murphy, JP, Goodman, MM and Stuber, CW (1998) Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Science 38: 10881098.CrossRefGoogle Scholar
Shehzad, T, Iwata, H and Okuno, K (2009) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breeding Science 59: 217227.CrossRefGoogle Scholar
Stępień, Ł, Mohler, V, Bocianowski, J and Koczyk, G (2007) Assessing genetic diversity of polish wheat (Triticum aestivum) varieties using microsatellite markers. Genetic Resources and Crop Evolution 54: 14991506.Google Scholar
Thudi, M, Senthilvel, S, Bottley, A, Hash, CT, Reddy, AR, Feltus, AF, Paterson, AH, Hoisington, DA and Varshney, RK (2010) A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica 174: 253260.CrossRefGoogle Scholar
Upadhyaya, HD, Pundir, RPS, Gowda, CLL, Reddy, VG and Singh, S (2008 a) Establishing a core collection of foxtail millet to enhance utilization of germplasm of an underutilized crop. Plant Genet Resources: Characterization and Utilization 7: 177184.CrossRefGoogle Scholar
Upadhyaya, HD, Dwivedi, SL, Baum, M, Varshney, RK, Udupa, SM, Gowda, CLL, Hoisinton, D and Singh, S (2008 b) Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biology 8: 106.Google Scholar
Upadhyaya, HD, Yadav, D, Dronavalli, N, Gowda, CLL and Singh, S (2010) Mini core germplasm collections for infusing genetic diversity in plant breeding programs. Electronic Journal of Plant Breeding 1: 12941309.Google Scholar
Wang, R, Yu, Y, Zhao, J, Shi, Y, Song, Y, Wang, T and Li, Y (2008) Population structure and linkage disequilibrium of a minicore set of maize inbred lines in China. Theoretical and Applied Genetics 117: 11411153.CrossRefGoogle Scholar
Wang, ML, Zhu, C, Barkley, NA, Chen, Z, Erpelding, JE, Murray, SC, Tuinstra, MR, Tesso, T, Pederson, GA and Yu, J (2009) Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum. Theoretical and Applied Genetics 120: 1323.CrossRefGoogle ScholarPubMed
Wang, C, Chen, J, Zhi, H, Yang, L, Li, W, Wang, Y, Li, H, Zhao, B, Chen, M and Diao, X (2010) Population genetics of foxtail millet and its wild ancestor. BMC Genetics 11: 90.Google Scholar
Yang, X, Yan, J, Shah, T, Warburton, ML, Li, Q, Li, L, Chai, Y, Fu, Z, Zhou, Y, Xu, S, Bai, G, Meng, Y, Zheng, Y and Li, J (2010) Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theoretical and Applied Genetics 121: 417431.CrossRefGoogle ScholarPubMed
Zhang, H, Zhang, D, Wang, M, Sun, J, Qi, Y, Li, J, Wei, X, Han, L, Qiu, Z, Tang, S and Li, Z (2011) A core collection and mini core collection of Oryza sativa L. in China. Theoretical and Applied Genetics 122: 4961.Google Scholar
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