Abstract
Cotton (Gossypium spp.) is the world’s most important natural textile fiber crop, and Gossypium hirsutum L. has been responsible for 90 % of the annual cotton crop in the world. Few studies are conducted about the population structure and genetic diversity of elite cotton (G. hirsutum) germplasm based on a worldwide collection. In this study, we analyzed population structure and genetic diversity of 157 elite G. hirsutum cultivar accessions collected from China, American, Africa, Former Soviet Union, and Australia using 146 SSR markers randomly distributed on the 26 chromosomes of cotton. The average allele number and PIC were 2.26 and 0.2857, respectively, indicating a relatively low degree of genetic diversity. By predefining the total cotton panel as three groups according to their geographic origin, we proved that the predefined American-origin group had higher average genetic diversity than China-origin group, but the China-origin group had the widest range of genetic variation, and the highest genetic distance happened between the varieties from America and from China, implying a direction for genetic improvement. Population structure analysis revealed two groups existed in the whole cotton panel, but the two groups inferred from structure were not consistent with the predefined three groups, indicating that the exchange and domestication of germplasm all over the world. Further independent STRUCTURE run on the two inferred groups indicated that they could be subdivided into three and two subgroups. Analysis of molecular variance showed that the American-origin group had higher population substructure than China-origin group, and only a little variation between groups was explained by population structure, suggesting that our population was suitable for association mapping. Finally, the evolutionary implication of cotton population structure was discussed. These results have provided valuable information for the association mapping of important agronomic traits, as well as for the breeding and exploit of new cotton germplasms.
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References
Abdurakhmonov IY, Saha S, Jenkins JN, Buriev ZT, Shermatov SE, Scheffler BE, Pepper AE, Yu JZ, Kohel RJ, Abdukarimov A (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136:401–417
Ahoton L, Lacape JM, Baudoin JP, Mergeai G (2003) Introduction of Australian diploid cotton genetic variation into upland cotton. Crop Sci 43:1999–2005
Akagi H, Yokozeki Y, Nagaki A, Fujimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeats and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94:61–67
Bertini CHCM, Schuster I, Sediyama T, Barros EG, Moreira MA (2006) Characterization and genetic diversity analysis of cotton cultivars using microsatellites. Genet Mol Biol 2:321–329
Chen G, Du XM (2006) Genetic diversity of source germplasm of upland cotton in China as determined by SSR marker analysis. Acta Genet Sin 33(8):733–745
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Fang DD, Hinze LL, Percy RG, Li P, Deng D, Thyssen G (2013) A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum L.) cultivars from major cotton-growing countries. Euphytica 191:391–401
Flint-Garcia SA, Thuillet AC, Yu JM, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44:1054–1064
Hardy OJ, Vekemans X (2002) SpaGeDi: a versatile computer program to analyze spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
Hussain M, Khan MSI, Khanl AI, Akhtar KP, Gong WK (2002) Induced mutagenesis as a genetic improvement tool of cotton (Gossypium hirsutum L.) in conformance with needs in Pakistan. Cotton Sci 14(6):374–377
Iqbal J, Ouk Reddy, Km El-Zik, Pepper AEA (2001) Genetic bottleneck in the evolution under domestication of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting. Theor Appl Genet 103:547–554
Kantartzi SK, Ulloa M, Sacks E, Stewart JM (2009) Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites. Genetica 136:141–147
Lacape JM, Dessauw D, Rajab M, Noyer JL, Hau B (2007) Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Mol Breed 19:45–58
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129
Liu S, Cantrell RG, Mcarty JCJ, Stewart JM (2000) Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions. Crop Sci 40:1459–1469
Moiana LD, Filho PSV, Goncalves-Vidigal MC, Lacanallo GF et al (2012) Genetic diversity and population structure of cotton (Gossypium hirsutum L. race latifolium H.) using microsatellite markers. Afr J Biotechnol 11(54):11640–11647
Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Report 11:122–127
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multi-locus genotype data. Genetics 155:945–959
Rungis D, Llewellyn D, Dennis ES, Lyon BR (2005) Simple sequence repeat (SSR) markers reveal low levels of polymorphism between cotton (Gossypium hirsutum L.) cultivars. Aust J Agric Res 56:301–307
Schneider S, Roessll D, Excoffier L (2000) ARLEQUIN: a software for population genetics data analysis, version 2.0. Genetics and Biometry Laboratory, Department of Anthropology, Geneva, Switzerland, University of Geneva
Stewart JM (1992) Germplasm resources and enhancement strategies for disease. Proc Beltwide Cotton Conf 3:1323–1325
Sun JL, Du XM, Zhou ZL, Pan ZE, Pang BY (2004) Innovation of elite cotton germplasm. CHINA COTTON 31(4) (in Chinese)
Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V (2014) Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 127:283–295
Van-Esbroeck G, Bownam DT (1998) Cotton germplasm diversity and its importance to cultivar development. J Cotton Sci 2:121–129
Wendel JF, Cronn RC (2003) Polyploidy and the evolutionary history of cotton. Adv Agron 78:139–186
Zhai XJ, Luo GT (1994) The characteristics of cotton Verticillium wilt breaking out and control methods of this disease. Hebei Agricultural Sciences 2:32 (in Chinese)
Zhang DL, Zhang HL, Wang MX, Sun JL, Qi YW, Wang FM, Wei XH, Han LZ, Wang XK, Li ZC (2009) Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet 119:1105–1117
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This research was supported by the National Natural Science Foundation of China (Grant No. 31000733) and by the National Hi-Tech Research and Development Program of China (Grant No. 2012AA101108-02-02).
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Zhao, Y., Wang, H., Chen, W. et al. Genetic diversity and population structure of elite cotton (Gossypium hirsutum L.) germplasm revealed by SSR markers. Plant Syst Evol 301, 327–336 (2015). https://doi.org/10.1007/s00606-014-1075-z
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DOI: https://doi.org/10.1007/s00606-014-1075-z