Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)
- 2k Downloads
Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton.
Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.
KeywordsSimple Sequence Repeat Marker Allelic Richness Polymorphism Information Content Simple Sequence Repeat Locus Upland Cotton
We thank Dr. Gina Brown-Guedira for providing access to the genotyping facility and Jared Smith, Kim Howell and Blake Bowen for their technical assistance. We are grateful to Cotton Incorporated, NC Agricultural Research Service and NC Cotton Producers Association for funding support. The authors would like to thank NC State University Plant Breeding Center and Monsanto Company for providing PhD assistantship to Priyanka Tyagi.
Conflict of interest
The authors declare that there are no conflicts of interest in the reported research.
The authors note that this research is performed and reported in accordance with ethical standards of the scientific conduct.
- Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA, Kushanov FN, Salakhutdinov LB, Buriev ZT, Saha S, Scheffler BE, Jenkins JN, Abdukarimov A (2008) Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics 92:478–487PubMedCrossRefGoogle Scholar
- Abdurakhmonov IY, Buriev ZT, Shermatov SE, Abdullaev AA, Urmonov K, Kushanov F, Egamberdiev SS, Shapulatov U, Abdukarimov A, Saha S, Jenkins JN, Kohel RJ, Yu JZ, Pepper AE, Kumpatla SP, Ulloa M (2012) Genetic Diversity in Gossypium genus. In: Caliskan M (ed) Genetic Diversity in Plants, ISBN: 978-953-51-0185-7, InTech, pp 313–338. doi: 10.5772/2640
- Blott S et al (2003) Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 16:253–266Google Scholar
- Bowman DT, Gutierrez OA, Percy RG, Calhoun DS, May OL (2006) Pedigrees of upland and pima cotton cultivars released between 1970 and 2005. Miss Agric For Exp Stn Bull 1155Google Scholar
- Brubaker CL, Bourland FM, Wendel JF (1999) The origin and domestication of cotton. In: Smith CW, Cothren JT (eds) Cotton: origin, history, technology, and production. Wiley, New York, pp 3–32Google Scholar
- 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 1–11Google Scholar
- Frankel OH (1984) Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P (eds) Genetic manipulation: impact on man and society. Cambridge University Press, Cambridge, pp 161–170Google Scholar
- Kuraparthy V, Bowman DT (2013) Gains in breeding Upland cotton for fiber quality. J Cotton Sci (in press)Google Scholar
- Kuroda Y, Tomooka N, Kaga A, Wanigadeva SMSW, Vaughan DA (2009) Genetic diversity of wild soybean (Glycine soja Sieb. et Zucc.) and Japanese cultivated soybeans [G. max (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection. Genet Res Crop Evol 56:1045–1055CrossRefGoogle Scholar
- Meuwissen THE, Karlsen A, Lien S, Olsaker I, Goddard ME (2002) Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genetics 16:373–379Google Scholar
- Niles GA, Feaster CV (1984) Breeding. In: Kohel RJ, Lewis CF (eds) Cotton, agronomy monograph no. 24. CSSA, Madison, pp 201–231Google Scholar
- Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends in Plant Sci 1:215–222Google Scholar
- Rohlf FJ (2000) Numerical taxonomy and multivariate analysis system, ver. 2.11. Applied Biostatistics, New YorkGoogle Scholar
- Smith CW, Cantrell RG, Moser HS, Oakley SR (1999) History of cultivar development in the United States. In: Smith CW, Cothren JT (eds) Cotton: origin, history, technology, and production. Wiley, New York, pp 99–171Google Scholar
- Staten G (1970) Breeding Acala 1517 cottons, memoir series no. 4. New Mexico State University, Las Cruces, pp 1926–1970Google Scholar
- Van Esbroeck GA, Bowman DT (1998) Cotton improvement. Cotton germplasm diversity and its importance to cultivar development. J Cotton Sci 2:121–129Google Scholar
- Van Esbroeck GA, Bowman DT, May OL, Calhoun DS (1999) Genetic similarity indices for ancestral cotton cultivars and their impact on genetic diversity estimates of modern cultivars. Crop Sci 39:323–328Google Scholar