Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

KEY MESSAGE : 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 variat...

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Veröffentlicht in:Theoretical and applied genetics Jg. 127; H. 2; S. 283 - 295
Hauptverfasser: Tyagi, Priyanka, Gore, Michael A, Bowman, Daryl T, Campbell, B. Todd, Udall, Joshua A, Kuraparthy, Vasu
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Berlin/Heidelberg Springer-Verlag 01.02.2014
Springer Berlin Heidelberg
Springer
Springer Nature B.V
Schlagworte:
Agriculture
Alleles
Biochemistry
Biological diversity
Biomedical and Life Sciences
Biotechnology
classification
Cotton
Cultivars
Domestication
Epidemics
Fabric analysis
genetic distance
Genetic diversity
Genetic Markers
Genetic Variation
genetics
Genomes
genomics
Germplasm
Gossypium
Gossypium - classification
Gossypium - genetics
Gossypium hirsutum
Life Sciences
loci
microsatellite repeats
Original Paper
pedigree
Phylogenetics
Phylogeny
Physiological aspects
Plant Biochemistry
plant breeding
Plant Breeding/Biotechnology
Plant Genetics and Genomics
population structure
tetraploidy
United States
United States
North Carolina
United States > US
Upland Cotton
Simple Sequence Repeat Locus
Simple Sequence Repeat Marker
Allelic Richness
Polymorphism Information Content
ISSN:0040-5752, 1432-2242, 1432-2242
Online-Zugang:Volltext
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Zusammenfassung:KEY MESSAGE : 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.
Bibliographie:http://dx.doi.org/10.1007/s00122-013-2217-3
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ISSN:0040-5752
1432-2242
1432-2242
DOI:10.1007/s00122-013-2217-3