Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association-Mapping Panel Revealed by Genome-Wide SNP Markers in Sesame

The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype–genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1 × 10-3, with averages of 1.0 × 10-4, 2.7 × 10-4, and 3.6 × 10-4 obtained, respectively for three identified subgroups of the panel: Pop 1, Pop 2, and the Mixed. The genetic structure analysis revealed that these sesame germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in the panel. The genome-wide linkage disequilibrium (LD) analysis showed that an average LD extended up to ∼99 kb. The genetic diversity and population structure revealed in this study should provide guidance to the future design of association studies and the systematic utilization of the genetic variation characterizing the sesame panel

Favorable QTL Alleles for Yield and Its Components Identified by Association Mapping in Chinese Upland Cotton Cultivars

<div><p>Linkage disequilibrium based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 356 representative Upland cotton cultivars was constructed, evaluated in three environments and genotyped using 381 SSRs to detect molecular markers associated with lint yield and its components. The results showed that abundant phenotypic and moderate genetic diversities existed within this germplasm panel. The population could be divided into two subpopulations, and weak relatedness was detected between pair-wise accessions. LD decayed to the background (<i>r</i>² = 0.1182, P≤0.01), <i>r</i>² = 0.1 and <i>r</i>² = 0.2 level within 12–13 cM, 17–18 cM and 3–4 cM, respectively, providing the potential for association mapping of agronomically important traits in Chinese Upland cotton. A total of 55 marker-trait associations were detected between 26 SSRs and seven lint yield traits, based on a mixed linear model (MLM) and Bonferroni correction (<i>P</i>≤0.05/145, −log₁₀<i>P</i>≥3.46). Of which 41 could be detected in more than one environment and 17 markers were simultaneously associated with two or more traits. Many associations were consistent with QTLs identified by linkage mapping in previous reports. Phenotypic values of alleles of each loci in 41 stably detected associations were compared, and 23 favorable alleles were identified. Population frequency of each favorable allele in historically released cultivar groups was also evaluated. The QTLs detected in this study will be helpful in further understanding the genetic basis of lint yield and its components, and the favorable alleles may facilitate future high-yield breeding by genomic selection in Upland cotton.</p></div

Allele frequency for each favorable QTL allele in historically released Chinese Upland cotton cultivar groups.^a

<p>^a CK, I, II, III, IV, V and VI indicates the founder parent group (CK), and the Chinese cultivars released in 1930–1960, 1961–1970, 1971–1980, 1981–1990, 1991–2000 and 2000–2005, respectively.</p

Scatter plots of <i>r</i>² values against genetic distance among linked loci (P≤0.01) in 356 <i>G. hirsutum</i> L. accessions.

<p>The trend line is a non-linear logarithmic regression curve of <i>r</i>² on genetic distance. LD decayed to the background (<i>r</i>² = 0.1182, P≤0.01), <i>r</i>² = 0.1 and <i>r</i>² = 0.2 level within about 12–13 cM, 17–18 cM and 3–4 cM, respectively.</p

Estimated LnP(D) and Δ<i>K</i> over five repeats of STRUCTURE analysis.

<p>(a) LnP(D) for <i>k</i> from 1 to 10 for 356 accessions. LnP(D) value of each hypothetical <i>k</i> kept increasing with <i>k</i> value and did not show any peak. (b) Δ<i>K</i> for <i>k</i> from 2 to 9 for 356 accessions. The <i>Δk</i> value showed a much higher likelihood at <i>k</i> = 2 than at <i>k</i> = 3–10, suggesting that the total panel should be divided into two major subpopulations.</p

Phenotypic correlations among lint yield and its components based on trait means of 356 upland cotton accessions across three environments.

<p>^a See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082193#pone-0082193-t002" target="_blank">Table 2</a> for abbreviations.</p