Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans

Abstract

Plant height (PH) and the number of nodes on the main stem (NN) serve as major plant architecture traits affecting soybean seed yield. Although many quantitative trait loci for the two traits have been reported, their genetic controls at different developmental stages in soybeans remain unclear. Here, 368 soybean breeding lines were genotyped using 62,423 single nucleotide polymorphism (SNP) markers and phenotyped for the two traits at three different developmental stages over two locations in order to identify their quantitative trait nucleotides (QTNs) using compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) approaches. As a result, 11 and 13 QTNs were found by CMLM to be associated with PH and NN, respectively. Among these QTNs, 8, 3, and 4 for PH and 6, 6, and 8 for NN were found at the three stages, and 3 and 6 were repeatedly detected for PH and NN. In addition, 34 and 30 QTNs were found by mrMLM to be associated with PH and NN, respectively. Among these QTNs, 11, 13, and 16 for PH and 11, 15, and 8 for NN were found at the three stages. A majority of these QTNs overlapped with the previously reported loci. Moreover, one QTN within the known E2 locus for flowering time was detected for the two traits at all three stages, and another that overlapped with the Dt1 locus for stem growth habit was also identified for the two traits at the mature stage. This may explain the highly significant correlation between the two traits. Our findings provide evidence for mixed major plus polygenes inheritance for dynamic traits and an extended understanding of their genetic architecture for molecular dissection and breeding utilization in soybeans.

Keywords: dynamic development; genome-wide association study; number of nodes on the main stem; plant height; quantitative trait nucleotide; soybean.

FIGURE 1

Characterization of the SNPs in the soybean genome. (A) Minor allele frequency of SNPs across the whole genome. (B) Distribution of LD blocks (>50 kb) in the whole genome. (C) Chromosomal region with pericentromeric regions in a darker color and whole chromosome in a lighter color (distance unit is Mb).

FIGURE 2

Population structure of 368 soybean accessions. (A) Calculation of the true K of the SBL population according to Evanno et al. (2005). (B) A neighbor-joining tree of the tested accessions that could be divided into three subpopulations. (C) Population structure was estimated by ADMIXTURE. Three colors represent three subpopulations, respectively. Each vertical column represents one individual and each colored segment in each column represents the percentage of the individual in the population. (D) PCA plot of the 368 accessions; two-dimensional scales were used to reveal population stratification.

FIGURE 3

Average LD decay rates in euchromatic and heterochromatic regions of the whole genome. The mean LD decay rate was estimated as the squared correlation coefficient (r²) using all pairs of SNPs located within 5 Mb of physical distance in euchromatic (red) and heterochromatic (green) regions in the SBL population.

FIGURE 4

Manhattan plots and quantile–quantile plots for PH1 (A), PH2 (B), PH3 (C), NN1 (D), NN2 (E), and NN3 (F) over three stages in the SBL population. The major loci for PH3 (left) and NN3 (right) in their Manhattan plots were located on chromosomes 10 and 19, respectively (G).

FIGURE 5

Candidate regions of the genome showing significant association signals near identified major loci for PH and NN. The top of each panel shows the Manhattan plot indicating the level of SNP association with PH (A) or NN (B). Gray horizontal dashed lines indicate the genome-wide suggestive threshold. The bottom of each panel shows the local LD of the chromosomal regions containing the peak SNP (SNP with the lowest P-value), whose position is indicated by a green asterisk. Nearby haplotype blocks are outlined in black triangles.

FIGURE 6

Venn diagrams for loci associated with PH (A) and NN (B) over three stages.