A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis

Abstract

Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information. The soybean cultivars (N = 169) were field-evaluated across four locations of southern Brazil. The genome-wide haplotype association analysis (941 haplotypes) identified eleven, seventeen and fifty-nine SNP-based haplotypes significantly associated with SY, SW and PH, respectively. Although most marker-trait associations were environment and trait specific, stable haplotype associations were identified for SY and SW across environments (i.e., haplotypes Gm12_Hap12). The haplotype block 42 on Chr19 (Gm19_Hap42) was confirmed to be associated with PH in two environments. These findings enable us to refine the breeding strategy for tropical soybean, which confirm that haplotype-based GWAS can provide new insights on the genetic determinants that are not captured by the single-marker approach.

Fig 1

Manhattan plots of GWAS for seed yield (SY) evaluated in a soybean association mapping panel across the following environments of southern Brazil, A) Cascavel, B) Palotina, C) Primavera do Leste and D) Rio Verde. Negative log10-transformed P-values of SNPs from a genome-wide scan for SY using a mixed linear model that includes both kinship and populations structure are plotted against positions on each of the 20 chromosomes. The significant SNPs associated with the trait (P > 3.0 × 10⁻³) are distinguished by the threshold line.

Fig 2. Putative region (SNPs ss715613192 ss715613203, ss715613207 and ss715613219 on Gm12_Hap12) associated with seed weight (SW) and seed yield (SY) in soybean.

Gm12_Hap12 is in the same region of gene glyma12g075700 annotated as a double-stranded RNA-binding protein 2-like, which encodes a Ribonuclease III protein (BT097697). Glyma12g075600 is another gene near of this LD block region (Gm12_Hap12) which encodes protein for senescence regulator in soybean. SSR markers have been involved to seed protein synthesis (Liang et al. 2010) and associated with QTLs of seed glycitein, glycitein, pod maturity and reproductive stage. Bottom panel depicts a haplotype region of 412 kb associated with SY and SW (Red color intensity indicates the intensity of r², i.e., higher color intensity means higher r²).

Fig 3

Manhattan plots of GWAS for 100-seed weight (SW) evaluated in a soybean association mapping panel across the following environments of southern Brazil, A) Cascavel, B) Palotina, C) Primavera do Leste and D) Rio Verde. Negative log10-transformed P-values of SNPs from a genome-wide scan for SW using a mixed linear model that includes both kinship and populations structure are plotted against positions on each of the 20 chromosomes. The significant associations (P > 3.0 × 10⁻³) are distinguished by the threshold line.

Fig 4

Manhattan plot of GWAS for plant height (PH) evaluated in a soybean association mapping panel across the following environments of southern Brazil, A) Cascavel, B) Palotina, C) Primavera do Leste and D) Rio Verde. Negative log10-transformed P-values of SNPs from a genome-wide scan for PH using a mixed linear model that includes both kinship and populations structure are plotted against positions on each of the 20 chromosomes. The significant associations (P > 3.0 × 10⁻³) are distinguished by the threshold line.

Fig 5. Putative region (SNPs ss715635403, ss715635425, ss715635433, ss715635454 and ss715635468 located on Gm19_Hap42; and loci ss715635494, ss715635506 and ss715635520 located on Gm19_Hap43) associated to traits of interest.

Gm19_Hap42 was associated with PH, SY and SCN in soybean. QTLs are in the same genomic region of gene Glyma19g37890 (Dt1 or GmFLT1), which is involved in the stem growth habit in soybean. Gene Glyma19g194500 encodes an abscisic acid-insensitive protein; Glyma19g38160 encodes a beta-fructofuranosidase isoenzyme and Glyma19g196000 encodes a spindly-related enzyme. Bottom panel depicts haplotypes regions of 494 (Gm19_Hap42) and 163 kb (Gm19_Hap43) associated with the mentioned traits (Red color intensity indicates the intensity of r², i.e., higher color intensity means higher r²).