A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis.
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.
Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, PR, Brasil.
Rodrigo Iván
http://orcid.org/0000-0001-6468-9394
RI
Contreras-Soto
Institute of Biological Sciences, University of Talca, Casilla, Talca, Chile.
Freddy
F
Mora
COODETEC, BR, Cascavel, PR, Brasil.
Marco Antônio Rott
MA
de Oliveira
COODETEC, BR, Cascavel, PR, Brasil.
Wilson
W
Higashi
Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo, Maringá, PR, Brasil.
Carlos Alberto
CA
Scapim
Dow Agrosciences, Rod. Anhanguera, Cravinhos, SP, Brazil.
Ivan
I
Schuster
D001938:Brazil; D001947:Breeding; D002874:Chromosome Mapping; D059647:Gene-Environment Interaction; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics / Q000254:growth & development; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development*