Genome-wide association study reveals genomic regions impacting yield-related traits in allohexaploid Brassica with AABBCC genomes

Abstract Background and Aims Brassica is an important genus with economic value. Allopolyploids generally possess abundant genetic diversity, which, when combined with selective breeding, can lead to yield improvement. Previously, we have derived a novel allohexaploid Brassica doubled haploid (DH) population from two genetically different synthetic Brassica allohexaploid parents (2n = AABBCC). However, the underlying mechanisms of seed yield in novel Brassica allohexaploids are unclear. In this study, we aim to explore the genetic basis of yield-related traits controlling seed yield in this allohexaploid Brassica DH population. Methods We assessed genetic variations, phylogenetic and population structure, and selection signals of 149 individual plants in this novel allohexaploid Brassica DH population based on restriction-site associated DNA sequencing. A genome-wide association study (GWAS) in three different environments was performed to identify single nucleotide polymorphism (SNP) markers and candidate genes associated with seed yield and eight yield-related traits. Key Results Phylogenetic and population structure analyses divided the 149 individual plants into two genetically diverse subgroups plus an intersected subgroup, and revealed genetic differentiation and character separation in progenies. We identified 142 significant SNPs associated with four agronomically important traits and 17 haplotype blocks containing multiple SNPs. Two genes, BhLecRK and BhCABIN1, were identified as candidate genes associated with silique length. We further tested the mRNA level of these two genes, and found that their expression level peaked at 21 days after pollination. Conclusions We propose that the two genes, BhLecRK and BhCABIN1, may regulate silique development by abundant expression in silique tissues at the critical stage during Brassica development. The results of phylogenetic analysis and GWAS provide a genetic and molecular foundation for yield improvement of allohexaploid Brassica.