Identification of a candidate QTG for seed number per silique by integrating QTL mapping and RNA-seq in Brassica napus L.

Abstract

Seed number per silique (SNPS) is one of seed yield components in rapeseed, but its genetic mechanism remains elusive. Here a double haploid (DH) population derived from a hybrid between female 6Q006 with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017, 2018, 2019 and 2021, and genotyped with Brassica 60K Illumina Infinium SNP array. An overlapping major QTL (qSNPS.C09) explaining 51.50% of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq. Subsequently, two DEGs in this interval were detected between extreme individuals in DH and F2 populations by transcriptome sequencing at 7 and 14 days after pollination siliques. Of which, BnaC09g45400D encoded an adenine phosphoribosyltransferase 5 (APT5) has a 48-bp InDel variation in the promoter of two parents. Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed, where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than 103 accessions carrying the same haplotype as parent 6W26. Collectively, the findings are helpful for rapeseed molecular breeding of SNPS, and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.