Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (<italic>Brassica napus</italic> L.)

Abstract

Plant height (PH) and the first branch height (BH) are important agronomic traits closely related to thickness of pod canopy and harvest index of Brassica napus . There are many reports on quantitative trait locus (QTL) and genome-wide association study (GWAS) for PH, but few reports on QTL and GWAS localization and candidate gene screening for BH. In this study, QTLs for PH and BH using the 186 recombinant inbred lines (RIL) in the two environments of 2016 and 2017 were detected based on the high-density genetic linkage map. A total of eight PH QTLs located on chromosomes A03, A04, and A09 were detected in the two environments of 2016 and 2019, with the explained phenotypic variation of individual QTL range from 4.60% to 13.29%, among which overlapped QTLs (q-2017PH-A04-2 and q-BLUP-PH-A04-2) were detected both in 2017 and based on Best Linear Unbiased Prediction (BLUP). Nine BH QTLs located on chromosomes A01, A02, A05, A09, C01, and C05 were detected, in which a single QTL explained 5.12% to 19.10% of phenotypic variation. Among them, q-2017BH-A09-1, q-BLUP-BH-A09-2, and q-BLUP-BH-A09-3 were overlapped. GWAS for PH and BH was performed using 588 resequencing natural populations established by our previous study. A total of 50 SNPs associated with PH and 12 SNPs associated with BH were detected in two years. Thirteen PH candidate genes involved in cell proliferation, cell multiplication, cell cycle and cell wall activity and eleven BH candidate genes involved in the synthesis and metabolism of gibberellin and spermidine, ribosome composition, photosynthesis and germination were screened based on the physical locations of SNPs, and their expressions in extreme phenotypes by qRT-PCR. This result will provide a theoretical basis for improving plant architecture and subsequent functional studies of genes.