Genome-wide identification of silique-related traits based on high-density genetic linkage map in Brassica napus

Abstract

The yield of rapeseed is directly and indirectly influenced by silique-related traits, the genetic dissection, and improvement of the silique-related traits are thus the most important research project in rapeseed. Seven silique-related traits, including seed number per silique (SPS), silique length (SL), silique width (SW), silique thickness (ST), silique volume (SV), silique density (SD), and thousand seed weight (TSW) were further analyzed through quantitative trait locus (QTL) mapping based on a high-density genetic linkage map in KN population. A total of 273 identified QTLs were integrated into 230 consensus QTLs, in which 84.78% of consensus QTLs were considered to be environment-specific QTLs and 15.22% of consensus QTLs were considered to be environmentally stable expression QTLs. Two major QTLs, including cqSW.C6-5 for SW and cqSPS.C6-3 for SPS were identified on C06. According to QTLs integrated from different silique traits, 48 unique QTLs were identified with pleiotropy that involved in 2–5 silique-related traits. In addition, 185 epistatic locus pairs were identified with the PV ranging from 0.96 to 15.98%. QTL comparison were made between the KN population and other mapping populations, a total of 164 QTLs for silique-related traits (48 for SPS, 31 for SL, 7 for SD, and 78 for TSW) from nine previously reported researches were aligned to the Brassica napus reference genome, in which 23 QTLs were considered as new QTLs (8 for SD, 4 for SL, 7 for SPS, 4 for TSW). More importantly, cqSPS.C6-3 for SPS might be a novel major QTL. Furthermore, 82 candidate genes in B. napus corresponding to 48 candidate genes in Arabidopsis thaliana were identified, which were involved in transcription factors, enzymes, protein structure units, phytohormone response factors, and transporters, etc. These findings not only provided more comprehensive insights into the genetic basis for silique-related traits but also new cues for improving silique and increasing seed yield in B. napus.