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As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed ( Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38–13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.

Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed ( L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. is a crucifer with long siliques, many SS, and heavy seeds. A novel introgression line with many SS was previously selected from multiple crosses ( ssp. × ) × . In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs ( , and ) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.

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 .