Mining favorable alleles for five agronomic traits from the elite rapeseed cultivar Zhongshuang 11 by QTL mapping and integration

Zhongshuang 11 (ZS11) is an elite inbred rapeseed (Brassica napus L.) cultivar widely planted in the Yangtze River basin for its favorable characteristics including high seed oil content (SOC), low seed glucosinolate content (SGC), long siliques, and stable yield. To transfer the ideal traits from ZS11 into 195-14A, a Polima (pol)-type cytoplasmic male sterile line with high general combining ability, a doubled haploid population derived from the cross of ZS11 and 195-14A was developed. Based on this population, a high-density genetic linkage map covering 2553 cM with an average marker interval of 0.81 cM, was constructed using the Brassica 60K SNP array and simple sequence repeats. In seven environments, 64, 29, 35, 37, and 33 QTL were identified for silique length, seeds per silique, seed density per silique, SOC, and SGC, respectively. Most favorable alleles were from ZS11. Seventy-one consensus QTL were identified by a QTL meta-analysis, eight of which (cqSL–A9–2, cqSL–C7, cqSGC–C2, cqSOC–A5–2, cqSOC–A5–3, cqSPS–A6–2, cqSPS–A7–2, and cqSDPS–A9–2) were assigned as major QTL. Comparative genomics and expression analysis predicted 72 candidate genes underlying the 21 consensus QTL for the five traits. These findings suggest the genetic basis of the superior performance of ZS11 and suggest favorable alleles for development of cultivars with improved yield and quality. These results will assist in cloning these promising alleles in the future.