Mapping QTLs and candidate genes introgressed from Sinapis alba for siliquae related traits in second backcross progeny of allohexaploid brassica

Siliquae length (SL), beak length (BL), and seeds per siliqua (SPS) are critical for oilseed Brassica crop suitability. Breeding and biotechnology focus on genetic manipulation of the crop to enhance crop productivity. To identify QTL regions and genes contributing to SL, BL, and SPS, we developed a panel of 94 BCILs (BC₂F_3-4) with segregating traits and genotyped by 192 donor genome-specific SSRs. We developed a linkage map spanning 12 linkage groups with a total length of 1349.8 cM. We detected 1 quantitative trait locus (QTL) on Chromosome 04 with the log of odd (LOD) value of 2.68 and phenotypic variance explained (PVE) of 13.88%. Two QTLs were mapped for BL with LOD and PVE values of 5.72–20.44 and 12.75–37.48%, respectively. In addition to these, a QTL for SPS was mapped on chromosome 04 with LOD and PVE values of 7.50 and 31.35%, respectively. Moreover, a total of three QTLs for SL were identified at LOD scores of 2.99 (9.93% PVE), 3.03 (3.27% PVE), and 3.01 (6.76% PVE) in the second crop season (CS-II). Additionally, one QTL for BL at LOD 10.19 (21.69% PVE) was detected along with two QTLs of SPS at LOD 6.13 and 3.08 cumulatively controlling > 40% phenotypic variations. Among all these QTLs, the QTL of BL and SPS were major and controlling > 10% phenotypic variations. A total of 17 potential genes were predicted from all the QTL regions, out of which PG-3 was found orthologous to Brassica rapa receptor protein kinase CLAVATA1 regulating the development of multiple locules. To the best of our knowledge, this is the first report on the detection of QTLs for SL, BL, and SPS in BCILs introgressed from S. alba.