Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals OTL Hotspots and Epistatic Interactions

The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 OIL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (OIL) of seed weight, seed germination, and root and shoot lengths. A OIL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between OIL hotspots for seed germination on A02 and A10 and with a salt tolerance OIL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.