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

Abstract

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 QTL 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 (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL 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 QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL 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.

Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

“…Therefore, this approach not only detects the expression of a specific gene and the genotype at that gene's locus, but it also reveals clustered trans -eQTLs that are simultaneously regulated by a large fraction of the transcriptome (Brem et al, 2002; Schadt et al, 2003; Morley et al, 2004). This approach has been successfully used in crop plants to detect transcript-level variation and downstream phenotypic trait variation (Jordan et al, 2007; Shi et al, 2007; West et al, 2007; Potokina et al, 2008; Xiao et al, 2013, 2014; Del Carpio et al, 2014; Basnet et al, 2015, 2016). Although eQTLs have successfully been cloned in plants (Werner et al, 2005; Zhang et al, 2006), global eQTL analysis in a large mapping population of plants has not hitherto been performed.…”

A Statistical Framework for QTL Hotspot Detection

“…To detect the QTL for these traits, Silva Pereira et al 2020). In QTL mapping for either the traditional or molecular traits, it has been observed that QTL are highly abundant in some of the genomic regions, and that QTL responsible for correlated traits are frequently clustered closely together in some specific genetic regions as compared to other regions (Goffinet and Gerber 2000;Schadt et al 2003;Chardon et al 2004;West et al 2007;Breitling et al 2008;Wu et al 2008;Wang et al 2014;Basnet et al 2015;Yang et al 2019). These regions enriched in QTL are referred to as QTL hotspots, and, statistically, they harbor a significantly higher number of QTL than expected by random chance.…”

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

“…However, success in improving salt tolerance in rice is made by identifying a major quantitative trait locus (QTL), which contributes to salt tolerance in rice. QTL analysis of seed germination have been reported in rice [ 18 ], soybean [ 19 ], wheat [ 20 ], Arabidopsis [ 21 ], and Brassica rapa [ 22 ]. However, it is difficult to develop rice elite varieties with a high level of salt tolerance due to a lack of understanding the mechanisms of salt tolerance during the seed germination stage.…”