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

Abstract

Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.

Transcriptomic Analysis of Seed Coats in Yellow-Seeded Brassica napus Reveals Novel Genes That Influence Proanthocyanidin Biosynthesis

“…Flavonoids including anthocyanins and PAs are the major secondary metabolites that can influence leaf, flower, fruit, and seed color in plants and the flavonoid biosynthesis is controlled by a complex regulatory network with diverse TFs (Xu et al, 2014 ). Qu et al ( 2016b ) proposed that some TFs in two expression quantitative trait locus (eQTLs) hotspots, which harbor many trans -eQTLs for flavonoid TT genes, might be involved in the flavonoid pathway through different regulatory networks; these are represented by MYB51, bZIP25 , and MYC1 on chromosome A09. These eQTL hotspots were located around a major QTL for seed coat color on chromosome A09.…”

Fine mapping of the major QTL for seed coat color in Brassica rapa var. Yellow Sarson by use of NIL populations and transcriptome sequencing for identification of the candidate genes

“…To date, several researchers, such as Lou et al [30], Rahman et al [70, 71], Zhang et al [72], Li et al [17], Xiao et al [33], Bagheri et al [32], Padmaja et al [24], Stein et al [73], Qu et al [74, 75], Hong et al [48], Wang et al[76] and Wang et al [23, 34] have reported a major seed coat color gene or QTL on the chromosome A9 of B . rapa , B .…”

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

“…One example is represented by the non-smoky glycosyltransferase1 ( NSGT1 ) gene, that takes part in the phenylpropanoid pathway, which was shown to prevent the “smoky” aroma attribute (Tikunov et al, 2013 ). Similar glycosylation/glycosidation mechanisms operate in grape varieties that usually accumulate large amounts of volatile precursors as conjugated compounds that are released following tissue maceration (Rambla et al, 2016 , 2017b ). Using target approaches based on knowledge of metabolic pathways has led to the characterization of several genes involved in the biosynthesis of phenylpropanoids (Tieman et al, 2010 ; Mageroy et al, 2012 ), fatty acid-derived volatiles (Speirs et al, 1998 ; Chen et al, 2004 ; Matsui et al, 2007 ; Shen et al, 2014 ), apocarotenoids (Simkin et al, 2004 ), esters (Goulet et al, 2015 ), and other phenylalanine-derived volatile compounds (Tieman et al, 2010 ), and in the conjugation and/or deconjugation and emission of volatiles (Tikunov et al, 2013 ).…”

“…It also seems that metabolite composition, although genetically based, is heavily influenced by environmental factors, much more, even, than enzyme activity (Biais et al, 2014 ). Reassuring results have proved that the hereditability of the tomato fruit metabolome, including that part of the metabolome affecting flavor, in terms of mQTL, was relatively high, in both primary metabolites (sugars and acids) (Schauer et al, 2008 ) and volatiles (Rambla et al, 2016 ). Obviously, flavor-related traits have attracted much attention.…”