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

Huiyan Zhao; Urmila Basu; Berisso Kebede; Cunmin Qu; Jiana Li; Habibur Rahman

doi:10.1371/journal.pone.0209982

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

PLoS One. 2019 Feb 4;14(2):e0209982. doi: 10.1371/journal.pone.0209982. eCollection 2019.

Authors

Huiyan Zhao^{1

2}, Urmila Basu¹, Berisso Kebede¹, Cunmin Qu², Jiana Li², Habibur Rahman¹

Affiliations

¹ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
² Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, People's Republic of China.

Abstract

Yellow seed is a desirable trait in Brassica oilseed crops. The B. rapa var. Yellow Sarson carry unique yellow seed color genes which are not only important for the development of yellow-seeded oilseed B. rapa cultivars but this variant can also be used to develop yellow-seeded B. napus. In this study, we developed near-isogenic lines (NILs) of Yellow Sarson for the major seed coat color QTL SCA9-2 of the chromosome A9 and used the NILs to fine map this QTL region and to identify the candidate genes through linkage mapping and transcriptome sequencing of the developing seeds. From the 18.4 to 22.79 Mb region of SCA9-2, six SSR markers showing 0.63 to 5.65% recombination were developed through linkage analysis and physical mapping. A total of 55 differentially expressed genes (DEGs) were identified in the SCA9-2 region through transcriptome analysis; these included three transcription factors, Bra028039 (NAC), Bra023223 (C2H2 type zinc finger), Bra032362 (TIFY), and several other genes which encode unknown or nucleic acid binding protein; these genes might be the candidates and involved in the regulation of seed coat color in the materials used in this study. Several biosynthetic pathways, including the flavonoid, phenylpropanoid and suberin biosynthetic pathways were significantly enriched through GO and KEGG enrichment analysis of the DEGs. This is the first comprehensive study to understand the yellow seed trait of Yellow Sarson through employing linkage mapping and global transcriptome analysis approaches.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brassica napus / genetics
Brassica rapa / genetics*
Chromosome Mapping*
Gene Expression Profiling
Genes, Plant
Phenotype
Pigmentation
Polymorphism, Single Nucleotide
Quantitative Trait Loci*
Seeds / genetics*
Transcriptome*

Grants and funding

This study was supported by the Genome Canada; DOTM; HR; https://www.genomecanada.ca/; Genome Alberta; DOTM; HR; http://genomealberta.ca/; Natural Science and Engineering Research Council of Canada (NSERC); 298778-2011 RGPIN; HR; http://www.nserc-crsng.gc.ca/; China Scholarship Council; HZ; Ministry of Education, State Administration of Foreign Experts Affairs; B12006; JL; http://www.moe.gov.cn/http://www.safea.gov.cn/; Chongqing Science and Technology Bureau; cstc2016shms-ztzx80010, cstc2017jcyjAX0321; CQ; http://www.cstc.gov.cn/; Southwest University; XDJK2016B030; CQ; http://kjc.swu.edu.cn/s/kjc/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.