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Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.).

ABSTRACT: Background:Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. Results:To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions:The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments.

SUBMITTER: Wang T

PROVIDER: S-EPMC7397576 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (<i>Brassica napus</i> L.).

Wang Tengyue T Wei Lijuan L Wang Jia J Xie Ling L Li Yang Yang YY Ran Shuyao S Ren Lanyang L Lu Kun K Li Jiana J Timko Michael P MP Liu Liezhao L

Biotechnology for biofuels 20200803

<h4>Background</h4><i>Brassica napus</i> is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in <i>B. napus</i>.<h4>Results</h4>To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days ...[more]

PMID: 32774455

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Project description:BACKGROUND: Seed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.). However, the genetic basis of both traits is poorly understood. The main objectives of this study were to dissect the genetic basis of SW and SL in rapeseed through the preliminary mapping of quantitative trait locus (QTL) by linkage analysis and fine mapping of the target major QTL by regional association analysis. RESULTS: Preliminary linkage mapping identified thirteen and nine consensus QTLs for SW and SL, respectively. These QTLs explained 0.7-67.1% and 2.1-54.4% of the phenotypic variance for SW and SL, respectively. Of these QTLs, three pairs of SW and SL QTLs were co-localized and integrated into three unique QTLs. In addition, the significance level and genetic effect of the three co-localized QTLs for both SW and SL showed great variation before and after the conditional analysis. Moreover, the allelic effects of the three QTLs for SW were highly consistent with those for SL. Two of the three co-localized QTLs, uq.A09-1 (mean R(2) = 20.1% and 19.0% for SW and SL, respectively) and uq.A09-3 (mean R(2) = 13.5% and 13.2% for SW and SL, respectively), were detected in all four environments and showed the opposite additive-effect direction. These QTLs were validated and fine mapped (their confidence intervals were narrowed down from 5.3 cM to 1 cM for uq.A09-1 and 13.2 cM to 2.5 cM for uq.A09-3) by regional association analysis with a panel of 576 inbred lines, which has a relatively rapid linkage disequilibrium decay (0.3 Mb) in the target QTL region. CONCLUSIONS: A few QTLs with major effects and several QTLs with moderate effects might contribute to the natural variation of SW and SL in rapeseed. The meta-, conditional and allelic effect analyses suggested that pleiotropy, rather than tight linkage, was the genetic basis of the three pairs of co-localized of SW and SL QTLs. Regional association analysis was an effective and highly efficient strategy for the direct fine mapping of target major QTL identified by preliminary linkage mapping.

Dataset Information

Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.).

Publications

Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (<i>Brassica napus</i> L.).

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