Dissecting Genetic Architecture Underlying Seed Traits in Multiple Environments

Qi, Ting; Cao, Yujie; Zhang, Yingxin; Gao, Yujie; Zhu, Shuijin; Lou, Xiang‐Yang; Xu, Hongwei

doi:10.1534/genetics.114.168203

Cited by 4 publications

(1 citation statement)

References 31 publications

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“…Mixed linear model approach has been successfully applied in linkage mapping of complex traits, including seed traits in crops [ 32 , 40 , 41 ]. Because of the advantages of the mixed linear model approach in aggregating total genetic effects of numerous genetic variants scattered in the whole genome and dealing with covariates, such as age, sex and population stratification, many tools have been developed based on mixed linear model for estimating total genetic heritability and performing genome wide association mapping [ 42 – 45 ].…”

Section: Discussionmentioning

confidence: 99%

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Liu

Sun

et al. 2018

BMC Genomics

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BackgroundCottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement.ResultsA genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines.ConclusionsThis study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4837-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Liu

Sun

et al. 2018

BMC Genomics

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Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed (Brassica napus L.)

Shen

Yang

et al. 2017

Theor Appl Genet

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A high-density SNP map was constructed and several novel QTL for branch angle across six environments in Brassica napus were identified. Branch angle is a major determinant for the ideotype of a plant, while the mechanisms underlying this trait in Brassica napus remain elusive. Herein, we developed one doubled haploid population from a cross involving one Capsella bursa-pastoris derived B. napus intertribal introgression line with the compressed branches and wooden stems, and constructed a high-density SNP map covering the genetic distance of 2242.14 cM, with an average marker interval of 0.73 cM. After phenotypic measurements across six environments, the inclusive composite interval mapping algorithm was conducted to analyze the QTL associated with branch angle. In single-environment analysis, a total of 17 QTL were detected and mainly distributed on chromosomes A01, A03, A09 and C03. Of these, three major QTL, qBA.A03-2, qBA.C03-3 and qBA.C03-4 were steadily expressed, each explaining more than 10% of the phenotypic variation in at least two environments. Compared with other results on rapeseed branch angle, these major QTL were newly detected. In QTL by environment interactions (QEI) mapping, 10 QTL were identified, and the QTL average effect and QEI effect were estimated. Of these, 7 QTL were detected in both single-environment analysis and QEI mapping. Based on the physical positions of SNPs and the functional annotation of the Arabidopsis thaliana genome, 27 genes within the QTL regions were selected as candidate genes, including early auxin-responsive genes, small auxin-up RNA, auxin/indoleacetic acid and gretchenhagen-3. These results may pave the way for deciphering the genetic control of branch angle in B. napus.

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Joint association analysis method to dissect complex genetic architecture of multiple genetically related traits

Lin

et al. 2020

The Crop Journal

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Dissecting Genetic Architecture Underlying Seed Traits in Multiple Environments

Cited by 4 publications

References 31 publications

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed (Brassica napus L.)

Joint association analysis method to dissect complex genetic architecture of multiple genetically related traits

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