A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus

Liu, Sheng; Fan, Chuchuan; Li, Jiana; Cai, Guangqin; Yang, Qingyong; Wu, Jian; Yi, Xinqi; Zhang, Chunyu; Zhou, Yongming

doi:10.1007/s00122-016-2697-z

Cited by 150 publications

(166 citation statements)

References 56 publications

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“…In addition, the efficiencies of association analysis is determined by population size and maker density [63]. So the Brassica 60 K SNP array was performed for the genotype of 520 rapeseed accessions.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Jia

et al. 2017

BMC Genomics

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Background B. napus (oilseed) is an important source of edible vegetable oil, and its nutritional and economic value is determined by its fatty acid composition and content.ResultsUsing the Brassica 60 K SNP array, we performed a genome-wide association study of fatty acid composition in a population of 520 genetically diverse oilseed accessions. Using the PCA + K model in TASSEL 5.2.1, we identified 62 genomic regions that were significantly associated with the composition of seven fatty acids, and five consensus regions that mapped to the A2, A8, A9, C1, and C3 chromosomes, respectively, of the Brassica napus Darmor-bzh genome. We then identified 24 orthologs of the functional candidate genes involved in fatty acid biosynthesis, excluding BnaA.FAE1 and BnaC.FAE1 on the A8 and C3 homologous genome blocks, which are known to have critical roles in the fatty acid biosynthesis pathway, and potential orthologs of these genes (e.g., LACS9, KCR1, FAB1, LPAT4, KCS17, CER4, TT16, and ACBP5).ConclusionsOur results demonstrate the power of association mapping in identifying genes of interest in B. napus and provide insight into the genetic basis of fatty acid biosynthesis in B. napus. Furthermore, our findings may facilitate marker-based breeding efforts aimed at improving fatty acid composition and quality in B. napus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3607-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Jia

et al. 2017

BMC Genomics

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“…PCA was superior to the Q model in controlling false positives for the estimation of population structure5859. Therefore, a mixed linear model (MLM) was used to calculate the associations in all analyses by incorporating PCA and kinship data56.…”

Section: Methodsmentioning

confidence: 99%

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Pang

et al. 2016

Sci Rep

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Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.

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“…Previous studies have demonstrated that the OC of rapeseed is mainly controlled by genotype and genotype × environment interactions (GE) [4–6]; in addition, it is governed by multiple genes mainly through additive effect, and thus can be altered through breeding and selection [7–10]. …”

Section: Introductionmentioning

confidence: 99%

Genetic effects and genotype × environment interactions govern seed oil content in Brassica napus L.

Guo

Wang

et al. 2017

BMC Genet

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BackgroundAs seed oil content (OC) is a key measure of rapeseed quality, better understanding the genetic basis of OC would greatly facilitate the breeding of high-oil cultivars. Here, we investigated the components of genetic effects and genotype × environment interactions (GE) that govern OC using a full diallel set of nine parents, which represented a wide range of the Chinese rapeseed cultivars and pure lines with various OCs.ResultsOur results from an embryo-cytoplasm-maternal (GoCGm) model for diploid seeds showed that OC was primarily determined by genetic effects (VG) and GE (VGE), which together accounted for 86.19% of the phenotypic variance (VP). GE (VGE) alone accounted for 51.68% of the total genetic variance, indicating the importance of GE interaction for OC. Furthermore, maternal variance explained 75.03% of the total genetic variance, embryo and cytoplasmic effects accounted for 21.02% and 3.95%, respectively. We also found that the OC of F1 seeds was mainly determined by maternal effect and slightly affected by xenia. Thus, the OC of rapeseed was simultaneously affected by various genetic components, including maternal, embryo, cytoplasm, xenia and GE effects. In addition, general combining ability (GCA), specific combining ability (SCA), and maternal variance had significant influence on OC. The lines H2 and H1 were good general combiners, suggesting that they would be the best parental candidates for OC improvement. Crosses H3 × M2 and H1 × M3 exhibited significant SCA, suggesting their potentials in hybrid development.ConclusionsOur study thoroughly investigated and reliably quantified various genetic factors associated with OC of rapeseed by using a full diallel and backcross and reciprocal backcross. This findings lay a foundation for future genetic studies of OC and provide guidance for breeding of high-oil rapeseed cultivars.

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A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus

Cited by 150 publications

References 56 publications

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

Genetic effects and genotype × environment interactions govern seed oil content in Brassica napus L.

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