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Genome wide analysis of flowering time trait in multiple environments via high-throughput genotyping technique in Brassica napus L.

Li L, Long Y, Zhang L, Dalton-Morgan J, Batley J, Yu L, Meng J, Li M - PLoS ONE (2015)

Bottom Line: Next, we performed a large-scale mapping of FT related loci among three regions, and found 437 associated SNPs, some of which represented known FT genes, such as AP1 and PHYE.Epistasis analysis showed that significant interactions were found between detected loci, even among some known FT related genes.All the results showed that our large scale and high-density genotype data are of great practical and scientific values for B. napus.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, China.

ABSTRACT
The prediction of the flowering time (FT) trait in Brassica napus based on genome-wide markers and the detection of underlying genetic factors is important not only for oilseed producers around the world but also for the other crop industry in the rotation system in China. In previous studies the low density and mixture of biomarkers used obstructed genomic selection in B. napus and comprehensive mapping of FT related loci. In this study, a high-density genome-wide SNP set was genotyped from a double-haploid population of B. napus. We first performed genomic prediction of FT traits in B. napus using SNPs across the genome under ten environments of three geographic regions via eight existing genomic predictive models. The results showed that all the models achieved comparably high accuracies, verifying the feasibility of genomic prediction in B. napus. Next, we performed a large-scale mapping of FT related loci among three regions, and found 437 associated SNPs, some of which represented known FT genes, such as AP1 and PHYE. The genes tagged by the associated SNPs were enriched in biological processes involved in the formation of flowers. Epistasis analysis showed that significant interactions were found between detected loci, even among some known FT related genes. All the results showed that our large scale and high-density genotype data are of great practical and scientific values for B. napus. To our best knowledge, this is the first evaluation of genomic selection models in B. napus based on a high-density SNP dataset and large-scale mapping of FT loci.

No MeSH data available.


SNPs located in previously found QTLs.Five linkage groups were showed with the lines, and the black short lines represented the QTLs. The blue triangles showed the SNPs located in the confidence interval of QTLs.
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pone.0119425.g003: SNPs located in previously found QTLs.Five linkage groups were showed with the lines, and the black short lines represented the QTLs. The blue triangles showed the SNPs located in the confidence interval of QTLs.

Mentions: Besides association analysis, the 1674 polymorphic SNP markers were combined with some common SSR markers to construct a linkage map (S3 Table), and FT associated SNPs were included in the linkage map. It was found that 31 significant SNPs were mapped in the linkage map. Further QTL mapping showed that there were 19 flowering time related QTL detected. Among the QTLs, 6 QTLs were detected for North environment, 12 QTLs were detected for South environment, and 1 for East environment. Comparison of the FT associated SNPs with mapping QTLs, found that 23 SNPs could be detected in both QTL mapping and our method (Fig. 3), which meant that these SNPs were real genetic loci controlling flowering time.


Genome wide analysis of flowering time trait in multiple environments via high-throughput genotyping technique in Brassica napus L.

Li L, Long Y, Zhang L, Dalton-Morgan J, Batley J, Yu L, Meng J, Li M - PLoS ONE (2015)

SNPs located in previously found QTLs.Five linkage groups were showed with the lines, and the black short lines represented the QTLs. The blue triangles showed the SNPs located in the confidence interval of QTLs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4366152&req=5

pone.0119425.g003: SNPs located in previously found QTLs.Five linkage groups were showed with the lines, and the black short lines represented the QTLs. The blue triangles showed the SNPs located in the confidence interval of QTLs.
Mentions: Besides association analysis, the 1674 polymorphic SNP markers were combined with some common SSR markers to construct a linkage map (S3 Table), and FT associated SNPs were included in the linkage map. It was found that 31 significant SNPs were mapped in the linkage map. Further QTL mapping showed that there were 19 flowering time related QTL detected. Among the QTLs, 6 QTLs were detected for North environment, 12 QTLs were detected for South environment, and 1 for East environment. Comparison of the FT associated SNPs with mapping QTLs, found that 23 SNPs could be detected in both QTL mapping and our method (Fig. 3), which meant that these SNPs were real genetic loci controlling flowering time.

Bottom Line: Next, we performed a large-scale mapping of FT related loci among three regions, and found 437 associated SNPs, some of which represented known FT genes, such as AP1 and PHYE.Epistasis analysis showed that significant interactions were found between detected loci, even among some known FT related genes.All the results showed that our large scale and high-density genotype data are of great practical and scientific values for B. napus.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, China.

ABSTRACT
The prediction of the flowering time (FT) trait in Brassica napus based on genome-wide markers and the detection of underlying genetic factors is important not only for oilseed producers around the world but also for the other crop industry in the rotation system in China. In previous studies the low density and mixture of biomarkers used obstructed genomic selection in B. napus and comprehensive mapping of FT related loci. In this study, a high-density genome-wide SNP set was genotyped from a double-haploid population of B. napus. We first performed genomic prediction of FT traits in B. napus using SNPs across the genome under ten environments of three geographic regions via eight existing genomic predictive models. The results showed that all the models achieved comparably high accuracies, verifying the feasibility of genomic prediction in B. napus. Next, we performed a large-scale mapping of FT related loci among three regions, and found 437 associated SNPs, some of which represented known FT genes, such as AP1 and PHYE. The genes tagged by the associated SNPs were enriched in biological processes involved in the formation of flowers. Epistasis analysis showed that significant interactions were found between detected loci, even among some known FT related genes. All the results showed that our large scale and high-density genotype data are of great practical and scientific values for B. napus. To our best knowledge, this is the first evaluation of genomic selection models in B. napus based on a high-density SNP dataset and large-scale mapping of FT loci.

No MeSH data available.