Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds.
Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds.
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DOI：
10.1111/tpj.13767
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发表时间：
2018-01
期刊：
影响因子：
--
通讯作者：
Bancroft I
中科院分区：
文献类型：
--
作者：
Havlickova L;He Z;Wang L;Langer S;Harper AL;Kaur H;Broadley MR;Gegas V;Bancroft I
开发了一个更新的平台，以支持多倍体作物物种甘蓝型油菜（油菜）的关联遗传学研究。基于叶mRNAseq数据的1.92 × 1012个碱基，使用包含116 098个有序编码DNA序列（CDS）基因模型的转录组参考，在383个种质的遗传多样性小组中对包含355 536个单核苷酸多态性标记和转录本丰度的功能基因型进行评分。关联转录组学平台的使用首先通过分析种子芥酸含量变异的遗传结构进行测试，因为高芥酸菜籽油在工业中的各种应用中具有很高的价值。确定了已知的基因座，沿着先前未检测到的次要效应基因座。然后使用该平台分析种子中生育酚（维生素E）形式相对比例的变化，并使用取一法评估最重要标记物的有效性。此外，该分析涉及与观察到的性状变异相关的基因Bo2g050970.1的表达变异，Bo2g050970.1是VTE 4的直向同源物（其编码将γ-生育酚转化为α-生育酚的γ-生育酚甲基转移酶）。B. napus的第一个全规模关联转录组学平台的建立，使我们能够在理解这一重要物种性状变异的遗传结构方面取得快速进展，并为其他作物提供了范例。基于功能基因型的甘蓝型油菜全方位关联遗传学平台的可用性，使这一重要作物物种中基本上任何性状的遗传结构都能得到解决。
An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single‐nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high‐erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor‐effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take‐one‐out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ‐tocopherol methyl transferase converting γ‐tocopherol into α‐tocopherol) associated with the observed trait variation. The establishment of the first full‐scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops. The availability of a full‐scale association genetics platform for Brassica napus, based on functional genotypes, enables the genetic architecture of essentially any trait to be addressed in this important crop species.
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影响因子：
1.2
作者：
He Z;Cheng F;Li Y;Wang X;Parkin IA;Chalhoub B;Liu S;Bancroft I
通讯作者：
Bancroft I
影响因子：
4.4
作者：
Huang S;Deng L;Guan M;Li J;Lu K;Wang H;Fu D;Mason AS;Liu S;Hua W
通讯作者：
Hua W
DOI：
10.1093/dnares/dsu002
发表时间：
2014-08
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Li F;Chen B;Xu K;Wu J;Song W;Bancroft I;Harper AL;Trick M;Liu S;Gao G;Wang N;Yan G;Qiao J;Li J;Li H;Xiao X;Zhang T;Wu X
通讯作者：
Wu X
全基因组关联研究确定了与玉米内核中与α-生育酚含量相关的三种独立多态性。
影响因子：
3.7
作者：
Li Q;Yang X;Xu S;Cai Y;Zhang D;Han Y;Li L;Zhang Z;Gao S;Li J;Yan J
通讯作者：
Yan J
影响因子：
2
作者：
Dolde, D;Vlahakis, C;Hazebroek, J
通讯作者：
Hazebroek, J