Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus.
Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus.
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DOI：
10.1186/1471-2164-14-717
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发表时间：
2013-10-20
期刊：
影响因子：
4.4
通讯作者：
Hua W
中科院分区：
文献类型：
--
作者：
Huang S;Deng L;Guan M;Li J;Lu K;Wang H;Fu D;Mason AS;Liu S;Hua W
单核苷酸多态性（SNP）是最常见的遗传变异类型。大量SNP的鉴定有助于遗传多样性分析、图位克隆、全基因组关联分析和标记辅助育种。最近，由于甘蓝型油菜 (2n = AA) 和甘蓝 (2n = CC)（甘蓝型油菜 (2n = AACC) 的祖先物种）参考基因组的可用性，通过对许多种质进行重新测序来鉴定异源多倍体甘蓝型油菜（油菜籽、油菜）中的全基因组 SNP 已变得可行。尽管欧洲油菜中的许多 SNP 已被发布，但本研究的目标是产生更多、信息更丰富的 SNP 集，用于大规模、高效的基因型筛选。因此，为了发现 SNP，我们对 10 个优良甘蓝型油菜种质进行了短读长基因组测序。随机选择这些 SNP 的子集进行序列验证并使用 Illumina GoldenGate 检测进行基因分型效率测试。在整个甘蓝型油菜基因组中总共发现了 892,536 个双等位基因 SNP。总共 36,458 个推定氨基酸变异位于 13,552 个蛋白质编码基因中，预计这些变异将具有丰富的结合和催化活性。使用GoldenGate基因分型平台，采样的96个SNP中的94个可以有效地区分两个作图群体中130个品系的基因型，平均检出率为92%。尽管甘蓝型油菜具有多倍体性质，但全基因组重测序仍鉴定出了近 900,000 个简单的 SNP。这些 SNP 预计在高通量基因分型测定中有效（51% 多态性 SNP，使用 GoldenGate 测定的平均检出率为 92%，估计产生 >450 000 个有用的 SNP）。因此，开发更多信息丰富的 SNP 基因分型阵列是可行的。本研究中鉴定出的导致非同义氨基酸取代的 SNP 也可用于直接鉴定关联研究中的因果基因。
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Identification of large numbers of SNPs is helpful for genetic diversity analysis, map-based cloning, genome-wide association analyses and marker-assisted breeding. Recently, identifying genome-wide SNPs in allopolyploid Brassica napus (rapeseed, canola) by resequencing many accessions has become feasible, due to the availability of reference genomes of Brassica rapa (2n = AA) and Brassica oleracea (2n = CC), which are the progenitor species of B. napus (2n = AACC). Although many SNPs in B. napus have been released, the objective in the present study was to produce a larger, more informative set of SNPs for large-scale and efficient genotypic screening. Hence, short-read genome sequencing was conducted on ten elite B. napus accessions for SNP discovery. A subset of these SNPs was randomly selected for sequence validation and for genotyping efficiency testing using the Illumina GoldenGate assay. A total of 892,536 bi-allelic SNPs were discovered throughout the B. napus genome. A total of 36,458 putative amino acid variants were located in 13,552 protein-coding genes, which were predicted to have enriched binding and catalytic activity as a result. Using the GoldenGate genotyping platform, 94 of 96 SNPs sampled could effectively distinguish genotypes of 130 lines from two mapping populations, with an average call rate of 92%. Despite the polyploid nature of B. napus, nearly 900,000 simple SNPs were identified by whole genome resequencing. These SNPs were predicted to be effective in high-throughput genotyping assays (51% polymorphic SNPs, 92% average call rate using the GoldenGate assay, leading to an estimated >450 000 useful SNPs). Hence, the development of a much larger genotyping array of informative SNPs is feasible. SNPs identified in this study to cause non-synonymous amino acid substitutions can also be utilized to directly identify causal genes in association studies.
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影响因子：
13.8
作者：
Lai, Kaitao;Duran, Chris;Edwards, David
通讯作者：
Edwards, David
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
3.1
作者：
Durstewitz, G.;Polley, A.;Ganal, M. W.
通讯作者：
Ganal, M. W.
影响因子：
7
作者：
Lysak, MA;Koch, MA;Schubert, I
通讯作者：
Schubert, I
影响因子：
5.4
作者：
Hyten, David L.;Song, Qijian;Cregan, Perry B.
通讯作者：
Cregan, Perry B.