Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.
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DOI：
10.1371/journal.pone.0040563
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Francis DM
中科院分区：
文献类型：
--
作者：
Sim SC;Durstewitz G;Plieske J;Wieseke R;Ganal MW;Van Deynze A;Hamilton JP;Buell CR;Causse M;Wijeratne S;Francis DM
高通量基因分型平台和下一代测序（NGS）的同步发展增加了遗传标记的数量和密度，构建详细连锁图谱的效率，以及我们覆盖基因组重组和物理图谱的能力。我们开发了一个番茄阵列，其中包含8，784个主要基于NGS衍生转录组序列发现的单核苷酸多态性（SNP）。在SNPs中，7，720个（88%）通过了生产质量控制，可以在番茄种质中评分。利用该基因芯片构建了3个种间F2群体的高密度连锁图谱：EXPEN 2000（Solanum lycopersicum LA 0925 x S. pennellii LA 0716，79个个体）、EXPEN 2012（S. lycopersicum Moneymaker × S. pennellii LA 0716，160个个体）和EXPIM 2012（S. lycopersicum Moneymaker × S. pimpinellifolium LA 0121，183株）。EXPEN 2000-SNP和EXPEN 2012图谱分别由3，503和3，687个标记组成，分别代表1，076和1，229个独特的图谱位置（遗传箱）。EXPEN 2000-SNP图谱具有1.6 cM的平均标记物箱间隔，而EXPEN 2012图谱具有0.9 cM的平均箱间隔。EXPIM 2012图谱由4，491个标记（1，358个箱）和0.8 cM的平均箱间隔构建。所有三个连锁图显示了整个基因组的标记分布不均。密集的EXPEN 2012和EXPIM 2012图谱显示了所有12条染色体的高水平共线性，并且还揭示了LA 0716和LA 0121之间的小倒位的证据。相对于番茄基因组序列，鉴定了7，666个SNP的物理位置。遗传和物理位置基本一致。在3、10和12号染色体上观察到染色体畸变。比较遗传位置相对于物理位置显示，具有高重组率的基因组区域与已知的12条染色体上常染色质的分布一致，而在异染色质区域观察到非常低的重组率。
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
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影响因子：
1.7
作者：
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通讯作者：
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