Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America.
PLoS One. 2012;7(7):e40563. doi: 10.1371/journal.pone.0040563. Epub 2012 Jul 10.
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 F(2) 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.
高通量基因分型平台和下一代测序 (NGS) 的同时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。我们开发了一种用于番茄的阵列，其中包含 8784 个主要基于 NGS 衍生转录组序列发现的单核苷酸多态性 (SNP)。在这些 SNP 中，7720 个（88%）通过了制造质量控制，可以在番茄种质中进行评分。该阵列用于生成三个种间 F2 群体的高密度连锁图谱：EXPEN 2000（Solanum lycopersicum LA0925 x S. pennellii LA0716，79 个个体）、EXPEN 2012（S. lycopersicum Moneymaker x S. pennellii LA0716，160 个个体）和 EXPIM 2012（S. lycopersicum Moneymaker x S. pimpinellifolium LA0121，183 个个体）。EXPEN 2000-SNP 和 EXPEN 2012 图谱分别由 3503 和 3687 个标记组成，代表 1076 和 1229 个独特的图谱位置（遗传 bin）。EXPEN 2000-SNP 图谱的平均标记 bin 间隔为 1.6 cM，而 EXPEN 2012 图谱的平均 bin 间隔为 0.9 cM。EXPIM 2012 图谱由 4491 个标记（1358 个 bin）组成，平均 bin 间隔为 0.8 cM。这三个连锁图谱都显示了标记在基因组中的不均匀分布。密集的 EXPEN 2012 和 EXPIM 2012 图谱在所有 12 条染色体上显示出高度的共线性，并且还显示了 LA0716 和 LA0121 之间小反转的证据。7666 个 SNP 的物理位置相对于番茄基因组序列进行了鉴定。遗传和物理位置基本一致。3、10 和 12 号染色体例外。相对于物理位置比较遗传位置，发现高重组率的基因组区域与 12 条染色体上 euchromatin 的已知分布一致，而在异染色质区域观察到非常低的重组率。
