Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.
Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.
复制标题
使用新的高密度遗传图谱更新芝麻基因组组装以及株高和种皮颜色 QTL 的精细定位
DOI：
10.1186/s12864-015-2316-4
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发表时间：
2016-01-05
期刊：
影响因子：
4.4
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Wang L;Xia Q;Zhang Y;Zhu X;Zhu X;Li D;Ni X;Gao Y;Xiang H;Wei X;Yu J;Quan Z;Zhang X
研究背景芝麻是重要的优质油料作物。芝麻基因组于2014年重新测序并组装（1.0版）；然而，由于缺乏具有13个连锁群的高密度遗传图谱，锚定假分子的数量高于染色体数量（2n = 2x = 26）。结果我们对由430个重组自交系组成的永久群体进行了重新测序，并构建了遗传图谱以改进芝麻基因组组装。我们成功地将 327 个支架锚定到 13 个假分子上。新的基因组组装（2.0 版）包括组装版本 1.0 中 97.5% 大小大于 150 kb 的支架，并将总假分子长度从 233.7 Mb 增加到 258.4 Mb，组装了 94.3% 的基因组，锚定了 97.2% 的预测基因模型。基于新的基因组组装，生成了包含 1,522 个 bin、跨度为 1090.99 cM 的 bin 图，并用于识别芝麻株高的 41 个数量性状位点 (QTL) 和种皮颜色的 9 个位点。与株高相关的 QTL 解释了 3-24% 的表型变异（平均值为 8%），其中 29 个在至少两次田间试验中被检测到。贡献 23% 和 18% 株高的两个主要基因座（qPH-8.2 和 qPH-3.3）分别位于 Chr8 和 Chr3 上的 350 和 928 kb 空间。qPH-3.3 预计与半矮化芝麻植物表型有关，包含 102 个候选基因。这是芝麻半矮化位点的第一份报告，为芝麻的植物结构研究提供了一个有趣的机会。对于芝麻种皮颜色，检测到颜色空间 L*、a* 和 b* 的 QTL，贡献率为 3-46%。qSCb-4.1 贡献了 b* 值的约 39%，位于 199.9 kb 空间中的 Chr4 上。通过筛选新锚定的基因组，确定了该基因座的 32 个候选基因，包括预测的黑色种皮相关基因。结论这项研究提供了高密度遗传图谱和改进的芝麻基因组组装。该组装体中连锁基团和假分子的数量首次与芝麻染色体的数量相等。该图谱和更新的基因组组装预计将成为未来比较基因组学和遗传学研究的平台。
BackgroundSesame is an important high-quality oil seed crop. The sesame genome wasde novosequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups.ResultsWe resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3–24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2andqPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively.qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3–46 %.qSCb-4.1contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome.ConclusionsThis study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies.