Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.).
Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.).
复制标题
基于水稻群体全基因组重测序开发高通量基因型染色体片段替换系（Oryza sativa L.）
DOI：
10.1186/1471-2164-11-656
复制
发表时间：
2010-11-24
期刊：
影响因子：
4.4
通讯作者：
Liang G
中科院分区：
文献类型：
--
作者：
Xu J;Zhao Q;Du P;Xu C;Wang B;Feng Q;Liu Q;Tang S;Gu M;Han B;Liang G
背景
遗传群体为广泛的遗传和基因组研究提供了基础，并已广泛应用于遗传图谱、基因发现和基因组学辅助育种。染色体片段替换系 (CSSL) 是检测和精确定位数量性状基因座 (QTL) 的最强大工具，可用于分析植物分子遗传学中的复杂性状。
结果
在这项研究中，通过两个已测序的水稻品种的杂交和回交，开发了一个由 128 个 CSSL 组成的广泛群体：9311（作为受体的优良籼稻品种）和 Nipponbare（作为供体的粳稻品种）。首先，根据使用 254 个基于 PCR 的分子标记对替换染色体片段的长度和位置的估计，构建了 128 个 CSSL 的物理图谱。从该图谱中，群体中 142 个取代片段的总大小为 882.2 Mb，是水稻基因组的 2.37 倍。其次，每个CSSL均通过0.13×基因组序列的全基因组重测序进行高通量基因分型，并构建了超高质量的物理图谱。这个基于测序的物理图谱表明检测到了 117 个新片段；几乎所有的都短于 3 Mb，并且在分子标记图谱中不明显。此外，相对于基于分子标记的图谱，基于测序的图谱产生了更精确的重组断点确定和取代片段长度的更高准确性，并提供了更准确的背景信息。第三，利用128个CSSL与基于测序的物理图谱转换的bin-map相结合，多元线性回归QTL分析定位了9个QTL，这解释了89.50%的秆长度表型方差。一个大效应QTL位于包含水稻“绿色革命”基因的791,655 bp区域。
结论
目前的结果表明，高通量基因分型CSSL结合了超高质量物理图谱和高作图精度的优点，因此对于基因发现和遗传作图具有巨大的潜在价值。这些CSSL可能为未来水稻全基因组大规模基因发现提供强大的工具，并为开发优质水稻品种奠定基础。
Background
Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics.
Results
In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene.
Conclusions
The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.
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