Adapting Genotyping-by-Sequencing for Rice F2 Populations.
Adapting Genotyping-by-Sequencing for Rice F2 Populations.
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DOI：
10.1534/g3.116.038190
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发表时间：
2017-03-10
期刊：
影响因子：
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通讯作者：
Reuscher S
中科院分区：
文献类型：
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作者：
Furuta T;Ashikari M;Jena KK;Doi K;Reuscher S
快速和具有成本效益的基因分型的大型绘图群体可以通过测序的每个人在一个给定的群体中的基因组的简化表示，并使用该信息来生成遗传标记。开发了定制的测序基因分型（GBS）管道，以对来自水稻亚种间杂交的水稻F2群体进行基因分型。日本日本晴和非洲野生稻O.长雄蕊的虽然大多数GBS管道旨在主要分析纯合群体，但我们试图对高度杂合的F2群体进行基因分型。我们展示了如何建立协议的物种和人口特定的改进，可以大大提高样品的吞吐量和基因型质量。对于一些个体使用少至50，000个读段（平均134，000个读段），我们能够在1081个F2个体中产生多达8154个信息SNP标记。此外，酶的选择，读取覆盖率和数据后处理的影响进行了评估。使用GBS衍生的标记，我们能够组装1536 cM的遗传图谱。为了证明我们的GBS管道的有用性，我们确定了分蘖数的数量性状基因座（QTL）。我们能够将四个QTL定位到第1、3、4和8染色体上，并使用渐渗系部分证实了它们的作用。我们提供了一个例子，如何成功地使用GBS与杂合子F2群体。通过使用成本相对较低的MiSeq平台，我们证明了GBS方法是灵活和具有成本效益的，即使对于较小的实验室。
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.