Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet

文献类型： 外文期刊

第一作者： Bai, Hui

作者： Bai, Hui;Quan, Jianzhang;Dong, Li;Li, Zhiyong;Zhu, Yanbin;Dong, Zhiping;Bai, Hui;Quan, Jianzhang;Dong, Li;Li, Zhiyong;Zhu, Yanbin;Dong, Zhiping;Bai, Hui;Cao, Yinghao;Zhu, Lihuang;Li, Dayong;Bai, Hui;Cao, Yinghao;Zhu, Lihuang;Li, Dayong;Zhu, Yanbin;Bai, Hui;Quan, Jianzhang;Dong, Li;Li, Zhiyong;Zhu, Yanbin;Dong, Zhiping

作者机构：

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2013 年 8 卷 9 期

页码：

收录情况： SCI

摘要： Foxtail millet (Setaria italica) is a drought-resistant, barren-tolerant grain crop and forage. Currently, it has become a new model plant for cereal crops and biofuel grasses. Although two reference genome sequences were released recently, comparative genomics research on foxtail millet is still in its infancy. Using the Solexa sequencing technology, we performed genome re-sequencing on one important foxtail millet Landrace, Shi-Li-Xiang (SLX). Compared with the two reference genome sequences, the following genetic variation patterns were identified: 762,082 SNPs, 26,802 insertion/deletion polymorphisms of 1 to 5 bp in length (indels), and 10,109 structural variations (SVs) between SLX and Yugu1 genomes; 915,434 SNPs, 28,546 indels and 12,968 SVs between SLX and Zhang gu genomes. Furthermore, based on the Yugu1 genome annotation, we found out that similar to 40% SNPs resided in genes containing NB-ARC domain, protein kinase or leucine-rich repeats, which had higher non-synonymous to synonymous SNPs ratios than average, suggesting that the diversification of plant disease resistance proteins might be caused by pathogen pressure. In addition, out of the polymorphisms identified between SLX and Yugu1, 465 SNPs and 146 SVs were validated with more than 90% accuracy, which could be used as DNA markers for whole-genome genotyping and marker-assisted breeding. Here, we also represented an example of fine mapping and identifying a waxy locus in SLX using these newly developed DNA markers. This work provided important information that will allow a deeper understanding of the foxtail millet genome and will be helpful for dissecting the genetic basis of important traits in foxtail millet.

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