Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China ; National Foxtail Millet Improvement Center, Shijiazhuang, Hebei, China ; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ; Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, Hebei, China.
PLoS One. 2013 Sep 10;8(9):e73514. doi: 10.1371/journal.pone.0073514. eCollection 2013.
Foxtail millet (Setariaitalica) 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 ~ 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.
谷子（Setaria italica）是一种耐旱、耐瘠薄的粮食作物和饲料。目前，它已成为谷类作物和生物燃料草的新模式植物。尽管最近发布了两个参考基因组序列，但谷子的比较基因组学研究仍处于起步阶段。我们使用 Solexa 测序技术对一个重要的谷子地方品种石-黎-香（SLX）进行了基因组重测序。与两个参考基因组序列相比，鉴定出以下遗传变异模式：SLX 和豫谷 1 基因组之间有 762,082 个 SNP、1 到 5 bp 长度的 26,802 个插入/缺失多态性（indels）和 10,109 个结构变异（SVs）；SLX 和张谷基因组之间有 915,434 个 SNP、28,546 个 indels 和 12,968 个 SVs。此外，基于豫谷 1 基因组注释，我们发现大约 40%的 SNP 位于含有 NB-ARC 结构域、蛋白激酶或富含亮氨酸重复的基因中，这些基因的非同义到同义 SNP 比值高于平均值，表明植物抗病蛋白的多样化可能是由病原体压力引起的。此外，在 SLX 和豫谷 1 之间鉴定的多态性中，有 465 个 SNP 和 146 个 SVs的验证准确率超过 90%，可作为全基因组基因型鉴定和标记辅助育种的 DNA 标记。在这里，我们还展示了一个使用这些新开发的 DNA 标记精细定位和鉴定 SLX 中蜡质基因座的例子。这项工作提供了重要的信息，将有助于深入了解谷子基因组，并有助于解析谷子重要性状的遗传基础。
