蒺藜苜蓿、天蓝苜蓿、金花菜基因组SNP穿梭标记开发

doi:10.11686/cyxb2016400

摘要/Abstract

摘要： 蒺藜苜蓿是继拟南芥和水稻之后又一个进行全基因组测序的植物,利用蒺藜苜蓿的基因组序列,开发出可以在其他豆科植物上应用的分子标记,即穿梭标记,已成为缺乏基因组信息或基因组复杂的豆科植物基因组学及分子遗传学研究的有效手段。天蓝苜蓿和金花菜是我国最重要的两种一年生苜蓿,由于缺乏有效的分子标记,这两种苜蓿在基因组水平上的研究很少。SLAF-seq是近年来开发出的一种简化基因组测序技术,具有高通量、准确性、成本低、周期短的优点,已在众多物种的全基因组SNP标记开发上得到应用。本研究通过SLAF-seq技术对12份蒺藜苜蓿、天蓝苜蓿和金花菜材料进行简化基因组测序,共得到28.04×10⁶个读长的测序数据,276432个高质量的SLAF标签,其中58748个SLAF标签为多态性标签,平均测序深度为17.44。在58748个多态性SLAF标签中,共检测出次要基因型频率(MAF)大于0.05的SNP标记189133个。本研究开发出的SNP标记可用于一年生苜蓿的遗传多样性、遗传图谱构建和重要农艺性状的QTL定位等的研究,其种间穿梭的特性可为苜蓿属种间基因组排列顺序、系统进化关系、比较图谱构建等方面的研究提供帮助。

Abstract: Medicago truncatula is another whole genome sequenced species next to Arabidopsis thaliana and Oryza sativa. Studying genomics and genetics using cross-species markers developed from M. truncatula has become an important strategy for species with more complex genomes or for legumes with less well understood genome. M. lupulina and M. polymorpha are the most important annual medics in China. However, limited by molecular marker, little research has been done on genome scales in these species. Specific length amplification fragment sequencing (SLAF-seq) possesses significant advantages including development of markers with high throughput, high accuracy, low cost and time saving which has been successfully used in single nucleotide polymorphism (SNP) development in many species. In this study, 28.04×10⁶ reads were obtained from a collection of twelve of M. truncatula, M. lupulina and M. polymorpha accessions using SLAF-seq. The average sequencing depth was 17.44, and 276432 high-quality SLAFs were developed, among which 58748 SLAFs were polymorphic. Further 189133 cross-species SNPs were identified from these polymorphic SLAFs with minor allele frequencies (MAFs)>0.05. These SNPs can be used in genetic diversity, genetic linkage mapping and QTL mapping of important agronomic traits in annual medic. They will also convey benefits for the study of genome orders, system evolution, and comparative map construction.

任海龙, 魏臻武, 陈祥. 蒺藜苜蓿、天蓝苜蓿、金花菜基因组SNP穿梭标记开发[J]. 草业学报, 2017, 26(4): 188-195.

REN Hai-Long, WEI Zhen-Wu, CHEN Xiang. Cross-species markers developed from genome sequencing in Medicago truncatula, Medicago lupulina and Medicago polymorpha[J]. Acta Prataculturae Sinica, 2017, 26(4): 188-195.

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