用于羊草基因分型的SNP分子标记技术研究

doi:10.11686/cyxb2015466

草业学报 ›› 2016, Vol. 25 ›› Issue (2): 105-113.DOI: 10.11686/cyxb2015466

用于羊草基因分型的SNP分子标记技术研究

侯莉娟^1**, 齐晓^2,3**, 齐冬梅¹, 陈双燕^1*, 刘公社^1*

1.中国科学院植物研究所北方资源植物重点实验室,北京100093;
2.中国农业科学院草原研究所,内蒙古呼和浩特 010010;
3.全国畜牧总站,北京 100125

收稿日期:2015-09-29 出版日期:2016-02-20 发布日期:2016-02-20
通讯作者: E-mail: sychen@ibcas.ac.cn, liugs@ibcas.ac.cn
作者简介:侯莉娟(1989-),女,山西太原人,硕士。E-mail: jennifer_hou762@163.com。齐晓(1982-),男,河北泊头人,硕士。E-mail: tq07mms@sina.com。**共同第一作者These authors contributed equally to this work.
基金资助:
国家草品种区域试验项目-羊草新品种“三性”测试(农财发[2015]36号)和国家重点基础研究发展计划(973计划)项目(2014CB138704)资助

A study of SNP molecular marker technology for Leymus chinensis genotyping

HOU Li-Juan^1,**, QI Xiao^2,3,**, QI Dong-Mei¹, CHEN Shuang-Yan^1,*, LIU Gong-She^1,*

1.Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China;
2.Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot 010010, China;
3.National Animal Husbandry Service, Beijing 100125, China

Received:2015-09-29 Online:2016-02-20 Published:2016-02-20

摘要/Abstract

摘要： 以我国广泛分布的多年生优势禾本科牧草羊草为研究材料,针对羊草目前尚无SNP标记技术的报道,基于实验室已有的转录组数据,挖掘其中的SNP分子标记,建立一种利用高分辨率熔解曲线(high-resolution melting, HRM)进行羊草SNP基因分型的方法。结果表明,从羊草转录组数据中获得41843个SNPs,转换的数量是颠换数量的2倍;建立了基于SNP的HRM基因分型方法,设计了112对SNP引物,其中有98对(87.5%)能扩增出明亮单一条带,扩增条带大小符合预期的有72对(64.29%),适宜进行HRM基因分型的引物有46对,占41.07%;用其中的7对引物可将羊草48份种质区分开,并绘制出指纹图谱。通过对部分HRM基因分型结果进行测序验证,表明测序分析的基因型结果与HRM基因分型结果一致,证明HRM基因分型结果是可靠的。本研究首次建立的基于SNP的HRM基因分型方法,可用于羊草种质资源的指纹图谱绘制、育种亲本的选配、基因关联分析、分子标记辅助育种、功能分子标记开发、新品种的保护等育种工作。

Abstract: Leymus chinensis, is a widely distributed and often ecologically dominant perennial grass in China, frequently used as research material. Because we know of no previous reports of markers in L. chinensis, we performed single nucleotide polymorphism (SNP) mining of 48 genotypes, based on the transcriptome data in the laboratory and established a method using high resolution melting (HRM) curves for L. chinensis SNP genotyping. A total of 41843 SNPs were detected from the transcriptome data by bioinformatics analysis. Transitions were nearly twice as frequent as transversions. Among 112 pairs of designed SNP primers, 98 SNP primer pairs (87.5%) were able to amplify bright single bands, 72 primer pairs (64.29%) had a suitable amplified band size, and 46 SNP primer pairs (41.07%) were suitable for HRM genotyping. The 48 germplasm genotypes of L. chinensis could be separated by 7 primer pairs and the fingerprint of each identified. The partial HRM genotyping results were verified by sequencing. The results of genotype by sequencing analysis were consistent with the results of HRM genotyping, so confirming that the HRM genotyping was reliable. HRM for SNP genotyping first established in this study can also be used in other breeding work with L. chinensis, including parent selection, gene correlation analysis, molecular marker assisted breeding, development of functional molecular markers and new variety protection.

侯莉娟, 齐晓, 齐冬梅, 陈双燕, 刘公社. 用于羊草基因分型的SNP分子标记技术研究[J]. 草业学报, 2016, 25(2): 105-113.

HOU Li-Juan, QI Xiao, QI Dong-Mei, CHEN Shuang-Yan, LIU Gong-She. A study of SNP molecular marker technology for Leymus chinensis genotyping[J]. Acta Prataculturae Sinica, 2016, 25(2): 105-113.

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用于羊草基因分型的SNP分子标记技术研究

A study of SNP molecular marker technology for Leymus chinensis genotyping

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