A study of SNP molecular marker technology for Leymus chinensis genotyping

doi:10.11686/cyxb2015466

Abstract

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.

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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