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Mining of genic SNPs and diversity evaluation of landraces in loquat

文献类型： 外文期刊

作者： Li, Xiaoying 1 ; Xu, Hongxia 1 ; Feng, Jianjun 2 ; Zhou, Xiaoyin 3 ; Chen, Junwei 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Hort, Hangzhou 310021, Zhejiang, Peoples R China

2.Ninghai Agr & Forestry Bur, Ningbo 315600, Zhejiang, Peoples R China

3.Lishui Agr Bur, Lishui 323000, Zhejiang, Peoples R China

关键词： Loquat;Genic SNPs;Characteristic analysis;Germplasm evaluation;Phylogenetic tree

期刊名称：SCIENTIA HORTICULTURAE （ 影响因子：3.463； 五年影响因子：3.672 ）

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收录情况： SCI

摘要： With the development of next-generation sequencing technologies, the exploitation of single nucleotide polymorphism (SNP) markers from transcriptome sequences has gained more attention and this kind of marker is widely utilized in plant genetic research. In this study, genic SNP markers derived from transcriptome sequences were identified from 26 loquat cultivars. A total length of 4183 bp using 9 sets of primers was sequenced and used for alignments. From this, 103 SNPs, with a frequency of one SNP per 41 bp, were found, which were comprised of 55 transitions, 37 transversions, 8 InDels and 3 other types. Among these SNPs, the percentage of transitions and transversions in A/G, C/T, G/T, A/T, G/C and A/C were 31.1% (32), 22.3% (23), 13.6% (14), 11.7% (12), 6.8%(7) and 3.9% (4), respectively. Of these SNP genotypes, 84 were detected as homozygotes in the 26 loquat cultivars, and 8 heterozygous SNPs were found in some cultivars. Cluster analysis of the 26 loquat cultivars was also carried out using the SNPs data, and a phylogenetic tree constructed showed that all the cultivars were separated well, and clustered into several groups which basically corresponds to the genetic background of them. The newly identified genic SNPs in this study will provide powerful tools in molecular studies for cultivar identification, genetic diversity analyses and marker-assisted selection breeding in loquat (C) 2015 Elsevier B.V. All rights reserved.

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