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Assessing the numbers of SNPs needed to establish molecular IDs and characterize the genetic diversity of soybean cultivars derived from Tokachi nagaha

文献类型： 外文期刊

作者： Liu, Zhangxiong 1 ; Li, Jun; Fa, Xuhong; Htwe, Nang Myint Phyu Sin 1 ; Wang, Shuming; Huang, Wen; Yang, Ji 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Gene Resources & Genet Improvement, Key Lab Crop Germplasm Utilizat,Minist Agr, Beijing 100081, Peoples R China

2.Chinese Acad Agr Sci, Inst Crop Sc

关键词： Soybean;SNP;Genetic diversity;Genetic distance;Molecular ID

期刊名称：CROP JOURNAL （ 影响因子：4.407； 五年影响因子：5.687 ）

ISSN： 2095-5421

年卷期： 2017 年 5 卷 4 期

页码：

收录情况： SCI

摘要： The development of a core set of SNP molecular markers that could be widely used in soybean genetic research would greatly facilitate research into the genetic diversity of soybean. We conducted an analysis of Tokachi nagaha and 137 of its descendant soybean cultivars using 4044 SNP markers with the goal of determining the appropriate number of single -nucleotide polymorphisms (SNPs) needed to construct unambiguous molecular IDs and characterize genetic diversity based on a genetic distance matrix correlation method. When the number of SNPs was held constant, the number of accession pairs that could be distinguished increased as the polymorphism informative content (PIC) value of the SNPs increased. A core panel of 20 selected SNPs from 11 linkage groups with a mean PIC value of 0.3703 and a range of 0.3640-0.3749 was able to identify almost all of the accession pairs in our study [9445 pairs (99.92%)]. The eight accession pairs that could not be identified with this core SNP set all originated from the sam Fe province and some of them had the same parental cultivars. The molecular IDs of the 138 accessions were constructed using the core 20 SNPs. It is known that both the number of SNPs and PIC values should be considered when SNPs are selected for use in the analysis of genetic diversity. In this study, when the PIC value was 0.3460, the correlation coefficient between the genetic distance matrices associated with a panel of 200 SNPs and the total population was >0.800, indicating satisfactory correlation. Our high -accuracy, high -resolution core SNP panel for germplasm fingerprinting and our findings about assessing genetic diversity will likely markedly improve the management and utilization efficiency of soybean germplasm resources. (C) 2017 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license.

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