Genetic diversity analysis of drought tolerant flax varieties based on genome-wide SNP

Fan Zhang; Jianhui Wu; Siqin Bateer; Liuxi Yi; Xiaoqing Zhao; Zhanyuan Lu

doi:10.1117/12.2660582

6 December 2022 Genetic diversity analysis of drought tolerant flax varieties based on genome-wide SNP

Fan Zhang, Jianhui Wu, Siqin Bateer, Liuxi Yi, Xiaoqing Zhao, Zhanyuan Lu

Proceedings Volume 12458, International Conference on Biomedical and Intelligent Systems (IC-BIS 2022); 124580Q (2022) https://doi.org/10.1117/12.2660582
Event: International Conference on Biomedical and Intelligent Systems, 2022, Chengdu, China

Abstract

To clarify the genetic diversity among typical drought tolerant flax varieties, in this study, the Single-nucleotide polymorphism sites (SNPs) of 29 drought tolerant flax varieties were identified by whole-genome resequencing, and their SNP characteristics and genetic relationships were analyzed. The results showed that 1069106 SNP sites were obtained from the genome of the 29 drought tolerant flax varieties, among which the variety with the largest number of SNP was Zhangya 2 (1027658) and the least was Shache flax (801300). Among the types of SNP variation that occurred, the number of transitions (671103) was higher than transversions(398003). Phylogenetic analysis divided all 29 flax varieties into three groups, each with a wide range of sources, and some flax originating from the same region were located in the same group, indicating a rich genetic diversity of these 29 flax varieties. PCA (Principal component analysis) also divided all the flax varieties into three groups, which showed similarity to the phylogenetic tree grouping, which provides evidence for the results of the phylogenetic analysis. Among them, five varieties, Linxiabai, Gaolanbai, Lingtaizhuangna, Shache flax and Shache precocious red, showed evidently close genetic relationship both in phylogenetic analysis and PCA. This study can prove that the 29 drought tolerant flax varieties have rich genetic diversity, which lays the foundation for the genetic breeding of drought tolerant flax, the development of specific molecular markers, and the identification of germplasm resources.

Citation Download Citation

Fan Zhang, Jianhui Wu, Siqin Bateer, Liuxi Yi, Xiaoqing Zhao, and Zhanyuan Lu "Genetic diversity analysis of drought tolerant flax varieties based on genome-wide SNP", Proc. SPIE 12458, International Conference on Biomedical and Intelligent Systems (IC-BIS 2022), 124580Q (6 December 2022); https://doi.org/10.1117/12.2660582

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KEYWORDS

Genetics

Principal component analysis

Agriculture

Biological research

Data conversion

Genomics

Genetic algorithms

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