基于KASP分子标记的木薯种质资源遗传多样性分析及DNA指纹图谱构建

Genetic diversity analysis and DNA fingerprint construction of cassava germplasm resources based on KASP molecular markers

  • 摘要: 【目的】 基于全基因组重测序数据开发木薯KASP分子标记,利用其对木薯种质进行遗传多样性分析及DNA指纹图谱构建,以期为木薯种质鉴定、优异资源挖掘及新品种选育提供分子工具和理论参考。【方法】 基于377份木薯种质全基因组重测序数据,以位点完整性、次要等位基因频率、杂合率、多态性信息含量(PIC)、GC含量、序列同源性、连续单碱基重复及位点分布密度等条件,筛选出高多态性KASP分子标记,并对184份木薯种质资源进行遗传多样性分析及DNA指纹图谱构建。【结果】 从木薯全基因组重测序数据中位于基因组不同位置的52722个SNP位点进行筛选,最终获得了9443个SNP位点。从木薯的18条染色体上分别选择分布相对均匀的20个SNP位点,共计360个位点。利用360对KASP引物对22份木薯种质进行引物初筛,筛选出27个高多态性KASP分子标记。通过27个KASP分子标记对184份木薯种质资源的遗传多样性分析,结果显示,主要等位基因频率(MAF)为0.440~0.842,平均为0.637;基因多样性(GD)为0.270~0.591,平均为0.464,有26个KASP分子标记的GD高于0.300;观测杂合度(Ho)为0.173~0.538,平均为0.344,45.3% KASP分子标记的Ho分布在0.300~0.400;PIC为0.234~0.545,85.18% KASP分子标记的PIC大于0.300,显示出较高的多态性。184份木薯种质被划分为9个类群,群体划分与其地理来源未呈明显相关性,说明木薯种质间存在较高程度的基因交流与混合。将27个KASP分子标记分型结果转为二元编码数据,构建184份木薯种质资源的DNA指纹图谱,有效地揭示不同木薯种质之间的遗传差异。【结论】 基于木薯全基因组重测序数据开发出27个KASP分子标记,能有效评估木薯种质遗传多样性,并鉴定种质间的亲缘关系,可用于木薯种质资源鉴定、基因定位及分子标记辅助育种。

     

    Abstract: 【Objective】 This study aimed to develop KASP (kompetitive allele-specific PCR) molecular markers based on whole-genome resequencing data and perform genetic diversity analysis and DNA fingerprint construction, thereby providing molecular tools and theoretical references for cassava germplasm identification, superior resource exploration, and breeding of new varieties. 【Method】 Based on whole-genome resequencing data of 377 cassava germplasms, highly polymorphic KASP molecular markers were screened according to conditions including locus integrity,minor allele frequency,heterozygosity,polymorphism information content (PIC),GC content,sequence homology,and distribution density of continuous single-base repeats and loci, and genetic diversity analysis and DNA fingerprint construction of 184 cassava germplasm resources were performed. 【Result】 A total of 9443 loci were screened from the 52722 SNP loci at different positions of genome of the whole-genome resequencing data of cassava. A total of 20 SNP loci that were evenly distributed were selected from 18 chromosomes of cassava, which were 360 loci in total. The 22 cassava germplasms were preliminarily screened using 360 pairs of KASP primers,and 27 highly polymorphic KASP molecular markers were identified. Genetic diversity analysis based on the 27 KASP molecular markers in 184 cassava germplasm resources showed that the major allele frequency (MAF) ranged from 0.440 to 0.842,with an average of 0.637; the gene diversity (GD) ranged from 0.270 to 0.591,with an average of 0.464; the GDs of 26 KASP molecular markers were higher than 0.300; observed heterozygosity (Ho) was 0.173-0.538, with an average of 0.344, and 45.3% of KASP molecular markers had Ho distributed in 0.300-0.400; PIC was 0.234-0.545, and 85.18% of KASP molecular markers had PIC higher than 0.300, exhibiting a high level of polymorphism. Cluster analysis grouped the 184 cassava germplasms into 9 major categories,but no clear correlation was observed between the clustering pattern and geographical origin,suggesting extensive gene flow and genetic admixture among cassava germplasms. The genotyping results of 27 KASP molecular markers were transferred to binary coding data for constructing a DNA fingerprint of 184 cassava germplasm resources, effectively revealing genetic differences among different cassava germplasms. 【Conclusion】 The 27 KASP molecular markers are developed based on whole-genome resequencing data of cassava, which can effectively evaluate the genetic diversity and identify genetic relationships among germplasms, therefore, they can be used for germplasm identification, gene localization, and molecular-assisted breeding of cassava.

     

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