Fu Yong-Bi, Cober Elroy R, Morrison Malcolm J, Marsolais Frédéric, Peterson Gregory W, Horbach Carolee
Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
Plants (Basel). 2021 Aug 5;10(8):1611. doi: 10.3390/plants10081611.
Genomic characterization is playing an increasing role in plant germplasm conservation and utilization, as it can provide higher resolution with genome-wide SNP markers than before to identify and analyze genetic variation. A genotyping-by-sequencing technique was applied to genotype 541 soybean accessions conserved at Plant Gene Resources of Canada and 30 soybean cultivars and breeding lines developed by the Ottawa soybean breeding program of Agriculture and Agri-Food Canada. The sequencing generated an average of 952,074 raw sequence reads per sample. SNP calling identified 43,891 SNPs across 20 soybean chromosomes and 69 scaffolds with variable levels of missing values. Based on 19,898 SNPs with up to 50% missing values, three distinct genetic groups were found in the assayed samples. These groups were a mixture of the samples that originated from different countries and the samples of known maturity groups. The samples that originated from Canada were clustered into all three distinct groups, but 30 Ottawa breeding lines fell into two groups only. Based on the average pairwise dissimilarity estimates, 40 samples with the most genetic distinctness were identified from three genetic groups with diverse sample origin and known maturity. Additionally, 40 samples with the highest genetic redundancy were detected and they consisted of different sample origins and maturity groups, largely from one genetic group. Moreover, some genetically duplicated samples were identified, but the overall level of genetic duplication was relatively low in the collection. These findings are useful for soybean germplasm management and utilization.
基因组特征分析在植物种质资源的保存和利用中发挥着越来越重要的作用，因为与以往相比，它可以利用全基因组SNP标记提供更高的分辨率来识别和分析遗传变异。采用一种简化基因组测序技术对加拿大植物基因资源库保存的541份大豆种质以及加拿大农业和农业食品部渥太华大豆育种项目培育的30个大豆品种和育种系进行基因分型。测序结果显示，每个样本平均产生952,074条原始序列读数。通过SNP检测，在20条大豆染色体和69个支架上共鉴定出43,891个SNP，缺失值水平各不相同。基于19,898个缺失值高达50%的SNP，在检测样本中发现了三个不同的遗传群体。这些群体是来自不同国家的样本和已知成熟组样本的混合。来自加拿大的样本被聚类到所有三个不同的群体中，但30个渥太华育种系仅分为两个群体。根据平均成对差异估计，从具有不同样本来源和已知成熟度的三个遗传群体中鉴定出40个遗传差异最大的样本。此外，还检测到40个遗传冗余度最高的样本，它们由不同的样本来源和成熟组组成，主要来自一个遗传群体。此外，还鉴定出一些基因重复的样本，但该种质库中基因重复的总体水平相对较低。这些发现对大豆种质资源的管理和利用具有重要意义。
