Data from: SSR-marker analysis of the intracultivar phenotypic variation discovered within 3 soybean cultivars

Genetic variation within homogeneous gene pools in various crops is assumed to be very limited. One objective of this study was to use 144 simple sequence repeat (SSR) markers to determine if the single-plant lines selected at ultra-low plant density in honeycomb designs within the soybean cultivars Benning, Haskell, and Cook had unique SSR genetic fingerprints. Another objective was to investigate if the variation found was the result of residual genetic heterozygosity that could be detected in the original gene pool where selection initiated. Our results showed that the phenotypic variation for seed protein content and seed weight has a genotypic component identified by the SSR band variation. The seven lines from Haskell had a total of 63 variant alleles, the five lines from Benning had 34 variant alleles, and the seven lines from Cook had 34 variant alleles, therefore, possessing unique genetic fingerprints. Most of the intra-cultivar SSR band variation discovered was the result of residual heterozygosity in the initial plant selected to become the cultivar. More specifically, 82% of the SSR variant alleles were traced in the Benning Foundation seed source, 93% in the Haskell seed source, and 82% in the Cook seed source. The remaining variant bands (18% for Benning, 7% for Haskell, and 18% for Cook) could not be detected in the Foundation seed source and were likely the result of mutation or some other mechanism generating de novo variation. These results provide evidence that genetic variation among individual plants is present even in homogeneous gene pools and can be further utilized in breeding programs.人们普遍认为，各类作物同质化基因库内的遗传变异极为有限。本研究的核心目标之一，是利用144个简单序列重复（simple sequence repeat, SSR）标记，探究在大豆品种Benning、Haskell与Cook中，通过蜂巢设计以超低种植密度筛选出的单株系是否具备独特的SSR遗传指纹。另一目标则是考察所发现的变异，是否源于初始选择群体中可被检测到的残留遗传杂合性。 研究结果显示，种子蛋白含量与种子重量的表型变异存在由SSR条带变异所鉴定的遗传组分。其中，来自Haskell的7个品系共检测到63个变异等位基因，来自Benning的5个品系检测到34个变异等位基因，来自Cook的7个品系亦检测到34个变异等位基因，因此这些品系均拥有独特的遗传指纹。 本次研究发现的品种内SSR条带变异，大多源自用于培育该品种的初始植株所携带的残留杂合性。具体而言，82%的SSR变异等位基因可在Benning的基础种子源中溯源，93%可在Haskell的种子源中溯源，82%可在Cook的种子源中溯源。剩余的变异条带（Benning为18%、Haskell为7%、Cook为18%）无法在基础种子源中被检测到，其成因大概率为突变或其他产生新生变异的机制。 上述结果证实，即便在同质化基因库中，单株间仍存在遗传变异，且该变异可进一步应用于作物育种项目中。