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.学界普遍认为，各类作物的同质化基因库内遗传变异程度极低。本研究的两大目标为：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的蜂巢设计超低种植密度下筛选出的单株株系是否具备独特的SSR遗传指纹；二是探明所观测到的遗传变异是否源自初始筛选所用原始基因库中可被检测到的残留遗传杂合性。本研究结果显示，种子蛋白含量与籽粒重量的表型变异存在可通过SSR条带变异表征的遗传组分。其中，来自Haskell的7个株系共携带63个变异等位基因，Benning的5个株系携带34个，Cook的7个株系亦携带34个，所有株系均具备独特的遗传指纹。本研究发现的品种内SSR条带变异，大多源于该品种初始选育单株携带的残留杂合性。具体而言，82%的SSR变异等位基因可在Benning基础种子种源中溯源，93%可在Haskell种源中溯源，82%可在Cook种源中溯源。剩余变异条带（Benning占18%、Haskell占7%、Cook占18%）无法在基础种子种源中被检测到，推测其源于突变或其他可产生新生变异的机制。本研究结果证实，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。