Department of Crop Sciences, University of Illinois at Urbana - Champaign, Urbana, IL, USA.
Honeybee Breeding, Genetics, and Physiology Research, U. S. Department of Agriculture, Baton Rouge, LA, USA.
Theor Appl Genet. 2022 May;135(5):1591-1602. doi: 10.1007/s00122-022-04056-5. Epub 2022 Feb 27.
Independent soybean breeding programs shape genetic diversity from unimproved germplasm to modern cultivars in similar ways, but distinct breeding populations retain unique genetic variation, preserving additional diversity. From the domestication of wild soybean (Glycine soja Sieb. & Zucc.), over 3,000 years ago, to the modern soybean (Glycine max L. Merr) cultivars that provide much of the world's oil and protein, soybean populations have undergone fundamental changes. We evaluated the molecular impact of breeding and selection using 391 soybean accessions including US cultivars and their progenitors from the USDA Soybean Germplasm Collection (CGP), plus two new populations specifically developed to increase genetic diversity and high yield in two alternative gene pools: one derived from exotic G. max germplasm (AGP) and one derived from G. soja (SGP). Reduction in nucleotide genetic diversity (π) was observed with selection within gene pools, but artificial selection in the AGP maintained more diversity than in the CGP. The highest F levels were seen between ancestral and elite lines in all gene pools, but specific nucleotide-level patterns varied between gene pools. Population structure analyses support that independent selection resulted in high-yielding elite lines with similar allelic compositions in the AGP and CGP. SGP, however, produced elite progeny that were well differentiated from, but lower yielding than, CGP elites. Both the AGP and SGP retained a significant number of private alleles that are absent in CGP. We conclude that the genomic diversity shaped by multiple selective breeding programs can result in gene pools of highly productive elite lines with similar allelic compositions in a genome-wide perspective. Breeding programs with different ancestral lines, however, can retain private alleles representing unique genetic diversity.
独立的大豆育种计划以相似的方式从未经改良的种质中塑造遗传多样性，形成现代品种，但不同的育种群体保留了独特的遗传变异，保留了额外的多样性。从野生大豆（Glycine soja Sieb. & Zucc.）的驯化，距今已有 3000 多年，到现代大豆（Glycine max L. Merr）品种为世界提供了大部分的油和蛋白质，大豆群体发生了根本性的变化。我们使用包括美国品种及其亲本在内的 391 份大豆种质评估了育种和选择的分子影响，这些亲本来自美国农业部大豆种质库（CGP），另外两个新群体是专门为增加两个替代基因库的遗传多样性和高产量而开发的：一个来自外来大豆种质（AGP），一个来自大豆（SGP）。在基因库内选择时观察到核苷酸遗传多样性（π）减少，但 AGP 的人工选择保持了比 CGP 更多的多样性。在所有基因库中，都可以看到祖先进化和精英系之间的 F 水平最高，但特定核苷酸水平的模式在基因库之间有所不同。种群结构分析支持独立选择导致了高产的精英系，这些系在 AGP 和 CGP 中具有相似的等位基因组成。然而，SGP 产生的精英后代与 CGP 精英系分化良好，但产量较低。AGP 和 SGP 都保留了大量在 CGP 中不存在的特有等位基因。我们得出的结论是，多个选择育种计划塑造的基因组多样性可以导致基因库中具有相似等位基因组成的高产精英系，但具有不同祖先的育种计划可以保留代表独特遗传多样性的特有等位基因。
