Soybean Research Institute; MARA National Center for Soybean Improvement; MARA Key Laboratory of Biology and Genetic Improvement of Soybean; National Key Laboratory for Crop Genetics and Germplasm Enhancement; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
Mudanjiang Research and Development Center for Soybean; Mudanjiang Experiment Station of the National Center for Soybean Improvement, Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, 157041, Heilongjiang, China.
Theor Appl Genet. 2020 Jun;133(6):1839-1857. doi: 10.1007/s00122-020-03558-4. Epub 2020 Feb 6.
This population genetic study is characterized with direct comparisons of days to flowering QTL-allele matrices between newly evolved and originally old maturity groups of soybeans to explore its evolutionary dynamics using the RTM-GWAS procedure. The Northeast China (NEC) soybeans are the major germplasm source of modern soybean production in Americas (> 80% of the world total). NEC is a relatively new soybean area in China, expanded after its nomadic status in the seventeenth century. At nine sites of four ecoregions in NEC, 361 varieties were tested for their days to flowering (DTF), a geography-sensitive trait as an indicator for maturity groups (MGs). The DTF reduced obviously along with soybeans extended to higher latitudes, ranging in 41-83 days and MG 000-III. Using the RTM-GWAS (restricted two-stage multi-locus model genome-wide association study) procedure, 81 QTLs with 342 alleles were identified, accounting for 77.85% genetic contribution (R = 0.01-7.74%/locus), and other 20.75% (98.60-77.85%, h = 98.60%) genetic variation was due to a collective of unmapped QTLs. With soybeans northward, breeding effort made the original MG I-III evolved to MG 0-00-000. In direct comparisons of QTL-allele matrices among MGs, the genetic dynamics are identified with local exotic introduction/migration (58.48%) as the first and selection against/exclusion of positive alleles causing new recombination (40.64%) as the second, while only a few allele emergence/mutation happened (0.88%, limited in MG 0, not in MG 00-000). In new MG emergence, 24 QTLs with 19 candidate genes are the major sources. A genetic potential of further DTF shortening (13-21 days) is predicted for NEC population. The QTL detection in individual ecoregions showed various ecoregion-specific QTLs-alleles/genes after co-localization treatment (removing the random environment shifting ones).
本群体遗传学研究的特点是直接比较新进化的和原本古老的大豆成熟期组的开花 QTL-等位基因矩阵，以使用 RTM-GWAS 程序探索其进化动态。东北大豆（NEC）是美洲现代大豆生产的主要种质资源（占世界总量的 80%以上）。NEC 是中国一个相对较新的大豆种植区，自 17 世纪以来从游牧状态扩展而来。在 NEC 的四个生态区的九个地点，测试了 361 个品种的开花日数（DTF），这是一个作为成熟度组（MG）指标的地理敏感性状。随着大豆向更高纬度地区扩展，DFT 明显减少，范围在 41-83 天和 MG 000-III 之间。使用 RTM-GWAS（限制两阶段多基因模型全基因组关联研究）程序，鉴定了 81 个 QTL，有 342 个等位基因，占 77.85%的遗传贡献（R=0.01-7.74%/位点），另外 20.75%（98.60-77.85%，h=98.60%）的遗传变异是由于未映射 QTL 的集体。随着大豆向北推进，育种工作使原本的 MG I-III 进化到 MG 0-00-000。在 MGs 之间的 QTL-等位基因矩阵的直接比较中，确定遗传动态与局部外来引种/迁移（58.48%）作为第一，选择淘汰正等位基因引起新重组（40.64%）作为第二，而只有少数等位基因出现/突变（0.88%，仅限于 MG 0，MG 00-000 中没有）。在新 MG 的出现中，24 个 QTL 和 19 个候选基因是主要来源。预测 NEC 群体进一步缩短开花日数（13-21 天）的遗传潜力。在个体生态区的 QTL 检测中，在共定位处理（去除随机环境转移的 QTL）后，显示了各种生态区特有的 QTL-等位基因/基因。
