Data from: Improvement in nitrogen fixation capacity could be part of the domestication process in soybean

Biological nitrogen fixation (BNF) in soybeans is a complex process involving the interplay between the plant host and the symbiotic rhizobia. As nitrogen supply has a crucial role in growth and development, higher nitrogen fixation capacity would be important to achieve bigger plants and larger seeds, which were important selection criteria during plant domestication by humans. To test this hypothesis, we monitored the nitrogen fixation-related performance in 31 cultivated and 17 wild soybeans after inoculation with the slow-growing Bradyrhizobium diazoefficiens sp. nov. USDA110 and the fast-growing Sinorhizobium (Ensifer) fredii CCBAU45436. Our results showed that, in general, cultivated soybeans gave better performance in BNF. Electron microscopic studies indicated that there was an exceptionally high accumulation of poly-β-hydroxybutyrate bodies in bacteroids in the nodules of all wild soybeans tested, suggesting that the C/N balance in wild soybeans may not be optimized for nitrogen fixation. Furthermore, we identified new quantitative trait loci (QTLs) for total ureides and total nodule fresh weight by employing a recombinant inbred population composed of descendants from a cross between a cultivated and a wild parent. Using nucleotide diversity (θπ), divergence index (Fst) and distribution of fixed single-nucleotide polymorphisms as parameters, we found that some regions in the total ureides QTL on chromosome 17 and the total nodule fresh weight QTL on chromosome 12 exhibited very low diversity among cultivated soybeans, suggesting that these were traits specially selected during the domestication and breeding process.

大豆生物固氮（Biological Nitrogen Fixation, BNF）是宿主植物与共生根瘤菌（symbiotic rhizobia）相互作用的复杂过程。氮素供应对植物生长发育至关重要，更高的固氮能力对于获得更大植株与更饱满种子具有重要意义，而这类性状亦是人类在植物驯化过程中的重要选择标准。为验证该假说，本研究分别以慢生型慢生根瘤菌（Bradyrhizobium diazoefficiens sp. nov.）USDA110与快生型弗雷氏中华根瘤菌（Sinorhizobium (Ensifer) fredii）CCBAU45436接种31份栽培大豆与17份野生大豆，对其固氮相关性状进行监测。研究结果表明，总体而言栽培大豆的生物固氮表现更优。电子显微镜观察显示，所有供试野生大豆的根瘤（nodules）内的类菌体（bacteroids）中均异常富集聚β-羟基丁酸酯颗粒（poly-β-hydroxybutyrate bodies），提示野生大豆的碳氮平衡可能未优化至适于高效固氮的状态。此外，本研究利用栽培大豆与野生大豆杂交获得的后代构建的重组自交系群体（recombinant inbred population），鉴定出与总尿囊素含量（total ureides）及总根瘤鲜重（total nodule fresh weight）相关的全新数量性状位点（Quantitative Trait Loci, QTLs）。本研究以核苷酸多样性（nucleotide diversity, θπ）、分化指数（divergence index, Fst）以及固定单核苷酸多态性（single-nucleotide polymorphisms）的分布作为分析参数，发现位于17号染色体的总尿囊素含量QTL区域与12号染色体的总根瘤鲜重QTL区域中的部分区段在栽培大豆中多样性极低，表明这些位点对应的性状是驯化与育种过程中受到定向选择的目标性状。