Multiple biotypes of soybean aphid, Aphis glycines, occur in North America adapted for survival (virulence) on soybean, Glycine max, with one or more different resistance to A. glycines (Rag) traits. The degree of genome-wide variance between biotypes and the basis of virulence remains unknown, but the latter is hypothesized to involve secreted effector proteins. Between 167,249 and 217,750 single nucleotide polymorphisms (SNPs) were predicted from whole genome re-sequencing of A. glycines avirulent biotype 1 (B1) and virulent B2, B3 and B4 colony-derived iso-female lines when compared to the draft B1 genome assembly, Ag_bt1_v6.0. Differences in nucleotide diversity indices (π) estimated within 1000 bp sliding windows demonstrated that 226 of 353 (64.0%) regions most differentiated between B1 and ≥ 2 virulent biotypes, representing < 0.1% of the 308 Mb assembled genome size, are located on 15 unordered scaffolds. Furthermore, these 226 intervals were coincident and show a significant association with 326 of 508 SNPs with significant locus-by-locus F_ST estimates between biotype populations (r = 0.6271; F_1,70 = 45.36, P < 0.001) and genes showing evidence of directions selection (πN/πS > 2.0; r = 0.6233; F_1,70 = 50.20, P < 0.001). A putative secreted effector glycoprotein is encoded in proximity to genome intervals of low estimated π (putative selective sweep) within avirulent B1 compared to all three virulent biotypes. Additionally, SNPs are clustered in or in proximity to genes putatively involved in intracellular protein cargo transport and the regulation of secretion. Results of this study indicate that factors on a small number of scaffolds of the A. glycines genome may contribute to variance in virulence towards Rag traits in G. max.

大豆蚜 ( Aphis sweetines ) 的多种生物型出现在北美，适合在大豆 ( Glycine max)上生存（毒力），对大豆蚜( Rag ) 具有一种或多种不同的抗性。生物型之间全基因组差异的程度和毒力的基础仍然未知，但推测后者涉及分泌的效应蛋白。与草图 B1 基因组组装相比，从甘氨酸无毒生物型 1 (B1) 和强毒B2、B3 和 B4 菌落来源的异雌性品系的全基因组重测序中预测出 167,249 至 217,750 个单核苷酸多态性 (SNP) ，Ag_bt1_v6.0。在 1000 bp 滑动窗口内估计的核苷酸多样性指数 ( π ) 的差异表明，353 个区域中的 226 个 (64.0%) 在 B1 和 ≥ 2毒力生物型之间差异最大，代表 < 308 Mb 组装基因组大小的 0.1%，位于 15无序的脚手架。此外，这 226 个间隔是一致的，并显示与 508 个 SNP 中的 326 个显着相关，与生物型群体之间逐个位点F _ST估计值显着相关（r = 0.6271； F _1,70 = 45.36， P < 0.001）和显示证据的基因方向选择（ π N/ π S > 2.0；r = 0.6233； F _1,70 = 50.20， P < 0.001）。与所有三种有毒生物型相比，无毒B1 中推定的分泌效应糖蛋白编码在接近低估计π （推定选择性扫描）的基因组间隔处。 此外，SNP 聚集在推测参与细胞内蛋白质货物运输和分泌调节的基因中或附近。这项研究的结果表明， A. 大豆基因组的少量支架上的因素可能会导致G. max中Rag性状的毒力差异。