Table_4_A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean.xlsx

Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using whole genome SNP sets and GWAS-based marker sets. Four SNPs, namely Gm18_57,223,391 (LOD = 2.69), Gm16_29,491,946 (LOD = 3.86), Gm06_45,035,185 (LOD = 4.74), and Gm18_51,994,200 (LOD = 3.60), were located near the reported P. pachyrhizi R genes, Rpp1, Rpp2, Rpp3, and Rpp4, respectively. Other significant SNPs, including Gm02_7,235,181 (LOD = 7.91), Gm02_7234594 (LOD = 7.61), Gm03_38,913,029 (LOD = 6.85), Gm04_46,003,059 (LOD = 6.03), Gm09_1,951,644 (LOD = 10.07), Gm10_39,142,024 (LOD = 7.12), Gm12_28,136,735 (LOD = 7.03), Gm13_16,350,701(LOD = 5.63), Gm14_6,185,611 (LOD = 5.51), and Gm19_44,734,953 (LOD = 6.02), were associated with abundant disease resistance genes, such as Glyma.02G084100, Glyma.03G175300, Glyma.04g189500, Glyma.09G023800, Glyma.12G160400, Glyma.13G064500, Glyma.14g073300, and Glyma.19G190200. The annotations of these genes included but not limited to: LRR class gene, cytochrome 450, cell wall structure, RCC1, NAC, ABC transporter, F-box domain, etc. The GWAS based markers showed more accuracies in genomic prediction than the whole genome SNPs, and Bayesian LASSO model was the ideal model in SBR resistance prediction with 44.5% ~ 60.4% accuracies. This study aids breeders in predicting selection accuracy of complex traits such as disease resistance and can shorten the soybean breeding cycle by the identified markers

大豆锈病（SBR），由Phakopsora pachyrhizi引起，是一种破坏性极强的真菌病害，对全球大豆产量构成严重威胁。本研究在3,082份大豆种质资源群体上，采用七种模型进行了全基因组关联研究（GWAS），通过30,314个高质量的单核苷酸多态性（SNPs）标记识别与SBR抗性相关的标记。随后，运用包括岭回归最佳线性无偏预测器（rrBLUP）、基因组最佳线性无偏预测器（gBLUP）、贝叶斯最小绝对收缩和选择算子（Bayesian LASSO）、随机森林（RF）和支持向量机（SVM）在内的五种基因组选择（GS）模型，利用全基因组SNP集和基于GWAS的标记集预测SBR抗性的育种值。在近P. pachyrhizi的R基因Rpp1、Rpp2、Rpp3和Rpp4处，分别定位了四个SNPs，即Gm18_57,223,391（LOD = 2.69）、Gm16_29,491,946（LOD = 3.86）、Gm06_45,035,185（LOD = 4.74）和Gm18_51,994,200（LOD = 3.60）。其他显著的SNPs，包括Gm02_7,235,181（LOD = 7.91）、Gm02_7234594（LOD = 7.61）、Gm03_38,913,029（LOD = 6.85）、Gm04_46,003,059（LOD = 6.03）、Gm09_1,951,644（LOD = 10.07）、Gm10_39,142,024（LOD = 7.12）、Gm12_28,136,735（LOD = 7.03）、Gm13_16,350,701（LOD = 5.63）、Gm14_6,185,611（LOD = 5.51）和Gm19_44,734,953（LOD = 6.02），均与丰富的抗病基因相关，例如Glyma.02G084100、Glyma.03G175300、Glyma.04g189500、Glyma.09G023800、Glyma.12G160400、Glyma.13G064500、Glyma.14g073300和Glyma.19G190200。这些基因的注释包括但不限于LRR类基因、细胞色素450、细胞壁结构、RCC1、NAC、ABC转运蛋白、F-box结构域等。基于GWAS的标记在基因组预测中的准确性高于全基因组SNPs，贝叶斯LASSO模型在SBR抗性预测中表现理想，准确率在44.5%至60.4%之间。本研究有助于育种者预测复杂性状如抗病性的选择准确性，并通过确定的标记缩短大豆育种周期。