Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean. Glycine max

Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practicalapproach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 conferring broad spectra of resistance to P. sojae isolates, were identified in a landrace PI 567139B and mapped to a 6.5-cM region on chromosome 3 and a 3.0-cM region on chromosome 16, corresponding to 840 kb and 600 kb of sequences, respectively,of the soybean reference genome. By analyzing ten and nine recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines of the mapping populations, RpsUN1 and RpsUN2 were further narrowed to a 151-kb region that harbors five genes including three NBS-LRR genes, and a 36-kb region that contains four genes including five NBS-LRR genes, respectively, according to the reference genome. Analysis of expressional changes of these nine genes before and after inoculation with the pathogen suggest that the counterparts of Glyma.03g034600 in the RpsUN1 region and the counterparts of Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between different NBS-LRR genes in the mapped regions may have occurred, resulting in the formation of two recombinants with inconsistent genotypes and phenotypes detected by molecular markers within the fine-mapped regions. The haplotypes of genomic regions surrounding RpsUN1 and RpsUN2 in the entire soybean germplasm deposited in the US soybean germplasm collection were analyzed towards a better understanding of the origins of these two novel sources of resistance and screening of effective markers for marker-assisted selectionof these two resistance genes for soybean breeding. Overall design: 2 samples were sequenced, 1 inoculated with P. sojae, the other 1 were mock-inoculated

由卵菌（oomycete）病原菌大豆疫霉菌（Phytophthora sojae）引起的疫霉根茎腐病，是大豆最具破坏性的病害之一。种植携带Rps基因（Rps gene）介导的小种专化抗性的大豆栽培品种，是防治该病害最实用的策略。此前，研究人员在地方品种PI 567139B中鉴定出两个对大豆疫霉菌分离物具有广谱抗性的Rps基因：RpsUN1与RpsUN2，二者分别被定位至大豆参考基因组3号染色体的6.5厘摩（cM）区域与16号染色体的3.0厘摩（cM）区域，对应基因组序列长度分别为840 kb与600 kb。本研究对由两个作图群体亲本正反交获得的826个F2:3家系开展基因型与表型筛选，获得10个与9个重组体，进而将RpsUN1与RpsUN2分别精细定位至参考基因组中的151 kb区域（包含5个基因，其中含3个NBS-LRR基因（NBS-LRR gene））与36 kb区域（包含4个基因，其中含5个NBS-LRR基因）。对病原菌接种前后这9个基因的表达变化进行分析后发现，PI 567139B的RpsUN1区域中Glyma.03g034600的同源基因，以及RpsUN2区域中Glyma.16g215200与Glyma.16g214900的同源基因，可能与大豆疫霉菌抗性相关。研究同时推测，定位区域内不同NBS-LRR基因间可能发生了不等交换，进而在精细定位区域内形成了2个经分子标记检测发现的基因型与表型不一致的重组体。为深入解析这两个新型抗性资源的起源，并筛选可用于这两个抗性基因标记辅助选择（marker-assisted selection）的有效分子标记，研究人员对美国大豆种质资源库中保存的所有大豆种质里RpsUN1与RpsUN2侧翼基因组区域的单倍型（haplotype）进行了分析。实验整体设计：共对2份样本进行测序，其中1份接种大豆疫霉菌，另1份施以模拟接种（mock-inoculated）。