Characterization and identification of Phytophthora resistance in soybean

Feng Lin, Purdue University

Abstract

Phytophthora root and stem rot (PRR), caused by the soil-borne oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. PRR can be effectively controlled by race-specific genes (Rps) conferring resistance to P. sojae. However, the Rps genes are usually non-durable, and it is needed to identify novel Rps genes with closely linked markers for marker assisted selection of resistant soybean cultivars. In addition, to better utilize Rps genes, it is important to understand the mechanism of resistance mediated by Rps genes, which remains largely unclear. In this thesis research, two independently inherited dominant resistant genes (designated as RpsUN1, and RpsUN2, respectively) were identified from a soybean landrace PI 567139B using a mapping population of 245 F2 individuals and 403 F2:3 families. RpsUN1 was mapped to a 6.5cM region between SSR markers Satt159 and BARCSOYSSR_03_0250 on chromosome 3, and RpsUN2 was mapped to a 3.0cM region between BARCSOYSSR_16_1275 and Sat_144 on chromosome 16. Marker assisted resistance spectrum analyses (MARS) with 16 isolates of P. sojae suggested that RpsUN1 was likely to be a novel allele at the Rps1 locus, and RpsUN2 was more likely to be a novel Rps gene. For a systematic understanding of the gene networks mediated by Rps genes, transcriptomes of 'Williams' and its 10 near isogenic lines (NIL) containing Rps genes were sequenced. A total of 4330 genes were differentially expressed in 'Williams' and 2075~5499 genes in NILs. The 10 NILs can be divided into three groups on the basis of expression of Rps mediated genes. Gene ontology (GO) analyses suggested that the different expression pattern of NILs was more likely due to intensity of gene expression rather than dramatic functional differences. Further analysis uncovered a whole picture of crosstalk of phytohormones during compatible or incompatible interactions. In addition, a vast majority of defense related gene networks were regulated by Rps genes, including phytoalexin biosynthesis, reactive oxygen species (ROS), Calcium signaling, mitogen-activated protein kinase (MAPK) cascade and transcription factors. Taking advantage of molecular mapping work and RNA sequencing data, we were able to establish a high resolution genetic and physical map for the novel Rps gene (RpsUN2) and characterize the expression and mutation of candidate genes towards providing valuable information for marker assisted selection and isolation of the gene. Using a total of 24 recombinants with heterozygous-susceptible genotype obtained from 826 F2:3 families, and additional SSR and CAPS markers, RpsUN2 were further narrowed down to a 64.5 kb region where seven genes were predicted on the basis of reference genome annotation, including five nucleotide binding-leucine rich repeat (NB-LRR) genes. Expression and mutation analysis from RNA-seq data suggested that Glyma16g34070 was the strongest candidate for RpsUN2, while Glyma16g34080 was less likely.

Degree

Ph.D.

Advisors

Ma, Purdue University.

Subject Area

Agronomy|Genetics|Plant Pathology

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