Transcriptome Profiling of the <i>Phaseolus vulgaris</i> - <i>Colletotrichum lindemuthianum</i> Pathosystem

<div><p>Bean (<i>Phaseolus vulgaris</i>) anthracnose caused by the hemi-biotrophic pathogen <i>Colletotrichum lindemuthianum</i> is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the <i>Co-1</i> gene on chromosome Pv01 during a time course following infection with race 73 of <i>C</i>. <i>lindemuthianum</i>. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the <i>Co-1</i> locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the <i>Co-1</i> locus. Through this analysis, we reduced the previous number of candidate genes reported at the <i>Co-1</i> locus from eight to three. These results suggest the dynamic nature of <i>P</i>. <i>vulgaris–C</i>. <i>lindemuthianum</i> interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.</p></div

Expression patterns of Phvul.001G241300 that encoding a Hs1pro-1 protein in resistant and susceptible near isogenic lines inoculated with <i>Colletotrichum lindemuthianum</i> race 73.

<p>Expression patterns of Phvul.001G241300 that encoding a Hs1pro-1 protein in resistant and susceptible near isogenic lines inoculated with <i>Colletotrichum lindemuthianum</i> race 73.</p

Heatmap of expression (FPKM) for nine genes encoding NB-ARC domains that were differentially expressed between resistant and susceptible near isogenic lines at 0, 24, 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.

<p>Expression for these nine genes ranged from 0 to 41 FPKM.</p

Genes encoding transcription factors differentially expressed between resistant and susceptible near isogenic lines at 24, 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.

<p>Genes encoding transcription factors differentially expressed between resistant and susceptible near isogenic lines at 24, 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.</p

Transcriptome Profiling of the <i>Phaseolus vulgaris</i> - <i>Colletotrichum lindemuthianum</i> Pathosystem - Fig 1

<p>Disease progression on the susceptible NIL genotype a) 0 hpi b) 24 hpi c) 72 hpi and d) 96 hpi. Water soaked lesions were seen at 72 hpi and plants exhibited necrotic lesions at 96 hpi.</p

Genes in <i>Co-1</i> and <i>Co-4</i> genomic regions that were differentially expressed between resistant and susceptible near isogenic lines at 24, 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.

<p>Genes in <i>Co-1</i> and <i>Co-4</i> genomic regions that were differentially expressed between resistant and susceptible near isogenic lines at 24, 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.</p

Genes encoding NB-ARC and leucine-rich repeat domains that were differentially expressed between resistant and susceptible near isogenic lines at 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.

<p>Genes encoding NB-ARC and leucine-rich repeat domains that were differentially expressed between resistant and susceptible near isogenic lines at 72 and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.</p

Number of genes up-regulated in resistant (R) and susceptible (S) near isogenic lines at 0, 24, 72, and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.

<p>Number of genes up-regulated in resistant (R) and susceptible (S) near isogenic lines at 0, 24, 72, and 96 hours post inoculation with <i>Colletotrichum lindemuthianum</i> race 73.</p

QQ and Manhattan Plots showing candidate SNPs and P-values from GWAS using MLM for anthracnose resistance.

<p>From top to bottom include results for anthracnose resistance to A) race 65, B) race 73, and C) race 3481 on Pv01. Red line on Manhattan Plots is the significance threshold of P = 1.03 x 10⁻⁵ after Bonferonni correction of α = 0.05.</p

Chromosome, position, p-value, proportion of phenotypic variation explained (R²) and minor allele frequency of the two most significant SNPs for seven races of anthracnose resistance measured on 226 Andean bean genotypes.

<p>Chromosome, position, p-value, proportion of phenotypic variation explained (R²) and minor allele frequency of the two most significant SNPs for seven races of anthracnose resistance measured on 226 Andean bean genotypes.</p