Candidate genes for ascochyta blight resistance and genome-wide association analysis for improvement of assisted-selection in chickpea
To examine the genetic variation of existing resistance genes controlling ascochyta blight resistance in chickpea and to understand their defence mechanism. The project will also identify new genes responsible for conferring resistance to ascochyta blight in chickpea.
Ascochyta blight caused by the fungus Ascochyta rabiei is one of the most devastating diseases of chickpea (Cicer arietinum L.) worldwide. The use of resistant varieties is considered the most economical and sustainable approach for controlling this disease. The project consisted of two major components. The first component was the identification of QTLs conferring partial resistance using sequence and gene expression analysis and the second component was the genetic evaluation across a wider genetic pool through genome wide association analysis (GWAS) to identify potential new genes that can be combined with resistance genes available in current cultivars. Four RIL mapping populations were genotyped using Illumina® GoldenGate assay and Genotyping by Sequencing (GBS). The populations were rated for their reaction o ascochyta blight under field and greenhouse conditions in 2013 and 2014. High density map was developed for each population. A total of 16 non-redundant QTLs across eight chickpea chromosomes were identified to be associated with AB resistance across the four mapping populations. The chickpea association mapping panel (CPAM) consisting of 268 diverse chickpea accessions were genotyped using 1,536 genic SNPs. A total of 27 SNP loci were found to be associated with ascochyta blight resistance either in one or multiple screenings under field and/or greenhouse conditions. These SNPs were located on 7 out of 8 chickpea chromosomes. To gain insight into the possible resistance mechanism, we generated transcriptomes from the ascochyta blight partial resistance lines and from the highly susceptible chickpea genotype at three different time points after Ascochyta rabiei inoculation using RNA-seq. We generated nearly 84.6 million RNA-Seq reads, totaling 96.5 Giga bases of sequence. We also sequenced 4.3 Gb transcripts of Ascochyta rabiei pathogen AR-170 isolate. More than 90% of chickpea transcriptome reads were mapped to the chickpea reference genome sequence. Differential expression analysis revealed that several pathogenesis-related genes, cell wall-mediated pathogen resistance genes, enzymes involved in defence mechanisms and different classes of stress responsive transcription factors were significantly up-regulated in Ascochyta rabiei inoculated chickpea samples. We also identified 6,549 genic SNPs among the three chickpea genotypes. These genic SNPs will be a valuable resource for development of gene based markers and genetic mapping of candidate genes. Overall this research has generated large amount of genomic and transcriptome sequence information. Genomic regions (QTLs) associated with AB resistance and differentially expressed genes in partially resistant chickpea varieties were identified. Several candidate genes and associated sequence variants were identified, which can be used as best marker for marker assisted selections
(MAS) for improvement of AB resistance in chickpea. The differentially expressed genes and candidate genes located within the QTL regions added important information in understanding the mechanisms that contribute to the expression of partial resistance to ascochyta blight in chickpea.