Research Objective
To make use of the chickpea genome assembly to accelerate chickpea varietal development through integration of genomic technologies into chickpea breeding program.
Chickpea production in Canada has been limited by susceptibility to Ascochyta blight as well as late maturity. Several moderately resistant and early maturing chickpea cultivars have been developed and released for cultivation in Western Canada. However, changing environmental conditions, such as wet conditions, increase disease pressure and cause significant yield losses, whereas warm conditions accompanied with high moisture may cause regrowth and delay maturity. Genomic tools (DNA markers) have been successfully used to expedite the development of disease resistant cultivars in many plant species. This research is aimed at characterizing the genetic variation available in chickpea germplasm and breeding lines by resequencing their genomes, followed by utilizing the resequencing data in association studies to identify genes and allelic variants associated with agronomically and economically important traits in chickpeas, and to use the data to facilitate the practical application of genomic selection in chickpea breeding.
To achieve these objectives, a set of chickpea experimental lines sampled from the CDC chickpea breeding program, and representative samples of the wild species together totaling 251 accessions, were re-sequenced. The panel accessions were evaluated for grain yield and other agronomic traits at one location each in 2015 and 2016. Assessment of intrinsic quality such as total protein, fat content, amino acid composition, carotenoid complex, and micronutrients is in progress.
The re-sequencing efforts were completed in 2016 and have generated millions of DNA markers, including single nucleotide variants, insertions and deletions, copy number variations, and structural variations in the Canadian chickpea collection including the Desi, Kabuli, and wild accessions. Whole genome sequencing of wild accessions provides information about potential novel alleles that can be used in the breeding program. The high sequencing depth (32X on average) provides good quality data for sequence variation characterization. Using large number SNP data and other variations in the genome generated from the resequencing effort, we are expecting to conduct robust association analysis to find a strong link between variations in the DNA sequence and the target traits. The markers associated with important traits will be used in the breeding program to expedite cultivar development. The large number of nucleotide variations identified in this analysis also allows us to selectively use the optimum subset of the data to increase the selection accuracy in the genome selection.
Developing disease resistant and early maturing chickpea cultivars can help to overcome production constraints and improve chickpea productivity in Canada. In the current project, we have developed genomic resources that can be used in genomic assisted breeding in chickpea. 251 accessions from the CDC chickpea collections were sequenced. An additional 12 wild relatives were also sequenced to analyze potential novel alleles from wild chickpea. Results of the analysis using the SNP information support the hypothesis that the wild, landraces (germplasm), and elite chickpea accessions originated from a common ancestor. The whole genome sequence information of the Canadian chickpea accessions and the SNPs associated with key traits identified in this project will be used for improving the selection program through assisted selection and genomic selection to shorten the delivery time of new cultivars with better adaptation to Canadian growing conditions.