Linkage QTL mapping and genome-wide association study on resistance in chickpea to Pythium ultimum

Authors: AGARWAL, CHITI - Washington State University; Chen, Weidong; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Vandemark, George

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2022
Publication Date: 8/20/2022
Citation: Agarwal, C., Chen, W., Varshney, R.K., Vandemark, G.J. 2022. Linkage QTL mapping and genome-wide association study on resistance in chickpea to Pythium ultimum. Frontiers in Genetics. 13. Article 390921. https://doi.org/10.3389/fgene.2022.945787.
DOI: https://doi.org/10.3389/fgene.2022.945787

Interpretive Summary: Chickpea has been a globally important source of nutrition for several thousand years. The fungicide mefenoxam has been used for at least 30 years as a seed coating to control several chickpea diseases. However, we recently identified the pathogen Pythium ultimum with mefenoxam resistance that caused severe losses to chickpea production throughout Washington and Idaho. Consequently, new approaches are needed to control this emerging pathogen that causes severe seed and root rot disease of chickpea. Initially, we evaluated different chickpea lines and identified several lines with resistance to the pathogen. However, our efforts to breed resistant varieties can be accelerated by developing technologies, such as molecular markers, to enable more efficient breeding procedures. The objectives of this study were to detect DNA markers associated with resistance in chickpea to diseases caused by Pythium, and identify genes that may be involved in disease resistance. We first studied a population of closely related chickpea lines and detected two DNA markers, one of which was responsible for nearly half of the differences observed in disease resistance. We also identified several genes that are candidates for being involved in disease resistance, including a gene involved in synthesis of plant hormones. Secondly, we studied a different population of loosely related chickpea lines and commercial varieties, and also identified several DNA markers and candidate genes for disease resistance. These candidates included several genes that have been proposed to be involved in disease resistance in other crops including corn, rice, and wheat. We will use the DNA markers detected in this study to help us more efficiently develop improved chickpea varieties and the candidate genes we identified contribute to understanding of plants combat a wide range of diseases.

Technical Abstract: The soilborne Oomycete plant pathogen Pythium ultimum causes seed rot and pre-emergence damping-off of chickpea (Cicer arietinum L.). The pathogen has been controlled for several decades using the fungicide metalaxyl as a seed treatment but has re-emerged as a severe problem with the detection of metalaxyl-resistant isolates of the pathogen from infested fields in the USA Pacific Northwest. The objective of this study was to identify genetic markers and candidate genes associated with resistance to P. ultimum in an interspecific recombinant inbred line population (CRIL-7) derived from a cross between C. reticulatum (PI599072) x C. arietinum (FLIP 84-92C) and conduct genome-wide association studies (GWAS) for disease resistance using a chickpea diversity panel consisting of 184 accessions. CRIL-7 was examined using 1029 SNP markers spanning eight linkage groups. A major QTL, “q4-1”, was detected on LG 4 that explained 41.8 % of phenotypic variation, and a minor QTL, “q8-1”, was detected on LG8 that explained 4.5% of phenotypic variance. Seven candidate genes were also detected using composite interval mapping, including several genes previously associated with disease resistance in other crop species. A total of 302,902 single nucleotide polymorphic (SNP) markers were used to determine population structure and Kinship of the diversity panel. Marker-trait associations were established by employing different combinations of principal components (PC) and kinships (K) in the FarmCPU model. Based on a Bonferroni cut-off, 11 significant SNPs and 7 candidate genes were identified for resistance based on GWAS. Significant SNP markers and candidate genes identified in this study may be useful for marker-assisted selection to develop superior chickpea varieties with improved resistance to seed rot and pre-emergence damping-off caused by metalaxyl-resistant P. ultimum.