Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes

Authors: WILLIAMSON-BENAVIDES, BRUCE - Washington State University; SHARPE, RICHARD - Washington State University; NELSON, GRANT - Washington State University; BODAH, ELIANE - Consultant; Porter, Lyndon; DHINGRA, AMIT - Washington State University

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2021
Publication Date: 8/5/2021
Citation: Williamson-Benavides, B.A., Sharpe, R., Nelson, G., Bodah, E.T., Porter, L.D., Dhingra, A. 2021. Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes. Frontiers in Genetics. 12. Article 629267. https://doi.org/10.3389/fgene.2021.629267.
DOI: https://doi.org/10.3389/fgene.2021.629267

Interpretive Summary: Pea is an important cool-season annual crop. Profitable production of pea is severely impacted by soilborne diseases. These diseases are commonly referred to as the pea root rot complex (PRRC) and are caused by a single or combination of pathogens, including, Aphanomyces euteiches, Fusarium spp, Mycosphaerella pinodes, Pythium spp. and Rhizoctonia solani. One of the predominant causal agents of PRRC is the fungus Fusarium solani f. sp. pisi (Fsp). Fsp occurs in most pea fields throughout the world, and the yields of P. sativum cultivars can be reduced up to 15-60% by this pathogen. Fsp infects the pea seeds during germination and symptoms of Fsp root rot begin at or near the seed attachment and progress under the soil to the upper region of the taproot. Round or irregular light brown lesions that progress to dark black lesions on below ground stems have also been reported along with stunting and death. Fsp can survive in the soil for more than one season and conditions that decrease root growth, such as soil compaction, extreme temperatures, and moisture levels can increase Fusarium-mediated root damage. The present research identified five locations on pea chromosomes associated with Fsp resistance in pea and potential genes associated with the resistance. Each of these locations explains 5.26 to 14.76% of the total variation in disease resistance and together they can add up to 33.21% of the variation associated with the observed resistance. To the best of our knowledge, this is the only study that has reported presence of genes associated with Fsp resistance on chromosomes II and III. This research will be used in marker-assisted breeding to determine pea lines having genetic resistance to Fsp that can help improve pea yields and reduce grower risk to this major root rot pathogen.

Technical Abstract: Pisum sativum (pea) yields have declined significantly over the last decades predominantly due to cultivar susceptibility to root rot diseases. One of the predominant causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp). Yield losses caused by Fsp range from 15 to 60%. Genetic resistance offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from differentially expressed genes (DEGs), which were identified in a preceding study, were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The total set of SNPs with validated polymorphisms was used to screen the two RIL populations. Five QTLs were identified using two disease reaction criteria: root disease severity and plant height. One QTL WB.Fsp-Ps 5.1, located on chromosome V, explained 14.76% of the variance with a confidence interval of 10.36'cM. The other four QTLs, located on chromosomes II, III, and V, explain 5.26–8.05% of the variance. With the identification of five QTLs, the use of DEGs as candidate genes for QTL mapping proved to be efficient to identify molecular markers associated with Fsp resistance in pea. SNPs associated with these QTLs make good targets for marker-assisted selection and pyramidying of QTLs to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.