Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance.

Dhiraj Kumar ,Sonia Sheoran,M Sivasamy,Anil Rai,Mir Asif Iquebal,Dinesh Kumar,Hanif Khan,Vinod Chhokar,Pradeep Sharma,Gyanendra Pratap Singh,Sarika Jaiswal,T L Prakasha,Animesh Kumar,S V Sai Prasad,Subhash Bhardwaj ,U B Angadi ,O P Gangwar ,R P Singh ,Ruchi Tiwari

doi:10.3389/fpls.2020.00748

Abstract

Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Highlights

Among the many foliar diseases of wheat, rusts are the economically most significant fungal diseases threatening the food security of the world’s growing population
The phenotypic data recorded for disease response to pathotypes of three Puccinia species on wheat at seedling stage (IT) under controlled conditions and adult plant stage under field conditions (IR, disease severity (DS), and coefficient of infection (COI)) have been provided in Supplementary Table S3
Except for YR_46S119, the infection type (IT) scores for other pathotypes were skewed toward susceptibility (Supplementary Table S4)

Summary

Introduction

Among the many foliar diseases of wheat, rusts are the economically most significant fungal diseases threatening the food security of the world’s growing population. There are three types of rusts in wheat, stripe, or yellow rust (YR) caused by the fungus Puccinia stritiformis Westend. (Pst), leaf, or brown rust (LR) caused by Puccinia triticina Eriks. (Pt), and stem or black rust (SR) caused by Puccinia graminis Pers. More than sixty wheat-producing countries distributed in all continents other than Antarctica have encountered the rusts proving their widespread presence. The damage caused by YR can be as high as 70% in case cultivars are susceptible and the climatic conditions are favorable for an early infection (Chen, 2005). LR has a widespread geographical presence causing considerable yield losses (Marasas et al, 2002). It causes much more damage to crop resulting in yield losses as compared to stem and stripe rusts (Bolton et al, 2008; Huerta-Espino et al, 2011). SR is contained mostly in the southern states of the country and survives throughout the year in the Nilgiri hills of southern India (Joshi et al, 1985; Nagarajan and Joshi, 1985)

Methods

Results

Conclusion