Genome-Wide Association and Genomic Prediction for Stripe Rust Resistance in Synthetic-Derived Wheats.

Zahid Mahmood,Zhonghu He,Francis Chuks Ogbonnaya,Awais Rasheed,Javed Iqbal Mirza,Khawar Majeed,Muhammad Fayyaz,Jesse Poland,Mohsin Ali,Lee Thomas Hickey,Muhammad Kashif Naeem,Abdul Aziz,Umar Masood Quraishi,Richard Trethowan

doi:10.3389/fpls.2022.788593

Abstract

Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds.

Highlights

Stripe or yellow rust caused by an obligate pathogen Puccinia striiformis tritici (Pst) is a major threat to wheat production and grain quality
The field experiments were conducted at the National Agricultural Research Centre (NARC), Islamabad (33◦ 0 N, 73◦ 4 E) and Cereal Crop Research Institute (CCRI), Nowshera (34◦ 1 N, 72◦ 2 E) Khyber Pakhtunkhwa, Pakistan, in the winter field seasons of 2015– 2016 and 2016–2017
Seedling screening against stripe rust was performed at the Crop Disease Research Institute (CDRI), Murree, Pakistan under controlled conditions

Summary

Introduction

Stripe or yellow rust caused by an obligate pathogen Puccinia striiformis tritici (Pst) is a major threat to wheat production and grain quality. Stripe rust epidemics have damaged wheat production in many wheat growing countries and regions including Australia, Ethiopia, China, United States, Europe, South Africa, and South Asia (Milus et al, 2006; Chen, 2007; Wellings, 2011). Since Airborne Pst urediniospores can migrate to other regions of the world using the climatic system termed the “Western Disturbance,” spreading new races. The Western Disturbance caused the spread of the (Pst) Yr9 virulent race in the Indian Subcontinent and Nepal from the East African highlands between 1985 and 1997. Virulence for Yr27 caused epidemics in Pakistan and India on the commonly growing mega cultivars, Inqlab-91, and PBW-343, respectively (Duveiller et al, 2007)

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