Genetic Diversity, Genotype-by-Environment Interaction and Genome Wide Association of Stripe Rust (Puccinia striiformis f.sp. tritici) in Bread Wheat (Triticum aestivum L.) Genotypes

Abstract

Wheat is Ethiopia's staple crop, accounting for 15% of daily calorie intake. However, due to population growth, changing food preferences, a strong urbanization trend, climate change, increased input costs, limited access to advanced production technologies, and increased intensity of abiotic and biotic stresses, which make the wheat demand-supply chain, is extremely volatile and can cause social instabilities. Fungal diseases, such as stripe rust, are severe bottlenecks in Ethiopian wheat production. Stripe rust caused by Puccinia striiformis f. sp. tritici, is a severe disease of wheat worldwide, including Ethiopia, causing up to 100% wheat yield loss in the worst season. The use of resistant cultivars is considered to be the most effective and durable management technique for controlling the disease. Accordingly, this study was aimed to explore genetic diversity, heritability, genotype-by-environment interaction (GxE) and genomic regions associated with stripe rust (Puccinia striiformis f.sp. tritici) resistance traits in bread wheat genotypes. Besides, genetic diversity and population structure of 180 bread wheat genotypes representing eight populations were analyzed using ten polymorphic inter simples sequence repeat (ISSR) markers. High within-populations genetic diversity with a mean allele values of 1.47, effective alleles of 1.33, Shannon’s information index of 0.29, Nei's gene diversity of 0.19, and percent polymorphic loci (PPL) of 80.5% were obtained. Analysis of molecular variance (AMOVA) revealed that 95% of the total genetic variation resides within populations, while the remaining 5% was accounted to among populations. Moreover, the extent of genetic variability, heritability and genotype-environment interaction in the 180 bread wheat genotypes were investigated using field-based phenotyping of 12 agro-morphological traits. This experiment was positioned at alpha lattice design in two replications in Ethiopia at Kulumsa Agricultural Research Center (KARC), Meraro (substation of KARC) and Holeta Agricultural Research Center (HARC). Moderate heritability and genetic advance were observed in plant height (50%, 5.5%), spike length (38%, 5.3%), number of kernels per spike (50%, 5.23%), and thousand kernel weights (41%, 4.38%), respectively. Moreover, combined analysis of variance and AMMI analysis showed highly significant differences for environment and genotype, in which grain yields were significantly affected by environment, accounting for 55.22% of the total variation. However, genotype and genotype-environment interaction (GxE) accounted for 27.46% and 17.44%, respectively. Moreover an investigation on virulence variability of four P. striiformis isolates from Ethiopia, efficiency of known Yr resistance genes and wheat cultivars against the isolates reviled presence of host-pathogen interaction. For instance in isolate 2, based on coefficient of infection 4 (2.25%), 136 (76.4%), 22 (12.36%), and 1 (0.56%) of the genotypes were immune, resistant, intermediate and susceptible to two or more isolates, respectively. In addition, Coatez Yr15 and Avocet Yr9 were immune to isolate 1. Furthermore, the additional component of the study was targeted to the study of the genetic architecture of adult plant resistance to yellow rust in 178 wheat association panels. The panel was phenotyped for yellow rust adult-plant resistance at three locations. Phonological, yield, yield-related and agro-morphological traits were recorded. The association panel was fingerprinted with genotyping-by-sequencing (GBS) platform, and a total of 6,788 polymorphic SNPs were used for genome-wide association analysis (GWAS) to identify effective yellow rust resistance genes. The marker-trait association (MTA) analysis was conducted using Genome Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability for the considered traits ranged from 74.52 to 88.64%, implying the presence of promising yellow rust resistance alleles in the association panel that could be deployed to improve wheat resistance to the disease. The overall linkage disequilibrium (LD) declined within average physical distance of 31.44 Mbp at r2 = 0.2. MTA analysis identified 148 loci significantly (p = 0.001) associated with yellow rust adult-plant resistance. Most of the detected resistance quantitative trait loci (QTLs) were located on same chromosomes as previously reported for yellow rust resistance and mapped on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6A, 6B, and 7A and 7D. Nevertheless, 12 of the discovered MTAs were not previously documented in the wheat literature, suggesting that they could represent novel loci for stripe rust resistance. Zooming into the QTL regions in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq Annotation v2.1 identified crucial disease resistance-associated genes that are key in plants' defence mechanisms against pathogen infections. The detected QTLs will be helpful for marker-assisted breeding of wheat to increase resistance to stripe rust in Ethiopia and beyond. However, the efficacy of newly found QTLs need functionally confirmed before they can be used for marker-assisted selection