Genetic characterization and genome-wide association mapping for stem rust resistance in spring bread wheat

Abstract

Background Emerging wheat stem rust races have become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economic and environmentally sound strategy to combat this problem. Thus, this study was aimed at characterizing the genetic diversity and identifying the genetic loci conferring resistance to the stem rust of wheat. To accomplish this, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were evaluated under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The single nucleotide polymorphisms (SNP) marker data was retrieved from a 15 K SNP wheat array. A mixed linear model was used to investigate the association between SNP markers and the best linear unbiased prediction (BLUP) values of the stem rust coefficient of infection (CI). Results Phenotypic analysis revealed that 46% of the lines had a coefficient of infection (CI) in a range of 0 to 19. Genome-wide average values of 0.38, 0.20, and 0.71 were recorded for Nei’s gene diversity, polymorphism information content, and major allele frequency, respectively. A total of 46 marker-trait associations (MTAs) encompassed within eleven quantitative trait loci (QTL) were detected on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A for CI. Two major QTLs with –log10 (p) ≥ 4 (EWYP1B.1 and EWYP1B.2) were discovered on chromosome 1B. Conclusions This study identified several novel markers associated with stem rust resistance in wheat with the potential to facilitate durable rust resistance development through marker-assisted selection. It is recommended that the resistant wheat genotypes identified in this study be used in the national wheat breeding programs to improve stem rust resistance.

Physiological specialization of Puccinia triticina and genome-wide association mapping provide insights into the genetics of wheat leaf rust resistance in Iran

“…Two QTLs on chromosome 1B were race-specific for resistance to MJTTS including QLr. iau-1B-1 was co-localized with different previously known APR resistance QTLs [44][45][46][47][48] as well as with four known resistance genes Lr33, Lr44, Lr71 and Lr75 49 . The QTL QLr.iau-1B-2 (276.30 cM) mapped on 1BL chromosome, but its chromosomal location is far (50 cM) from recently reported APR resistance QTL as well as a QTL found against THBL race form the USA on this chromosome arm 12,50 .…”

Wheat Genes Associated with Different Types of Resistance against Stem Rust (Puccinia graminis Pers.)

“…The QSr.umn-2B.2 QTL on chromosome 2B conferring APR against African and North American stem rust races (including the Ug99 race group) in four environments in the RB07/MN06113-8 population has been reported in the literature [ 166 ]. In addition, several minor QTLs on different chromosomes and major QTLs on chromosomes 1A and 1B were discovered [ 193 ].…”

Genome‐wide association analysis of coleoptile length and interaction with plant height in durum wheat

“…Li et al, 2016;Maccaferri et al, 2010;P. Zhang et al, 2021), yellow rust (L. Liu et al, 2020;Maccaferri et al, 2015), stem rust (Megerssa et al, 2020;Shewabez et al, 2021;L.-X. Yu et al, 2012), and for the improvement of grain yield (Alemu et al, 2020;Edae et al, 2014;Sehgal et al, 2020;Sukumaran et al, 2015), grain quality (Breseghello & Sorrells, 2006;Suliman et al, 2021;Talini et al, 2020) and other agro-morphological traits (Y.…”

“…This method efficiently identifies SNPs that cause phenotypic variation (Soto‐Cerda & Cloutier, 2012). To date, many successful GWASs have been performed in wheat to identify genomic regions for resistance/tolerance against mosaic viruses (Shubing et al., 2020; D. Zhang et al., 2011; Zheng et al., 2021), leaf rust (Kertho et al., 2015; G. Li et al., 2016; Maccaferri et al., 2010; P. Zhang et al., 2021), yellow rust (L. Liu et al., 2020; Maccaferri et al., 2015), stem rust (Megerssa et al., 2020; Shewabez et al., 2021; L.‐X. Yu et al., 2012), and for the improvement of grain yield (Alemu et al., 2020; Edae et al., 2014; Sehgal et al., 2020; Sukumaran et al., 2015), grain quality (Breseghello & Sorrells, 2006; Suliman et al., 2021; Talini et al., 2020) and other agro‐morphological traits (Y. Liu et al., 2015; Suliman et al., 2021; Wang et al., 2019; Zanke et al., 2014).…”