Characterization and mapping of leaf rust resistance in four durum wheat cultivars

Abstract

Widening the genetic basis of leaf rust resistance is a primary objective of the global durum wheat breeding effort at the International Wheat and Maize Improvement Center (CIMMYT). Breeding programs in North America are following suit, especially after the emergence of new races of Puccinia triticina such as BBG/BP and BBBQD in Mexico and the United States, respectively. This study was conducted to characterize and map previously undescribed genes for leaf rust resistance in durum wheat and to develop reliable molecular markers for marker-assisted breeding. Four recombinant inbred line (RIL) mapping populations derived from the resistance sources Amria, Byblos, Geromtel_3 and Tunsyr_2, which were crossed to the susceptible line ATRED #2, were evaluated for their reaction to the Mexican race BBG/BP of P. triticina. Genetic analyses of host reactions indicated that leaf rust resistance in these genotypes was based on major seedling resistance genes. Allelism tests among resistant parents supported that Amria and Byblos carried allelic or closely linked genes. The resistance in Geromtel_3 and Tunsyr_2 also appeared to be allelic. Bulked segregant analysis using the Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified two genomic regions for leaf rust resistance; one on chromosome 6BS for Geromtel_3 and Tunsyr_2 and the other on chromosome 7BL for Amria and Byblos. Polymorphic SNPs identified within these regions were converted to kompetitive allele-specific PCR (KASP) assays and used to genotype the RIL populations. KASP markers usw215 and usw218 were the closest to the resistance genes in Geromtel_3 and Tunsyr_2, while usw260 was closely linked to the resistance genes in Amria and Byblos. DNA sequences associated with these SNP markers were anchored to the wild emmer wheat (WEW) reference sequence, which identified several candidate resistance genes. The molecular markers reported herein will be useful to effectively pyramid these resistance genes with other previously marked genes into adapted, elite durum wheat genotypes.

Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance

“…Bulk segregant analysis (BSA) is the most commonly used, efficient, and rapid method to identify markers closely linked to a specific gene or any genomic regions (Michelmore et al, 1991) by genotyping a pool of DNA from selected individuals with two extreme phenotypes and the contrasting parents. Then the allelic frequency differences between the bulks will be analyzed and compared with the phenotype to ascertain the possible linkage between the markers and trait of interest (Kthiri et al, 2018). Earlier, in the decade, SSR markers evenly spanning the wheat chromosomes were very frequently used to screen for polymorphic markers but, it was time-consuming and laborious as it was done manually.…”

“…Earlier, in the decade, SSR markers evenly spanning the wheat chromosomes were very frequently used to screen for polymorphic markers but, it was time-consuming and laborious as it was done manually. In recent times, the integration of next-generation sequencing-based 90K SNP arrays with BSA approach has quickened the identification of polymorphic markers and chromosomal location of major genes or the QTLs ( Abe et al., 2012 ; Ramirez-Gonzalez et al., 2015 ; Qureshi et al., 2016 ; Kthiri et al., 2018 ; Wu et al., 2018 ; Pakeerathan et al., 2019 ). The BSA approach has also been combined with RNA-Seq to identify gene associated SNPs, NLR exome capture and sequencing (also called as MapRenSeq) to define NLRs associated with resistant genes ( Narang et al., 2020 ) and NGS-based SLAF-seq to locate the gene of interest/QTL ( Yin et al., 2018 ).…”

Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan

“…The search for additional sources of resistance to rust diseases can be conducted using extensive germplasm collections representing different genetic backgrounds and origins ( Kokhmetova et al, 2011 ; Badoni et al, 2017 ; Kumar et al, 2019 ). Linkage mapping has been commonly used to identify QTLs associated with resistance to SR ( Wang et al, 2015 ; Chen et al, 2018 ), LR ( Xue et al, 2018 ; Kthiri et al, 2018 ), and YR ( Zeng et al, 2019 ). This method was also successfully applied in QTL mapping for LR and SR resistance in Kazakhstan ( Genievskaya et al, 2019 ).…”

Mapping of Genetic Loci Conferring Resistance to Leaf Rust From Three Globally Resistant Durum Wheat Sources

“…The parental lines Gaza and ATRED #2 and check cultivars including the Lr61 -carrying Guyacan INIA were genotyped using the SSR marker Xwmc487 linked to Lr61 (Herrera-Foessel et al, 2008a). The four parental lines Gaza, Arnacoris, Saragolla, and ATRED #2 were also screened using the nucleotide-binding site leucine-rich repeat (NBS-LRR)-specific primers 4406F/4840R , previously determined to be linked to Lr14a (Kthiri et al, 2018). The durum cultivars Sachem and Somayoa were used as positive controls that carry Lr14a .…”

“…The durum cultivars Sachem and Somayoa were used as positive controls that carry Lr14a . The amplification reactions were performed according to published protocols (McCartney et al, 2005; William et al, 2006; Herrera-Foessel et al, 2008a; Kthiri et al, 2018). Polymorphisms for the SSR markers and the NBS-LRR-specific primers were scored on 2% agarose gels.…”