Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat “Kronos”
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ABSTRACT:
SUBMITTER: Li H
PROVIDER: S-EPMC8555631 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. 'Svevo'.
| S-EPMC9601996 | biostudies-literature
Project description: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.
| S-EPMC5945016 | biostudies-literature
Project description:Wheat stem rust caused by Puccinia graminis f. sp. tritici, can cause significant yield losses. To combat the disease, breeders have deployed resistance genes both individually and in combinations to increase resistance durability. A new race, TTKSK (Ug99), identified in Uganda in 1999 is virulent on most of the resistance genes currently deployed, and is rapidly spreading to other regions of the world. It is therefore important to identify, map, and deploy resistance genes that are still effective against TTKSK. One of these resistance genes, Sr13, was previously assigned to the long arm of chromosome 6A, but its precise map location was not known. In this study, the genome location of Sr13 was determined in four tetraploid wheat (T. turgidum ssp. durum) mapping populations involving the TTKSK resistant varieties Kronos, Kofa, Medora and Sceptre. Our results showed that resistance was linked to common molecular markers in all four populations, suggesting that these durum lines carry the same resistance gene. Based on its chromosome location and infection types against different races of stem rust, this gene is postulated to be Sr13. Sr13 was mapped within a 1.2-2.8 cM interval (depending on the mapping population) between EST markers CD926040 and BE471213, which corresponds to a 285-kb region in rice chromosome 2, and a 3.1-Mb region in Brachypodium chromosome 3. These maps will be the foundation for developing high-density maps, identifying diagnostic markers, and positional cloning of Sr13.
| S-EPMC4755715 | biostudies-literature
Project description:Leaf rust caused by Puccinia triticina Erikss. (Pt) and stem rust caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn (Pgt) are serious constraints to production of durum wheat (Triticum turgidum L). The objective of this study was to identify leaf rust resistance (Lr) and stem rust resistance (Sr) genes/QTL in Portuguese durum landrace PI 192051. Four Pt-isolates, representing three virulence phenotypes (BBBQJ, BBBSJ & EEEEE) and six Pgt-races TTKSK, JRCQC, TKTTF, QFCFC, TPMKC and TMLKC were used to evaluate 180 recombinant inbred lines (RILs) derived from the cross Rusty (rust susceptible) × PI 192051-1 (rust resistant) at the seedling stage. The RILs were also phenotyped at the adult-plant stage in a stem rust nursery in Ethiopia in 2017. The RILs were genotyped using the Illumina iSelect 9K wheat SNP array. PI 192051-1 carries a previously unidentified major Sr gene designated as QSr.ace-7A on chromosome arm 7AS and Lr gene Lr.ace-4A in the pericentromeric region of chromosome 4A. In addition, three minor Sr QTL QSr.ace-1A, QSr.ace-2B and QSr.ace-4A were mapped in PI 192051-1 on chromosomes 1AL, 2BL, and 4A, respectively Lr.ace-4A could be co-located or tightly linked to QSr.ace-4A Markers linked to the identified QTL/genes can be used for marker assisted selection. These findings enrich the genetic basis of rust resistance in both durum and common wheat.
| S-EPMC6686931 | biostudies-literature
Project description:Stem rust of wheat caused by Puccinia graminis Pers. f.sp. trtici Eriks and E. Henn., is the most damaging fungal disease of both common (Triticum aestivum L.) and durum (Triticum turgidum L., ssp. Durum) wheat. Continuously emerging races virulent to many of the commercially deployed qualitative resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 283 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and map loci associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year × season). The panel was genotyped using genotyping-by-sequencing. After filtering, 26,439 Single Nucleotide Polymorphism (SNP) markers and 280 lines and three checks were retained for analysis. Population structure was assessed using principal component analysis. Genome-wide association analysis (GWAS) was conducted using Genomic Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability of the phenotype data revealed that 64-83% of the variation in stem rust response explained by the genotypes and lines with multiple race resistance were identified. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported loci. Known stem rust resistance genes/alleles were postulated including Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22, and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus and potential markers for the known Sr13 alleles.
| S-EPMC7773921 | biostudies-literature
Project description:Key messageThe diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2AmL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.
| S-EPMC10140103 | biostudies-literature
Project description:The hexaploid wheat (Triticum aestivum) adult plant resistance gene, Lr34/Yr18/Sr57/Pm38/Ltn1, provides broad-spectrum resistance to wheat leaf rust (Lr34), stripe rust (Yr18), stem rust (Sr57) and powdery mildew (Pm38) pathogens, and has remained effective in wheat crops for many decades. The partial resistance provided by this gene is only apparent in adult plants and not effective in field-grown seedlings. Lr34 also causes leaf tip necrosis (Ltn1) in mature adult plant leaves when grown under field conditions. This D genome-encoded bread wheat gene was transferred to tetraploid durum wheat (T. turgidum) cultivar Stewart by transformation. Transgenic durum lines were produced with elevated gene expression levels when compared with the endogenous hexaploid gene. Unlike nontransgenic hexaploid and durum control lines, these transgenic plants showed robust seedling resistance to pathogens causing wheat leaf rust, stripe rust and powdery mildew disease. The effectiveness of seedling resistance against each pathogen correlated with the level of transgene expression. No evidence of accelerated leaf necrosis or up-regulation of senescence gene markers was apparent in these seedlings, suggesting senescence is not required for Lr34 resistance, although leaf tip necrosis occurred in mature plant flag leaves. Several abiotic stress-response genes were up-regulated in these seedlings in the absence of rust infection as previously observed in adult plant flag leaves of hexaploid wheat. Increasing day length significantly increased Lr34 seedling resistance. These data demonstrate that expression of a highly durable, broad-spectrum adult plant resistance gene can be modified to provide seedling resistance in durum wheat.
| S-EPMC5466443 | biostudies-literature
Project description:Key messageThe new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5AmS, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22. The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7AmL, completely linked to Sr22. SrTm5 displayed a different race specificity compared to Sr22 indicating that they are distinct. Sequencing of the Sr22 homolog in PI 306540 revealed a novel haplotype. Characterization of the segregating populations with Pgt race QFCSC revealed an additional resistance gene on chromosome arm 5AmS that was assigned the official name Sr60. This gene was also effective against races QTHJC and SCCSC but not against TTKSK (a Ug99 group race). Using two large mapping populations (4046 gametes), we mapped Sr60 within a 0.44 cM interval flanked by sequenced-based markers GH724575 and CJ942731. These two markers delimit a 54.6-kb region in Brachypodium distachyon chromosome 4 and a 430-kb region in the Chinese Spring reference genome. Both regions include a leucine-rich repeat protein kinase (LRRK123.1) that represents a potential candidate gene. Three CC-NBS-LRR genes were found in the colinear Brachypodium region but not in the wheat genome. We are currently developing a Bacterial Artificial Chromosome library of PI 306540 to determine which of these candidate genes are present in the T. monococcum genome and to complete the cloning of Sr60.
| S-EPMC5814525 | biostudies-literature
Project description:BackgroundEmerging 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).ResultsPhenotypic 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.ConclusionsThis 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.
| S-EPMC8845374 | biostudies-literature
Project description:Genetic resistance in the host plant is the most economical and environmentally friendly strategy for controlling wheat leaf rust, caused by Puccinia triticina Eriks. The durum wheat lines Gaza (Middle East), Arnacoris (France) and Saragolla (Italy) express high levels of resistance to the Mexican races of P. triticina. Three recombinant inbred line (RIL) populations, derived from crosses of each of these resistance sources to the susceptible line ATRED #2, were evaluated for leaf rust reactions at CIMMYT's leaf rust nurseries in Mexico. Genetic analyses of host reactions suggested oligogenic control of resistance in all populations. The F8 RILs from each cross were genotyped using the Illumina iSelect 90K array, and high-density genetic maps were constructed for each population. Using composite interval mapping, a total of seven quantitative trait loci (QTL) that provide resistance to leaf rust were identified. Two QTL designated as QLr.usw-6BS and QLr.usw-6BL were identified on chromosome 6B in Gaza, which explained up to 78.5% and 21.3% of the observed leaf rust severity variance, respectively. A major QTL designated as QLr.usw-7BL was detected on the long arm of chromosome 7B in Arnacoris, which accounted for up to 65.9% of the disease severity variance. Arnacoris also carried a minor QTL on chromosome 1BL, designated as QLr.usw-1BL.1 that explained up to 17.7% of the phenotypic variance. Three QTL conferred leaf rust resistance in Saragolla, namely QLr.usw-2BS, QLr.usw-3B, and QLr.usw-1BL.2, which accounted for up to 42.3, 9.4, and 7.1% of the phenotypic variance, respectively. Markers flanking each QTL were physically mapped against the durum wheat reference sequence and candidate genes involved in disease resistance were identified within the QTL intervals. The QTL identified in this study and their closely linked markers are useful resources for gene pyramiding and breeding for durable leaf rust resistance in durum wheat.
| S-EPMC6792298 | biostudies-literature