Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens

The locus Lr34/Yr18/Pm38 confers partial and durable resistance against the devastating fungal pathogens leaf rust, stripe rust, and powdery mildew. In previous studies, this broad-spectrum resistance was shown to be controlled by a single gene which encodes a putative ATP-binding cassette transporter. Alleles of resistant and susceptible cultivars differed by only three sequence polymorphisms and the same resistance haplotype was found in the three independent breeding lineages of Lr34/Yr18/Pm38. Hence, we used these conserved sequence polymorphisms as templates to develop diagnostic molecular markers that will assist selection for durable multi-pathogen resistance in breeding programs. Five allele-specific markers (cssfr1-cssfr5) were developed based on a 3bp deletion in exon 11 of the Lr34-gene, and one marker (cssfr6) was derived from a single nucleotide polymorphism in exon 12. Validation of reference genotypes, well characterized for the presence or absence of the Lr34/Yr18/Pm38 resistance locus, demonstrated perfect diagnostic values for the newly developed markers. By testing the new markers on a larger set of wheat cultivars, a third Lr34 haplotype, not described so far, was discovered in some European winter wheat and spelt material. Some cultivars with uncertain Lr34 status were re-assessed using the newly derived markers. Unambiguous identification of the Lr34 gene aided by the new markers has revealed that some wheat cultivars incorrectly postulated as having Lr34 may possess as yet uncharacterised loci for adult plant leaf and stripe rust resistanc

High-Density Mapping of Triple Rust Resistance in Barley Using DArT-Seq Markers

The recent availability of an assembled and annotated genome reference sequence for the diploid crop barley (Hordeum vulgare L.) provides new opportunities to study the genetic basis of agronomically important traits such as resistance to stripe [Puccinia striiformis f. sp. hordei (Psh)], leaf [P. hordei (Ph)], and stem [P. graminis f. sp. tritici (Pgt)] rust diseases. The European barley cultivar Pompadour is known to possess high levels of resistance to leaf rust, predominantly due to adult plant resistance (APR) gene Rph20. We developed a barley recombinant inbred line (RIL) population from a cross between Pompadour and the leaf rust and stripe rust susceptible selection Biosaline-19 (B-19), and genotyped this population using DArT-Seq genotyping by sequencing (GBS) markers. In the current study, we produced a high-density linkage map comprising 8,610 (SNP and in silico) markers spanning 5957.6 cM, with the aim of mapping loci for resistance to leaf rust, stem rust, and stripe rust. The RIL population was phenotyped in the field with Psh (Mexico and Ecuador) and Ph (Australia) and in the greenhouse at the seedling stage with Australian Ph and Pgt races, and at Wageningen University with a European variant of Psh race 24 (PshWUR). For Psh, we identified a consistent field QTL on chromosome 2H across all South American field sites and years. Two complementary resistance genes were mapped to chromosomes 1H and 4H at the seedling stage in response to PshWUR, likely to be the loci rpsEm1 and rpsEm2 previously reported from the cultivar Emir from which Pompadour was bred. For leaf rust, we determined that Rph20 in addition to two minor-effect QTL on 1H and 3H were effective at the seedling stage, whilst seedling resistance to stem rust was due to QTL on chromosomes 3H and 7H conferred by Pompadour and B-19, respectively

Quantitative trait loci mapping reveals the complexity of adult plant resistance to leaf rust in spring wheat ‘Copio’

The spring wheat (Triticum aestivum L.) line ‘Copio’ has exhibited high level of adult plant resistance (APR) to the leaf rust (Puccinia triticina) pathogen in Mexico during field evaluations. To elucidate the genetic basis of leaf rust resistance in Copio, 176 F4-derived F6-recombinant inbred lines (RILs) from a cross of wheat lines ‘Apav’ and Copio were phenotyped in the field for two seasons in the United States and Mexico. A total of 762 genotyping-by-sequencing (GBS) single nucleotide polymorphic (SNP) markers were used to develop linkage maps. Composite interval mapping identified seven quantitative trait loci (QTL), all contributed by Copio. Three QTL on chromosome arms 1BL (QLr.umn-1B), 2AS (QLr.umn-2A), and 3BS (QLr.umn-3B) were consistently expressed across all four environments. The QTL on 1BL represents Lr46, which is a pleiotropic APR gene, while the QTL on 2AS is colocated to the Lr37 gene in the 2NS/2AS translocation fragment. The QTL on 3BS, mapped to the Sr2/Yr30/Lr27 genomic region, is more likely to be a unique locus conferring APR to leaf rust races because all phenotyping environments had Lr27 virulent pathotypes. Moreover, the functionality of Lr27 is complimented by Lr31 on chromosome 4BS, which is lacking in both parents. Marker haplotypes identified seven RILs carrying a combination of resistance alleles at all three loci. This combination reduced leaf rust coefficient of infection up to 52 and 36% in the Mexican and U.S. environments, respectively. This study reports the complex genetic mechanism of APR to leaf rust in Copio and its importance as a potential resistance source for gene pyramiding through recombination breeding

Identification and characterization of resistance loci to wheat leaf rust and stripe rust in Afghan landrace “KU3067”

Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace “KU3067” displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5–17.2 and 12.6–19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9–20.5 and 5.4–12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases

Acción génica y genes que otorgan resistencia a roya de la hoja en trigo cristalino

La roya de la hoja, causada por el hongo Puccnia triticina E., es una enfermedad que cuando se presenta, genera pérdidas hasta del 100 % en el rendimiento de grano del trigo cristalino (Triticum turgidum ssp. durum L.). Como medida de protección genética en la construcción piramidal de nuevos genotipos resistentes es necesario identificar en el germoplasma con resistencia a esta enfermedad, el número de genes involucrados y su acción génica. Con este propósito, durante el ciclo de cultivo otoño-invierno 2017- 2018, se cruzaron los progenitores susceptibles Atred#1 y Atred#2 con las líneas resistentes de trigo cristalino procedentes de Etiopía WC-2 no. 100, DW-K2 no. 47, Oda, 2000/01 population FR. no. 43, 2000/01 population 37-30 BDI no. 63 y 2000/01 population 37-30 BDI no. 12. Las generaciones filiales de las cruzas se obtuvieron alternadamente en CIMMYT-Batán, Estado de México y CIMMYT-CENEB, Ciudad Obregón, Sonora, hasta obtener las Familias F3 y F4. Con base en los análisis de segregantes de tales familias, se encontró que, en las seis líneas etíopes, la resistencia a la roya de la hoja es conferida por dos genes dominantes

Frecuencia del marcador IWA7257-YR78 asociado con la resistencia a roya amarilla en trigo harinero mexicano

Yr78 es un gen de planta adulta que confiere resistencia a la roya amarilla del trigo y que fue recientemente identificado en la línea de trigo harinero PI520108 (HORK/KALYANSONA). El gen se encuentra localizado en el cromosoma 6BS y hasta antes de este estudio se desconocía su frecuencia. Dentro de la colección de trigo del banco de germoplasma del CIMMYT se identificaron 917 líneas que llevan a HORK como progenitor en el pedigrí. Aproximadamente el 12 % de las muestras (117 líneas) se probaron con el marcador molecular IWA7257-Yr78, ligado al gen de resistencia Yr78, y con las razas fisiológicas de roya amarilla MEX14.191 y MEX17.83. Se determinó que 76 % de las líneas fueron positivas para el marcador IWA7257-Yr78. Las líneas susceptibles en etapa de plántula mostraron una severidad final a la enfermedad que osciló entre 0 y 80 % en el campo, y una respuesta similar en las líneas resistentes en plántula de 1MR a 60M. El 24 % restante de líneas negativas para el marcador Yr78, susceptibles y resistentes en etapa de plántula, mostraron respuestas que oscilaban entre 5M y 50MR, indicando la presencia de otros genes de resistencia; además, el 64 % de 621 líneas de tres viveros de selección de trigo de primavera del CIMMYT analizadas molecularmente fueron positivas al marcador Yr78, lo que indica que este gen es más común de lo esperado en el germoplasma mexicano. Las evaluaciones de invernadero y de campo en planta adulta indicaron que Yr78 induce una fuerte clorosis y necrosis, pero no reduce el porcentaje de infección; por lo tanto, Yr78 debe utilizarse en combinación con otros genes de resistencia

Don Lupe Oro C2020: nueva variedad de trigo duro para el noroeste de México

El noroeste de México es la principal región productora de trigo cristalino (Triticum durum Desf.). Durante el año 2020 se cultivaron 159,229 ha con este tipo de trigo, las cuales representaron el 90.5 % de la superficie total sembrada en México. Dicha región alcanzó una producción de 1.19 millones de toneladas, con un valor de la producción de 5.25 mil millones de pesos (SIAP, 2021)

Multi-location trials identify stable high yielding spring bread and durum wheat cultivars in Mexico

Determining the stability and consistency of grain yield performance requires accurate evaluation of genotypes in different environments. In Mexico, annual national spring wheat irrigated trials are conducted to assess elite bread and durum wheat performance in different testing environments (TEs) in the main wheat-growing areas. These trials provide data supporting release of new cultivars and aim to also address Mexican wheat value chain grain needs. In this study we analyzed 30 bread and durum wheat trial results from the 2012/13 and 2013/14 growing cycles conducted across TEs in northwest, north and central Mexico. Environmental variability (location, sowing timing, and irrigation schemes) across the national spring wheat irrigated trials enabled genotype by environment interaction to be effectively evaluated. We identified genotypes with high and stable grain yield across TEs of the wheat-growing areas of Mexico. The bread cultivars Bacorehuis F2015 and Borlaug100 F2014, and the durum cultivars Barobampo C2015, CONASIST C2015 and Anatoly C2011 were high yielding and gave stable performance in most of the TEs. This analysis demonstrates the utility of multi-year, multi-environment testing and analysis to identify improved wheat cultivars to meet wheat production demand in Mexico

Effects of glutenins (Glu-1 and Glu-3) allelic variation on dough properties and bread-making quality of CIMMYT bread wheat breeding lines

Wheat dough characteristics and end-use quality are strongly influenced by the amount and specific composition of the glutenins, the major components of gluten. Such proteins are divided into high-molecular-weight glutenins, encoded by the Glu-A1, Glu-B1 and Glu-D1 loci; and low-molecular-weight glutenins, encoded by the Glu-A3, Glu-B3 and Glu-D3 loci. Allelic variation at each of these loci has been associated with changes in wheat functionality. However, most of the studies conducted so far included a relatively limited number of genotypes. Also for this reason, it is still unclear which locus contributes more to dough characteristics and how important are the interactions between the glutenin loci. To try to answer these questions, the quality data of 4623 grain samples derived from 2550 genotypes and generated across 10 years at the CIMMYT bread wheat breeding program, was used to estimate the effect of the glutenin loci and their interactions on gluten quality and bread-making potential. Gluten strength was the trait more strongly influenced by glutenin variations, with the Glu-B1, Glu-D1 and Glu-B3 loci having the greatest effect. Among the glutenin alleles, Glu-A1a, Glu-A1b, Glu-B1al, Glu-B1i, Glu-B1f, Glu-D1d, Glu-A3b, Glu-A3d, Glu-A3f, Glu-B3c and Glu-B3d were associated in general with greater gluten strength, good extensibility and higher bread loaf volume. Differently, alleles Glu-A1c, Glu-B1a, Glu-B1d, Glu-D1a, Glu-A3e and Glu-B3j were associated with an overall poor quality. Glutenin interactions were significantly associated with most of the analyzed quality traits even if their influence was often lower compared to the effect of the single glutenin loci. This is probably the largest study ever done on the effects of the glutenins on wheat quality. The results obtained confirm the importance of such proteins on wheat quality variation and corroborate the usefulness of determining the glutenin profile to improve the selection efficiency for wheat quality in breeding programs

Identification and Validation of a Common Stem Rust Resistance Locus in Two Bi-parental Populations

Races belonging to Ug99 lineage of stem rust fungus Pucciniagraminis f. sp. tritici (Pgt) continue to pose a threat to wheat (Triticumaestivum L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent ‘Cacuke’ with the resistant parents ‘Huhwa’ and ‘Yaye’ were phenotyped for resistance at the seedling stage to Pgt race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as SrH and SrY, were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations. SrH mapped between markers cim109 and cim114 at a distance of 0.9 cM proximal, and cim117 at 2.9 cM distal. SrY was flanked by markers cim109 and cim116 at 0.8 cM proximal, and IWB45932 at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat, Sr9h and Sr28, have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that Sr28 was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against Sr9h-virulent race TTKSF+ confirmed the presence of a common resistance locus Sr9h in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and Sr9h. Marker cim117 linked to SrH was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of Sr9h in breeding programs