Rust Resistance Genes Research Articles

Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower (Helianthus annuus L.).

Rust and downy mildew (DM) are two important sunflower diseases that lead to significant yield losses globally. The use of resistant hybrids to control rust and DM in sunflower has a long history. The rust resistance genes, R13a and R16, were previously mapped to a 3.4 Mb region at the lower end of sunflower chromosome 13, while the DM resistance gene, Pl33, was previously mapped to a 4.2 Mb region located at the upper end of chromosome 4. High-resolution fine mapping was conducted using whole genome sequencing of HA-R6 (R13a) and TX16R (R16 and Pl33) and large segregated populations. R13a and R16 were fine mapped to a 0.48 cM region in chromosome 13 corresponding to a 790 kb physical interval on the XRQr1.0 genome assembly. Four disease defense-related genes with nucleotide-binding leucine-rich repeat (NLR) motifs were found in this region from XRQr1.0 gene annotation as candidate genes for R13a and R16. Pl33 was fine mapped to a 0.04 cM region in chromosome 4 corresponding to a 63 kb physical interval. One NLR gene, HanXRQChr04g0095641, was predicted as the candidate gene for Pl33. The diagnostic SNP markers developed for each gene in the current study will facilitate marker-assisted selections of resistance genes in sunflower breeding programs.

Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat.

A stripe rust resistance gene YrZM175 in Chinese wheat cultivar Zhongmai 175 was mapped to a genomic interval of 636.4 kb on chromosome arm 2AL, and a candidate gene was predicted. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is a worldwide wheat disease that causes large losses in production. Fine mapping and cloning of resistance genes are important for accurate marker-assisted breeding. Here, we report the fine mapping and candidate gene analysis of stripe rust resistance gene YrZM175 in a Chinese wheat cultivar Zhongmai 175. Fifteen F1, 7,325 F2 plants and 117 F2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F2:3 lines were also evaluated for stripe rust reaction in the field using mixed PST races. Bulked segregant RNA-seq (BSR-seq) analyses revealed 13 SNPs in the region 762.50-768.52Mb on chromosome arm 2AL. By genome mining, we identified SNPs and InDels between the parents and contrasting bulks and mapped YrZM175 to a 0.72-cM, 636.4-kb interval spanned by YrZM175-InD1 and YrZM175-InD2 (763,452,916-764,089,317bp) including two putative disease resistance genes based on IWGSC RefSeq v1.0. Collinearity analysis indicated similar target genomic intervals in Chinese Spring, Aegilops tauschii (2D: 647.7-650.5Mb), Triticum urartu (2A: 750.7-752.3Mb), Triticum dicoccoides (2A: 771.0-774.5Mb), Triticum turgidum (2B: 784.7-788.2Mb), and Triticum aestivum cv. Aikang 58 (2A: 776.3-778.9Mb) and Jagger (2A: 789.3-791.7Mb). Through collinearity analysis, sequence alignments of resistant and susceptible parents and gene expression level analysis, we predicted TRITD2Bv1G264480 from Triticum turgidum to be a candidate gene for map-based cloning of YrZM175. A gene-specific marker for TRITD2Bv1G264480 co-segregated with the resistance gene. Molecular marker analysis and stripe rust response data revealed that YrZM175 was different from genes Yr1, Yr17, Yr32, and YrJ22 located on chromosome 2A. Fine mapping of YrZM175 lays a solid foundation for functional gene analysis and marker-assisted selection for improved stripe rust resistance in wheat.

Stripe rust and leaf rust resistance in CIMMYT wheat line “Mucuy” is conferred by combinations of race-specific and adult-plant resistance loci

Developing wheat varieties with durable resistance is a core objective of the International Maize and Wheat Improvement Center (CIMMYT) and many other breeding programs worldwide. The CIMMYT advanced wheat line “Mucuy” displayed high levels of resistance to stripe rust (YR) and leaf rust (LR) in field evaluations in Mexico and several other countries. To determine the genetic basis of YR and LR resistance, 138 F5 recombinant inbred lines (RILs) derived from the cross of Apav#1× Mucuy were phenotyped for YR responses from 2015 to 2020 at field sites in India, Kenya, and Mexico, and LR in Mexico. Seedling phenotyping for YR and LR responses was conducted in the greenhouse in Mexico using the same predominant races as in field trials. Using 12,681 polymorphic molecular markers from the DArT, SNP, and SSR genotyping platforms, we constructed genetic linkage maps and QTL analyses that detected seven YR and four LR resistance loci. Among these, a co-located YR/LR resistance loci was identified as Yr29/Lr46, and a seedling stripe rust resistance gene YrMu was mapped on the 2AS/2NS translocation. This fragment also conferred moderate adult plant resistance (APR) under all Mexican field environments and in one season in Kenya. Field trial phenotyping with Lr37-virulent Puccinia triticina races indicated the presence of an APR QTL accounting for 18.3–25.5% of the LR severity variation, in addition to a novel YR resistance QTL, QYr.cim-3DS, derived from Mucuy. We developed breeder-friendly KASP and indel molecular markers respectively for Yr29/Lr46 and YrMu. The current study validated the presence of known genes and identified new resistance loci, a QTL combination effect, and flanking markers to facilitate accelerated breeding for genetically complex, durable rust resistance.

The genetic basis and interaction of genes conferring resistance to Puccinia hordei in an ICARDA barley breeding line GID 5779743.

Leaf rust of barley causes significant losses in crops of susceptible cultivars. Deploying host resistance is the most cost-effective and eco-sustainable strategy to protect the harvest. However, most known leaf rust resistance genes have been overcome by the pathogen due to the pathogen’s evolution and adaptation. The discovery of novel sources of genetic resistance is vital to keep fighting against pathogen evolution. In this study, we investigated the genetic basis of resistance in barley breeding line GID 5779743 (GID) from ICARDA, found to carry high levels of seedling resistance to prevalent Australian pathotypes of Puccinia hordei. Multipathotype tests, genotyping, and marker-trait associations revealed that the resistance in GID is conferred by two independent genes. The first gene, Rph3, was detected using a linked CAPS marker and QTL analysis. The second gene was detected by QTL analysis and mapped to the same location as that of the Rph5 locus on the telomeric region of chromosome 3HS. The segregating ratio in F2 (conforming to 9 resistant: 7 susceptible genetic ratio; p > 0.8) and F3 (1 resistant: 8 segregating: 7 susceptible; p > 0.19) generations of the GID × Gus population, when challenged with pathotype 5477 P− (virulent on Rph3 and Rph5) suggested the interaction of two genes in a complementary fashion. This study demonstrated that Rph3 interacts with Rph5 or an additional locus closely linked to Rph5 (tentatively designated RphGID) in GID to produce an incompatible response when challenged with a pathotype virulent on Rph3+Rph5.

Marker-assisted transfer of leaf and stripe rust resistance from Triticum turgidum var. durum cv. Trinakria to wheat variety HD2932.

A marker-assisted backcrossing program initiated to transfer leaf rust resistance gene LrTrk from Triticum turgidum cv. Trinakria to hexaploid wheat variety HD2932 cotransferred a stripe rust resistance gene, YrTrk, along with LrTrk. The cross of hexaploid recurrent parent HD2932 with tetraploid donor parent Trinakria produced pentaploid F1 plants. F1s were backcrossed with recurrent parent HD2932 to produce BC1F1 generation. Foreground and background selection was conducted in each backcross generation to identify plants for backcrossing or selfing. While foreground selection for LrTrk was carried out with linked and validated molecular marker Xgwm234, for background selection, 86 polymorphic SSR markers from the A and B genomes were used. Single selected plants from BC1F1 and BC2F1 generations backcrossed and selfed to produce BC2F1and BC2F2 generations, respectively. Background selection resulted in 83.72%, 91.86%, and 98.25% of RPG recovery in BC1F1, BC2F1, and BC2F2 generations, respectively. A total of 27 plants with LrTrk in homozygous state were identified in BC2F2 generation and selfed to produce 27 BC2F3 NILs. All the NILs were tested for leaf and stripe rust resistance at the seedling stage using seven Puccinia triticina and one Puccinia striiformis f.sp. tritici rust pathotypes. All the 27 NILs were found to be resistant to both leaf and stripe rust pathotypes. So, these NILs are designated to carry leaf and stripe rust resistance genes LrTrk/YrTrk.

Molecular and Cytogenetic Identification of Stem Rust Resistant Wheat-Thinopyrum intermedium Introgression Lines.

Thinopyrum intermedium (JJJsJsStSt, 2n = 6x = 42), a wild relative of common wheat, possesses many desirable agronomic genes for wheat improvement. The production of wheat-Thinopyrum intermedium introgression lines is a key step for transferring these beneficial genes into wheat. In this study, we characterized three wheat-Thinopyrum intermedium introgression lines TA3681, TA5566, and TA5567 using non-denaturing fluorescence in situ hybridization, genomic in situ hybridization, PCR-based landmark unique gene, and intron targeting markers. Our results showed that TA3681 is a wheat-Thinopyrum intermedium 1Stdisomic addition line, TA5566 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying two pairs of 3A-7Js translocation chromosomes, and that TA5567 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying a pair of 3A-7Js translocation chromosomes. We developed 13, 36, and 15 Thinopyrum intermedium chromosome-specific markers for detecting the introgressed Thinopyrum chromosomes in TA3681, TA5566, and TA5567, respectively. Stem rust assessment revealed that TA3681 exhibited ahigh level of seedling resistance to Chinese-prevalent Puccinia graminis f. sp. tritici pathotypes, and both TA5566 and TA5567 were highly resistant to Australian P. graminis f. sp. tritici pathotypes, indicating that Thinopyrum intermedium chromosomes 1St and 7Js might carry new stem rust resistance genes. Therefore, the new identified introgression lines may be useful for improving wheat stem rust resistance.

Establishment and identification of six wheat-Thinopyrum ponticum disomic addition lines derived from partial amphiploid Xiaoyan 7430.

Six wheat-Thinopyrum ponticum disomic addition lines derived from partial amphiploid Xiaoyan 7430 were identified using in situ hybridization and SNP microarray, the homoeologous group and stripe rust resistance of each alien chromosome were determined, and Th. ponticum chromosome-specific markers were developed. Xiaoyan 7430 is a significant partial amphiploid, which is used to set up a bridge for transferring valuable genes from Thinopyrum ponticum (Podp.) Barkworth & D.R. Dewey into common wheat. To accelerate the application of these useful genes in enriching the genetic variability of cultivated wheat by chromosome engineering, a complete set of derived addition lines has been created from Xiaoyan 7430. The chromosome composition of each line was characterized by the combination of genomic in situ hybridization and multicolor fluorescence in situ hybridization (mc-FISH), and the homoeology of each alien chromosome was determined by wheat SNP microarray analysis. Addition line WTA55 with alien group-6 chromosome was evaluated resistant to stripe rust isolates at both the seedling and grain-filling stages (Zadoks scale at z.11 and z.73). Diagnostic marker analysis proved that it could carry a novel stripe rust resistance gene derived from Th. ponticum. Furthermore, a FISH probe and 45 molecular markers specific for alien chromosomes were developed based on specific-locus amplified fragment sequencing (SLAF-seq). Of which 27 markers were separately located on single alien chromosome, and some of them could be used to identify the derived translocation lines. This set of addition lines as well as the molecular markers and the FISH probe will promote the introgression of abundant variation from Th. ponticum into wheat in wheat improvement programs.

Transfer of Durable Stripe Rust Resistance Gene Yr39 into Four Chinese Elite Wheat Cultivars Using Marker-Assisted Selection

Wheat gene Yr39 confers durable high-temperature adult-plant (HTAP) resistance to stripe rust caused by Puccinia striiformis f. sp. tritici, one of the most destructive diseases of wheat worldwide. The objective of this study was to transfer Yr39 into four Chinese elite wheat cultivars. Backcross inbred line populations were developed from four Chinese wheat cultivars Chuanmai 42 (CM42), Bainong Aikang 58 (AK58), Han 6172 (H6172) and Zhengmai 9023 (ZM9023) crossed with a Yr39 single-gene line. The F1, BC1F1 and BC1F6 lines were genotyped using resistance gene analogs polymorphism (RGAP) markers Xwgp36, Xwgp44 and Xwgp43, which are closely linked to Yr39. Progeny lines selected with the markers for Yr39 were evaluated in the field for stripe rust resistance and agronomic traits including plant height, tiller numbers, spike grain numbers and thousand-grain weight. Eleven lines were selected with stripe rust resistance and desirable agronomic traits. These lines with production potential can be used for further testing in various wheat production regions and as germplasm resources for breeding new wheat cultivars with durable stripe rust resistance, high yield, and adaptation to different production environments.

Cloning southern corn rust resistant gene RppK and its cognate gene AvrRppK from Puccinia polysora

Broad-spectrum resistance has great values for crop breeding. However, its mechanisms are largely unknown. Here, we report the cloning of a maize NLR gene, RppK, for resistance against southern corn rust (SCR) and its cognate Avr gene, AvrRppK, from Puccinia polysora (the causal pathogen of SCR). The AvrRppK gene has no sequence variation in all examined isolates. It has high expression level during infection and can suppress pattern-triggered immunity (PTI). Further, the introgression of RppK into maize inbred lines and hybrids enhances resistance against multiple isolates of P. polysora, thereby increasing yield in the presence of SCR. Together, we show that RppK is involved in resistance against multiple P. polysora isolates and it can recognize AvrRppK, which is broadly distributed and conserved in P. polysora isolates.

Identification of Novel Broad-Spectrum Leaf Rust Resistance Sources from Khapli Wheat Landraces.

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from “;”, “;N”, “;N1” to “;NC”. PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust.

Registration of two oilseed sunflower germplasms, HA‐R18 and HA‐R19, resistant to sunflower rust

AbstractSunflower rust, incited by the fungus Puccinia helianthi Schwein., is a serious fungal disease in the sunflower (Helianthus annuus L.) growing areas worldwide, with an increasing importance in North America in recent years due to the frequent evolution of new pathogen races. HA‐R18 (Reg. no. GP‐377, PI 698197) and HA‐R19 (Reg. no. GP‐378, PI 698198) are rust‐resistant germplasm lines that were developed and released cooperatively in 2020 by the USDA‐ARS, Sunflower and Plant Biology Research Unit and the Agricultural Experiment Station of North Dakota State University. The rust resistance in HA‐R18 and HA‐R19 originated from KP193 and KP199, respectively, which were identified segregating for rust resistance after screening of 58 sunflower lines introduced from South Africa. Rust evaluation of HA‐R18 and HA‐R19 with 11 P. helianthi races indicated that both lines exhibited resistance to the most rust races tested including the most predominant and the most virulent races currently identified in the United States. HA‐R18 and HA‐R19 possess the new rust resistance genes R17 and R18, respectively, both of which have been mapped to sunflower chromosome 13. The two new lines will diversify the pool of rust resistance genes and should serve as useful sources of rust resistance in sunflower.

Estimation results of the spring bread wheat varieties on disease resistance in the Kazan Research Center

In the Republic of Tatarstan, due to favorable soil-climatic and market conditions, spring wheat production is developed, but wheat grain yields are limited by a number of unfavorable factors, one of which is a spread of fungal diseases. At the same time, the pressure of pathogenic fungi makes it possible to carry out fruitful breeding work in Tatarstan on resistance to diseases, which is on of the main activity of the Kazan Research Center of the RAS. The purpose of the current study was to estimate ten new varieties for resistance to major fungal diseases. The study on resistance to leafy diseases, such as powdery mildew, stem rust, brown leaf rust, dark brown leaf blotch was carried out at a natural infectious background, to kernel smut on an artificial infectious background inoculating seeds with spores of kernel smut. The study was carried out between the years of 2017 and 2021. The analysis for the possible presence of stem rust resistance genes was performed by a PCR analysis. As a result of the study, there was found out that the varieties ‘Sto let TASSR’, ‘Balkysh’, ‘Khazine’, ‘Chistopolskaya’, ‘Bulyak’ had a complex resistance to all studied diseases. The variety ‘Sitara’ had a strong field resistance to powdery mildew and kernel smut. The variety ‘Barakat’ had a strong field resistance to powdery mildew and leaf rust. The variety ‘Nadira’ was moderately resistant to powdery mildew and dark brown leaf spot. The varieties ‘Ekada 265’ and ‘Ekada 282’ were highly resistant to local stem rust populations. The molecular genetic estimation of the stem rust resistant varieties of spring bread wheat ‘Chistopolskaya’, ‘Sto let TASSR’, ‘Balkysh’, ‘Ekada 282’ for the identification of effective Sr-genes has shown that their resistance is apparently regulated by the Sr31 gene.

Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat landrace Wudubaijian in multi-environment trials

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases on wheat worldwide. Wudubaijian, a wheat landrace released from Gansu Province in China since 1950, exhibits adult-plant resistance to stripe rust for several decades. To elucidate the genetic basis of stripe rust resistance, Wudubaijian was crossed with the high susceptible cultivar Mingxian 169, and stripe rust tests of both parents and the F2:3 lines were conducted in four environments of Yangling and Tianshui in 2015 and 2016, respectively. The relative area under disease progress curve (rAUDPC) of Mingxian 169/Wudubaijian F2:3 lines showed that the resistance of Wudubaijian was controlled by quantitative trait loci (QTL). Combined with phenotypic data and molecular markers, two stable QTLs were identified in Wudubaijian. QYrwdbj.nwafu-5A with the phenotypic variance of 15.02–40.26% was located between 5AS1–0.40–0.75 and 5AS3–0.75–0.98 of chromosome 5AS, and QYrwdbj.nwafu-2B.1 with the phenotypic variance of 9.54–10.40% was located in the bin C-2BS1–0.53 of chromosome 2BS. Through the location of flanking markers and epistasis analysis, QYrwdbj.nwafu-5A may be a new major QTL that can be used in conjunction with other stripe rust resistance genes (QTLs).

Development and Molecular Cytogenetic Characterization of Novel Primary Wheat-Rye 1RS.1BL Translocation Lines from Multiple Rye Sources with Resistance to Stripe Rust.

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases for wheat production. An important method to improve the stripe rust resistance of wheat is to introduce resistance genes from related species into the wheat genome. The 1RS.1BL wheat-rye translocation from Petkus rye has contributed substantially to wheat resistance breeding worldwide. However, given the breakdown of the stripe rust resistance gene Yr9 in 1RS, its importance for wheat improvement has decreased. In this study, we developed 166 new primary 1RS.1BL translocation lines by crossing rye varieties Weining, Baili, and Aigan with several wheat cultivars. Cytogenetic and molecular analyses indicated that all of these lines contained a pair of intact 1RS.1BL translocation chromosomes. The stripe rust resistance of these translocation lines and their wheat parents was evaluated in southwestern China during the severe stripe rust epidemics in 2015 and 2021. The results showed diverse effects of the 1RS.1BL translocations from different rye cultivars on resistance to stripe rust. The highest genetic diversity was observed in 1RS.1BL translocations derived from diverse rye varieties but in the same wheat background. The development of diverse 1RS.1BL translocation lines offers ample opportunities to introduce new variations into wheat for improving stripe rust resistance. Finally, 71 new translocation lines, including nine developed from the cross of MY11 × Aigan, four from MY11 × Baili, 40 from MY11 × Weining, 14 from A42912 × Baili, and four from A42912 × Weining. These lines showed consistent resistance to stripe rust in fields under frequent changes of the pathogen races and could be useful genetic stocks for breeding wheat cultivars with resistance to stripe rust.

Molecular Mapping of a Recessive Gene for Stripe Rust Resistance at the YrCf75 Locus Using Bulked Segregant Analysis Combined with Single Nucleotide Polymorphism Genotyping Arrays and Bulked Segregant RNA-Sequencing.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases in wheat worldwide. Planting resistant varieties is the most economical, effective, and environment-friendly measure to control wheat stripe rust. Changfeng 75, a Chinese winter wheat variety, shows high stripe rust resistance in both seedling and adult-plant stages. The seedling tests of F1, F2, and F2:3 populations derived from Mingxian 169/Changfeng 75 inoculated with Chinese predominant Pst race CYR34 showed that the stripe rust resistance of Changfeng 75 was controlled by a single recessive gene. The locus was temporarily designated as YrCf75. Bulked segregant analysis (BSA) combined with the wheat 660K single-nucleotide polymorphism (SNP) array and bulked segregant RNA-sequencing indicated that the proportion of polymorphic SNPs on wheat chromosome 2A was the highest, which suggested that YrCf75 was likely located on chromosome 2A. Two hundred and twenty-five Kompetitive allele-specific PCR (KASP) and 75 simple sequence repeat (SSR) markers on chromosome 2A were used to map YrCf75 using the BSA approach. Linkage analysis indicated that 31 KASP markers and one SSR marker were linked to YrCf75, and the genetic distances of the two closest flanking KASP markers, AX-1110060462 and AX-111004763, were 1.2 and 2.7 cM, respectively. YrCf75 was located on wheat chromosome 2AL. The molecular detection, resistance specificity, and chromosome location showed that YrCf75 is likely a new gene that is different from the known stripe rust resistance genes (Yr1 and Yr32) on wheat chromosome 2AL.

Structural Polymorphisms of Chromosome 3Am Containing Lr63 Leaf Rust Resistance Loci Reflect the Geographical Distribution of Triticum monococcum L. and Related Diploid Wheats

Wheat is one of the world’s crucial staple food crops. In turn, einkorn wheat (Triticum monococcum L.) is considered a wild relative of wheat (Triticum aestivum L.) and can be used as a source of agronomically important genes for breeding purposes. Cultivated T. monococcum subsp. monococcum originated from T. monococcum subsp. aegilopoides (syn. T. boeticum). For the better utilization of valuable genes from these species, it is crucial to discern the genetic diversity at their cytological and molecular levels. Here, we used a fluorescence in situ hybridization toolbox and molecular markers linked to the leaf rust resistance gene Lr63 (located on the short arm of the 3Am chromosome—3AmS) to track the polymorphisms between T. monococcum subsp. monococcum, T. boeticum and T. urartu (A-genome donor for hexaploid wheat) accessions, which were collected in different regions of Europe, Asia, and Africa. We distinguished three groups of accessions based on polymorphisms of cytomolecular and leaf rust resistance gene Lr63 markers. We observed that the cultivated forms of T. monococcum revealed additional marker signals, which are characteristic for genomic alternations induced by the domestication process. Based on the structural analysis of the 3AmS chromosome arm, we concluded that the polymorphisms were induced by geographical dispersion and could be related to adaptation to local environmental conditions.

The Physical Location of Stripe Rust Resistance Genes on Chromosome 6 of Rye (Secale cereale L.) AR106BONE.

It was reported that the chromosome 6R of rye (Secale cereale L.) carries stripe rust resistance gene Yr83, and the region with the candidate resistance gene(s) still needs to be narrowed down. This study confirmed that the chromosome 6RLAr derived from rye AR106BONE contains stripe rust resistance gene(s). A wheat-rye T6BS.6RLAr translocation chromosome, a wheat-rye small-segment translocation T6RLAr-6AS.6AL, and three kinds of deleted T6BS.6RLAr translocations, T6BS.6RLAr-1, T6BS.6RLAr-2, and T6BS.6RLAr-3, were identified. Translocations T6BS.6RLAr, T6BS.6RLAr-2, and T6RLAr-6AS.6AL were highly resistant to stripe rust and T6BS.6RLAr-1 and T6BS.6RLAr-3 were highly susceptible. The molecular markers specific to 6RL determined that the three regions of the 6RLAr arm from 732,999,830 bp to the telomere, from 735,010,030 to 848,010,414 bp, and from 848,011,262 bp to the telomere were deleted from T6BS.6RLAr-1, T6BS.6RLAr-2, and T6BS.6RLAr-3, respectively. T6BS.6RLAr-2 and T6RLAr-6AS.6AL contained the segment that was deleted in T6BS.6RLAr-3. Therefore, it can be concluded that about 37 Mb segment from 848,011,262 bp to the telomere carried stripe rust resistance gene(s), and it was smaller than that with the Yr83 gene. Gene annotation indicated that about 37 Mb region contains 43 potential resistance genes, and 42 of them are nucleotide-binding site and leucine-rich repeat (NBS-LRR)-like resistance protein genes. The results in this study narrowed down the size of the region with candidate stripe rust resistance gene(s) on the 6RL arm, and the T6RLAr-6AS.6AL is a promising small-segment translocation for improvement of wheat cultivars.

Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat.

Stem rust resistance genes, SrRL5271 and Sr672.1 as well as SrCPI110651, from Aegilops tauschii, the diploid D genome progenitor of wheat, are sequence variants of Sr46 differing by 1-2 nucleotides leading to non-synonymous amino acid substitutions. The Aegilops tauschii (wheat D-genome progenitor) accessions RL 5271 and CPI110672 were identified as resistant to multiple races (including the Ug99) of the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt). This study was conducted to identify the stem rust resistance (Sr) gene(s) in both accessions. Genetic analysis of the resistance in RL 5271 identified a single dominant allele (SrRL5271) controlling resistance, whereas resistance segregated at two loci (SR672.1 and SR672.2) for a cross of CPI110672. Bulked segregant analysis placed SrRL5271 and Sr672.1 in a region on chromosome arm 2DS that encodes Sr46. Molecular marker screening, mapping and genomic sequence analysis demonstrated SrRL5271 and Sr672.1 are alleles of Sr46. The amino acid sequence of SrRL5271 and Sr672.1 is identical but differs from Sr46 (hereafter referred to as Sr46_h1 by following the gene nomenclature in wheat) by a single amino acid (N763K) and is thus designated Sr46_h2. Screening of a panel of Ae. tauschii accessions identified an additional allelic variant that differed from Sr46_h2 by a different amino acid (A648V) and was designated Sr46_h3. By contrast, the protein encoded by the susceptible allele of Ae. tauschii accession AL8/78 differed from these resistance proteins by 54 amino acid substitutions (94% nucleotide sequence gene identity). Cloning and complementation tests of the three resistance haplotypes confirmed their resistance to Pgt race 98-1,2,3,5,6 and partial resistance to Pgt race TTRTF in bread wheat. The three Sr46 haplotypes, with no virulent races detected yet, represent a valuable source for improving stem resistance in wheat.

Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9.

Four stable QTL for adult plant resistance were identified in wheat line Changwu 357-9, including a new QTL on 2AL showing significant interaction with Yr29 to reduce stripe rust severity. Stripe rust (yellow rust) is a serious disease of bread wheat (Triticum aestivum L.) worldwide. Genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease and to minimize the use of fungicides. The current study focused on characterizing the components of stripe rust resistance and understanding the interactions in Changwu 357-9 (CW357-9)/Avocet S RIL population. A genetic linkage map constructed using a new GenoBaits Wheat 16K Panel and the 660K SNP array had 5104 polymorphic SNP markers spanning 3533.11cM. Four stable QTL, consistently identified across five environments, were detected on chromosome arms 1BL, 2AL, 3DS, and 6BS in Changwu357-9. The most effective QTL QYrCW357-1BL was Yr29. The 6BS QTL was identified as Yr78, which has been combined with the 1BL QTL in many wheat cultivars and breeding lines. The novel QTL on 2AL with moderate effect showed a stable and significant epistatic interaction with Yr29. The QTL on 3DL should be same as QYrsn.nwafu-3DL and enriches the overall stripe rust resistance gene pool for breeding. Polymorphisms of flanking AQP markers AX-110020417 (for QYrCW357-1BL), AX-110974948 (for QYrCW357-2AL), AX-109466386 (for QYrCW357-3DL), and AX-109995005 (for QYrCW357-6BS) were evaluated in a diversity panel including 225 wheat cultivars and breeding lines. These results suggested that these high-throughput markers could be used to introduce QYrCW357-1BL, QYrCW357-2AL, QYrCW357-3DL, and QYrCW357-6BS into commercial wheat cultivars. Combinations of these genes with other APR QTL should lead to higher levels of stripe rust resistance along with the beneficial effects of multi-disease resistance gene Yr29 on improving resistance to other diseases.

Identification and characterization of the novel leaf rust resistance gene Lr81 in wheat.

The novel, leaf rust seedling resistance gene, Lr81, was identified in a Croatian breeding line and mapped to a genomic region of less than 100Kb on chromosome 2AS. Leaf rust, caused by Puccinia triticina, is the most common and widespread rust disease in wheat. Races of Puccinia triticina evolve rapidly in the southern Great Plains of the USA, and leaf rust resistance genes often lose effectiveness shortly after deployment in wheat production. PI 470121, a wheat breeding line developed by the University of Zagreb in Croatia, showed high resistance to Puccinia triticina races collected from Oklahoma, suggesting that PI 470121 could be a leaf rust resistance source for the southern Great Plains of the USA. Genetic analysis based on an F2 population and F2:3 families derived from the cross PI 470121 × Stardust indicated that PI 470121 carries a dominant seedling resistance gene, designated as Lr81. Linkage mapping delimited Lr81 to a genomic region of 96,148bp flanked by newly developed KASP markers Xstars-KASP320 and Xstars-KASP323 on the short arm of chromosome 2A, spanning 67,030,206-67,132,354bp in the Chinese Spring reference assembly (IWGSC RefSeq v1.0). Deletion bin mapping assigned Lr81 to the terminal bin 2AS-0.78-1.00. Allelism tests indicated that Lr81 is a distinctive leaf rust resistance locus with the physical order Lr65-Lr17-Lr81. Marker-assisted selection based on a set of markers closely linked to leaf rust resistance genes in PI 470121 and Stardust enabled identification of a recombinant inbred line RIL92 carrying Lr81 only. Lr81 is a valuable leaf rust resistance source that can be rapidly introgressed into locally adapted cultivars using KASP markers Xstars-KASP320 and Xstars-KASP323.