Mapping of QTLs prolonging the latent period of Puccinia triticina infection in wheat

Characterization of Quantitative Trait Loci for Leaf Rust Resistance from CI 13227 in Three Winter Wheat Populations

Leaf rust is a widespread foliar wheat disease causing substantial yield losses worldwide. Slow rusting is "adult plant" resistance that significantly slows epidemic development and thereby reduces yield loss. Wheat accession CI 13227 was previously characterized as having slow-rusting resistance. To validate the quantitative trait loci (QTLs) and develop diagnostic markers for slow rusting resistance in CI 13227, a new population of recombinant inbred lines of CI 13227 × Everest was evaluated for latent period, final severity, area under the disease progress curve, and infection type in greenhouses and genotyped using genotyping-by-sequencing. Four QTLs were identified on chromosome arms 2BL, 2DS, 3BS, and 7BL, explaining 6.82 to 28.45% of the phenotypic variance for these traits. Seven kompetitive allele-specific polymorphism markers previously reported to be linked to the QTLs in two other CI 13227 populations were validated. In addition, the previously reported QLr.hwwg-7AL was remapped to 2BL (renamed QLr.hwwg-2BL) after adding new markers in this study. Phenotypic data showed that the recombinant inbred lines harboring two or three of the QTLs had a significantly longer latent period. QLr.hwwg-2DS on 2DS showed a major effect on all rust resistance traits and was finely mapped to a 2.7-Mb interval by two newly developed flanking markers from exome capture. Three disease-resistance genes and two transporter genes were identified as the putative candidates for QLr.hwwg-2DS. The validated QTLs can be used as slow-rusting resistance resources, and the markers developed in this study will be useful for marker-assisted selection.

Characterization of Quantitative Trait Loci for Leaf Rust Resistance in the Uzbekistani Wheat Landrace Teremai Bugdai

Leaf rust, caused by Puccinia triticina, is a major cause of wheat yield losses globally, and novel leaf rust resistance genes are needed to enhance wheat leaf rust resistance. Teremai Bugdai is a landrace from Uzebekistan that is highly resistant to many races of P. triticina in the United States. To unravel leaf rust resistance loci in Teremai Bugdai, a recombinant inbred line (RIL) population of Teremai Bugdai × TAM 110 was evaluated for response to P. triticina race Pt54-1 (TNBGJ) and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). Quantitative trait loci (QTL) analysis using 5,130 high-quality GBS-SNPs revealed three QTLs, QLr-Stars-2DS, QLr-Stars-6BL, and QLr.Stars-7BL, for leaf rust resistance in two experiments. QLr-Stars-2DS, which is either a new Lr2 allele or a new resistance locus, was delimited to an ∼19.47-Mb interval between 46.4 and 65.9 Mb on 2DS and explained 31.3 and 33.2% of the phenotypic variance in the two experiments. QLr-Stars-6BL was mapped in an ∼84.0-kb interval between 719.48 and 719.56 Mb on 6BL, accounting for 33 to 36.8% of the phenotypic variance in two experiments. QLr.Stars-7BL was placed in a 350-kb interval between 762.41 and 762.76 Mb on 7BL and explained 4.4 to 5.3% of the phenotypic variance. Nine GBS-SNPs flanking these QTLs were converted to kompetitive allele specific PCR (KASP) markers, and these markers can be used to facilitate their introgression into locally adapted wheat lines.

Influence of new sulfur-containing fertilizers on performance of wheat yield

Wheat is the main cereal crop in Kazakhstan and fertilizers play an important role in enhancing harvest growth. In this study, the impact of new sulfur-containing fertilizers on the growth and yield of wheat was evaluated, and the resistance of varieties to Puccinia triticina Erikss was also investigated. (also known as Puccinia recondite Rob. ex Desm.) for recommendations in agriculture. The study was conducted from 2017 to 2020 in a nursery and greenhouse. The sulfur-containing fertilizer contains nutrients that allow you to extend the duration of absorption by the plant, thereby extending the period of their availability to plants, compared to conventional preparations. By encapsulating molten elemental sulfur and impregnating with a solution of calcium polysulfide, a long-acting compound based on amorphous and monocalcium phosphate was developed. The sulfur is in a water-soluble sulfate form, which, in turn, is slowly oxidized by bacteria and retained in the soil. Three different types of the developed sulfur-containing nano-particle have been used to test in greenhouses and nurseries: powdered, pasty sulfur-containing composition, and a solution of calcium polysulfide. The results showed that the use of powdered and dissolved sulfur-containing fertilizers contributed to the early ripeness and increased productivity of wheat. Wheat varieties were tested for the presence of key Lr genes that determine resistance to brown rust. The Omskaya 29 sample showed an immune response according to phytopathological assessment, and molecular screening revealed four resistance genes. The new sulfur-containing product is recommended for improving wheat productivity in agriculture, and the Omskaya 29 variety can also be used as a valuable breeding material resistant to brown rust.

Mapping of a QTL with major effect on reducing leaf rust severity at the adult plant growth stage on chromosome 2BL in wheat landrace Hongmazha

A major QTL (QLr.cau-2BL) for APR to leaf rust was detected on 2BL; an SSR marker was developed to closely link with QLr.cau-2BL and validated for effectiveness of MAS. The wheat landrace Hongmazha (HMZ) possesses adult plant resistance (APR) to leaf rust. To detect and validate quantitative trait locus (QTL) for the APR, four wheat populations were assessed for leaf rust severity in a total of eight field and greenhouse experiments. The mapping population Aquileja × HMZ (120 recombinant inbred lines, RILs) was genotyped using 90 K SNP markers. A major QTL (QLr.cau-2BL) was detected between the markers IWB3854 and IWB21922 on chromosome 2BL. IWB3854 and IWB21922 were positioned at approximately 531.14 Mb and 616.48 Mb, respectively, on 2BL of IWGSC RefSeq v1.0 physical map. Based on the sequences between 531.14 and 616.48 Mb on 2BL of IWGSC RefSeq v1.0, 415 simple sequence repeat (SSR) markers were developed. These markers and 28 previously published SSR makers were screened; the resulted polymorphic markers were used to genotype the relatively larger population RL6058 × HMZ (371 RILs). QLr.cau-2BL was mapped within a 1.5 cM interval on 2BL map of RL6058 × HMZ, and a marker (Ta2BL_ssr7) was identified to closely link with QLr.cau-2BL. Effectiveness of selection for QLr.cau-2BL based on Ta2BL_ssr7 was validated using two populations (RL6058 × HMZ F_2:3 and Jimai22 × HMZ BC₄F_2:3). In addition, polymorphism at Ta2BL_ssr7 was detected among a panel of 282 commercial wheat cultivars. We believe, therefore, that Ta2BL_ssr7 should be useful for introducing QLr.cau-2BL into commercial wheat cultivars and for accumulating QLr.cau-2BL with other APR QTL.

Fusarium Head Blight and Rust Diseases in Soft Red Winter Wheat in the Southeast United States: State of the Art, Challenges and Future Perspective for Breeding

Among the biotic constraints to wheat (Triticum aestivum L.) production, fusarium head blight (FHB), caused by Fusarium graminearum, leaf rust (LR), caused by Puccinia triticina, and stripe rust (SR) caused by Puccinia striiformis are problematic fungal diseases worldwide. Each can significantly reduce grain yield while FHB causes additional food and feed safety concerns due to mycotoxin contamination of grain. Genetic resistance is the most effective and sustainable approach for managing wheat diseases. In the past 20 years, over 500 quantitative trait loci (QTLs) conferring small to moderate effects for the different FHB resistance types have been reported in wheat. Similarly, 79 Lr-genes and more than 200 QTLs and 82 Yr-genes and 140 QTLs have been reported for seedling and adult plant LR and SR resistance, respectively. Most QTLs conferring rust resistance are race-specific generally conforming to a classical gene-for-gene interaction while resistance to FHB exhibits complex polygenic inheritance with several genetic loci contributing to one resistance type. Identification and deployment of additional genes/QTLs associated with FHB and rust resistance can expedite wheat breeding through marker-assisted and/or genomic selection to combine small-effect QTL in the gene pool. LR disease has been present in the southeast United States for decades while SR and FHB have become increasingly problematic in the past 20 years, with FHB arguably due to increased corn acreage in the region. Currently, QTLs on chromosome 1B from Jamestown, 1A, 1B, 2A, 2B, 2D, 4A, 5A, and 6A from W14, Ning7840, Ernie, Bess, Massey, NC-Neuse, and Truman, and 3B (Fhb1) from Sumai 3 for FHB resistance, Lr9, Lr10, Lr18, Lr24, Lr37, LrA2K, and Lr2K38 genes for LR resistance, and Yr17 and YrR61 for SR resistance have been extensively deployed in southeast wheat breeding programs. This review aims to disclose the current status of FHB, LR, and SR diseases, summarize the genetics of resistance and breeding efforts for the deployment of FHB and rust resistance QTL on soft red winter wheat cultivars, and present breeding strategies to achieve sustainable management of these diseases in the southeast US.

Mapping of Stripe Rust and Leaf Rust Resistance Quantitative Trait Loci in the Chinese Spring Wheat Line Mianyang351-15

Stripe rust and leaf rust cause wheat yield losses of up to 70% worldwide. The employment of resistant cultivars is the major method to reduce losses from these diseases. The objective of this study was to detect quantitative trait loci (QTL) for stripe rust and leaf rust resistance in 150 F₆ recombinant inbred lines (RIL) derived from a cross between Mianyang351-15 and Zhengzhou 5389. Both parents and the RIL population were genotyped with the Wheat55K single nucleotide polymorphism (SNP) array and simple sequence repeat markers, and phenotyped for stripe rust severity at Mianyang in Sichuan Province and Baoding in Hebei Province, and for leaf rust severity at Zhoukou in Henan Province and at Baoding in 2014 to 2017 cropping seasons. Seven and four QTL all contributed from Mianyang351-15 were identified for resistance to stripe rust and leaf rust, respectively. Four of these QTL on chromosomes 1BL, 2AS, 2DS, and 7BL conferred resistance to both stripe rust and leaf rust. The QTL on 1BL, 2AS, and 7BL were identified as Lr46/Yr29, Lr37/Yr17, and Lr68, respectively. QYr.hbau-2DS/QLr.hbau-2DS was detected at similar positions to previously reported loci. QYr.hbau-1DL, QYr.hbau-3AS, and QYr.hbau-3DL are likely to be new. Combined effects of QTL in the RIL population indicated RIL combining all QTL had the highest resistance level compared with those of lower numbers or no QTL. These QTL, with their closely linked SNP markers, are applicable for marker-assisted breeding and candidate gene discovery.

Gb8, a new gene conferring resistance to economically important greenbug biotypes in wheat

A new greenbug resistance gene Gb8 conferring broad resistance to US greenbug biotypes was identified in hard red winter wheat line PI 595379-1 and was mapped to the terminal region of chromosome 7DL. Greenbug [Schizaphis graminum (Rondani)] is a worldwide insect pest that poses a serious threat to wheat production. New greenbug resistance genes that can be readily used in wheat breeding are urgently needed. The objective of this study was to characterize a greenbug resistance gene in PI 595379-1, a single plant selection from PI 595379. Genetic analysis of response to greenbug biotype E in an F_2:3 population derived from a cross between PI 595379-1 and PI 243735 indicated that a single gene, designated Gb8, conditioned resistance. Linkage analysis placed Gb8 in a 2.7-Mb interval in the terminal bin of chromosome 7DL (7DL3-082-1.0), spanning 595.6 to 598.3 Mb in the Chinese Spring IWGSC RefSeq version 1.0 reference sequence. Gb8 co-segregated with a newly developed SSR marker Xstars508, positioned at 596.4 Mb in the reference sequence. Allelism tests showed that Gb8 was different from three permanently named genes on the same chromosome arm and the estimated genetic distance between Gb8 and Gb3 was 15.35 ± 1.35 cM. Gb8 can be directly used in wheat breeding to enhance greenbug resistance.

Quantitative Trait Loci Conferring Leaf Rust Resistance in Hexaploid Wheat

Leaf rust, caused by the fungal pathogen Puccinia triticina, is a major threat to wheat production in many wheat-growing regions of the world. The introduction of leaf rust resistance genes into elite wheat germplasm is the preferred method of disease control, being environmentally friendly and crucial to sustained wheat production. Consequently, there is considerable value in identifying and characterizing new sources of leaf rust resistance. While many major, qualitative leaf rust resistance genes have been identified in wheat, a growing number of valuable sources of quantitative resistance have been reported. Here we review the progress made in the genetic identification of quantitative trait loci (QTL) for leaf rust resistance detected primarily in field analyses, i.e., adult plant resistance. Over the past 50 years, leaf rust resistance loci have been assigned to genomic locations through chromosome analyses and genetic mapping in biparental mapping populations, studies that represent 79 different wheat leaf rust resistance donor lines. In addition, seven association mapping studies have identified adult plant and seedling leaf rust resistance marker trait associations in over 4,000 wheat genotypes. Adult plant leaf rust resistance QTL have been found on all 21 chromosomes of hexaploid wheat, with the B genome carrying the greatest number of QTL. The group 2 chromosomes are also particularly rich in leaf rust resistance QTL. The A genome has the lowest number of QTL for leaf rust resistance. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Quantitative Trait Loci for Slow-Rusting Resistance to Leaf Rust in Doubled-Haploid Wheat Population CI13227 × Lakin

CI13227 is a U.S. winter wheat line with adult-plant slow-rusting resistance that has been the subject of several studies on the characteristics and components of slow rusting. Previous genetic studies used different populations and approaches and came to different conclusions about the genetic basis of resistance in CI13227. To clarify the situation, a new doubled-haploid (DH) population of CI13227 × Lakin was produced and a linkage map was constructed using 5,570 single-nucleotide polymorphism (SNP) markers derived from wheat 90K SNP assays and 84 simple sequence repeat markers. Three quantitative trait loci (QTL) were identified for three slow-rusting traits on chromosome arms 2DS, 7AL, and 7BL from CI13227. A fourth QTL mapped on chromosome 3BS was from Lakin. The QTL on 2DS, designated QLr.hwwg-2DS, explained 11.2 to 25.6% of the phenotypic variation. It was found in the same position as a slow-rusting QTL in the CI13227 × Suwon 92 population in a previous study and, thus, verified the 2DS QTL. The QTL on chromosome 7BL explained 8.1 and 19.3% of the phenotypic variation and is likely to be Lr68. The other two QTL showed a minor effect on some of the traits evaluated in a single experiment. Flanking SNP closely linked to all QTL were converted to Kompetitive allele-specific polymerase chain reaction markers that can be used in marker-assisted selection to transfer these QTL into adapted wheat cultivars.

Characterization and Mapping of Leaf Rust and Stripe Rust Resistance Loci in Hexaploid Wheat Lines UC1110 and PI610750 under Mexican Environments

Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by the globally important wheat leaf rust (LR) and stripe rust (YR) diseases. In this study, a population of 186 F8 recombinant inbred lines (RILs) derived from a cross between a synthetic wheat derivative (PI610750) and an adapted common wheat line (cv. "UC1110") were phenotyped for LR and YR response at both seedling and adult plant stages over multiple seasons. Using a genetic linkage map consisting of single sequence repeats and diversity arrays technology markers, in combination with inclusive composite interval mapping analysis, we detected a new LR adult plant resistance (APR) locus, QLr.cim-2DS, contributed by UC1110. One co-located resistance locus to both rusts, QLr.cim-3DC/QYr.cim-3DC, and the known seedling resistance gene Lr26 were also mapped. QLr.cim-2DS and QLr.cim-3DC showed a marginally significant interaction for LR resistance in the adult plant stage. In addition, two previously reported YR APR loci, QYr.ucw-3BS and Yr48, were found to exhibit stable performances in rust environments in both Mexico and the United States and showed a highly significant interaction in the field. Yr48 was also observed to confer intermediate seedling resistance against Mexican YR races, thus suggesting it should be re-classified as an all-stage resistance gene. We also identified 5 and 2 RILs that possessed all detected YR and LR resistance loci, respectively. With the closely linked molecular markers reported here, these RILs could be used as donors for multiple resistance loci to both rusts in wheat breeding programs.

Genetic analysis and mapping of adult plant resistance loci to leaf rust in durum wheat cultivar Bairds

New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds. CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5-60.8%, 9.0-14.3%, 2.8-13.9%, and 11.6-29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.

Mapping of quantitative adult plant field resistance to leaf rust and stripe rust in two European winter wheat populations reveals co-location of three QTL conferring resistance to both rust pathogens

KEY MESSAGE

We detected several, most likely novel QTL for adult plant resistance to rusts. Notably three QTL improved resistance to leaf rust and stripe rust simultaneously indicating broad spectrum resistance QTL. The rusts of wheat (Puccinia spp.) are destructive fungal wheat diseases. The deployment of resistant cultivars plays a central role in integrated rust disease management. Durability of resistance would be preferred, but is difficult to analyse. The Austrian winter wheat cultivar Capo was released in the 1989 and grown on a large acreage during more than two decades and maintained a good level of quantitative leaf rust and stripe rust resistance. Two bi-parental mapping populations: Capo × Arina and Capo × Furore were tested in multiple environments for severity of leaf rust and stripe rust at the adult plant stage in replicated field experiments. Quantitative trait loci associated with leaf rust and stripe rust severity were mapped using DArT and SSR markers. Five QTL were detected in multiple environments associated with resistance to leaf rust designated as QLr.ifa-2AL, QLr.ifa-2BL, QLr.ifa-2BS, QLr.ifa-3BS, and QLr.ifa-5BL, and five for resistance to stripe rust QYr.ifa-2AL, QYr.ifa-2BL, QYr.ifa-3AS, QYr.ifa-3BS, and QYr.ifa-5A. For all QTL apart from two (QYr.ifa-3AS, QLr.ifa-5BL) Capo contributed the resistance improving allele. The leaf rust and stripe rust resistance QTL on 2AL, 2BL and 3BS mapped to the same chromosome positions, indicating either closely linked genes or pleiotropic gene action. These three multiple disease resistance QTL (QLr.ifa-2AL/QYr.ifa-2AL, QLr.ifa.2BL/QYr.ifa-2BL, QLr.ifa-3BS/QYr.ifa.3BS) potentially contribute novel resistance sources for stripe rust and leaf rust. The long-lasting resistance of Capo apparently rests upon a combination of several genes. The described germplasm, QTL and markers are applicable for simultaneous resistance improvement against leaf rust and stripe rust.

Assessing quantitative resistance against Leptosphaeria maculans (phoma stem canker) in Brassica napus (oilseed rape) in young plants

Quantitative resistance against Leptosphaeria maculans in Brassica napus is difficult to assess in young plants due to the long period of symptomless growth of the pathogen from the appearance of leaf lesions to the appearance of canker symptoms on the stem. By using doubled haploid (DH) lines A30 (susceptible) and C119 (with quantitative resistance), quantitative resistance against L. maculans was assessed in young plants in controlled environments at two stages: stage 1, growth of the pathogen along leaf veins/petioles towards the stem by leaf lamina inoculation; stage 2, growth in stem tissues to produce stem canker symptoms by leaf petiole inoculation. Two types of inoculum (ascospores; conidia) and three assessment methods (extent of visible necrosis; symptomless pathogen growth visualised using the GFP reporter gene; amount of pathogen DNA quantified by PCR) were used. In stage 1 assessments, significant differences were observed between lines A30 and C119 in area of leaf lesions, distance grown along veins/petioles assessed by visible necrosis or by viewing GFP and amount of L. maculans DNA in leaf petioles. In stage 2 assessments, significant differences were observed between lines A30 and C119 in severity of stem canker and amount of L. maculans DNA in stem tissues. GFP-labelled L. maculans spread more quickly from the stem cortex to the stem pith in A30 than in C119. Stem canker symptoms were produced more rapidly by using ascospore inoculum than by using conidial inoculum. These results suggest that quantitative resistance against L. maculans in B. napus can be assessed in young plants in controlled conditions. Development of methods to phenotype quantitative resistance against plant pathogens in young plants in controlled environments will help identification of stable quantitative resistance for control of crop diseases.

Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet × Pastor wheat population

Leaf rust and stripe rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar 'Pastor' originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf rust and stripe rust pressures. As a consequence, Pastor has good resistance to both rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible 'Avocet'. All 148 F(5) recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf rust (3 environments) and stripe rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for stripe rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf rust resistance were located on 1B, 2A and 2D and for stripe rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for stripe rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.

Lr68: a new gene conferring slow rusting resistance to leaf rust in wheat

The common wheat cultivar Parula possesses a high level of slow rusting, adult plant resistance (APR) to all three rust diseases of wheat. Previous mapping studies using an Avocet-YrA/Parula recombinant inbred line (RIL) population showed that APR to leaf rust (Puccinia triticina) in Parula is governed by at least three independent slow rusting resistance genes: Lr34 on 7DS, Lr46 on 1BL, and a previously unknown gene on 7BL. The use of field rust reaction and flanking markers identified two F(6) RILs, Arula1 and Arula2, from the above population that lacked Lr34 and Lr46 but carried the leaf rust resistance gene in 7BL, hereby designated Lr68. Arula1 and Arula2 were crossed with Apav, a highly susceptible line from the cross Avocet-YrA/Pavon 76, and 396 F(4)-derived F(5) RILs were developed for mapping Lr68. The RILs were phenotyped for leaf rust resistance for over 2 years in Ciudad Obregon, Mexico, with a mixture of P. triticina races MBJ/SP and MCJ/SP. Close genetic linkages with several DNA markers on 7BL were established using 367 RILs; Psy1-1 and gwm146 flanked Lr68 and were estimated at 0.5 and 0.6 cM, respectively. The relationship between Lr68 and the race-specific seedling resistance gene Lr14b, located in the same region and present in Parula, Arula1 and Arula2, was investigated by evaluating the RILs with Lr14b-avirulent P. triticina race TCT/QB in the greenhouse. Although Lr14b and Lr68 homozygous recombinants in repulsion were not identified in RILs, γ-irradiation-induced deletion stocks that lacked Lr68 but possessed Lr14b showed that Lr68 and Lr14b are different loci. Flanking DNA markers that are tightly linked to Lr68 in a wide array of genotypes can be utilized for selection of APR to leaf rust.

Identification and validation of a major quantitative trait locus for slow-rusting resistance to stripe rust in wheat

Stripe (yellow) rust, caused by Puccinia striiformis Westend. f. sp. tritici Eriks (Pst), is one of the most important wheat (Triticum aestivum L.) diseases and causes significant yield losses. A recombinant inbred (RI) population derived from a cross between Yanzhan 1 and Xichang 76-9 cultivars was evaluated for resistance to wheat stripe rust strain CYR32 at both the seedling and adult plant stages. Four resistance quantitative trait loci (QTLs) were detected in this population, in which the major one, designated as Yrq1, was mapped on chromosome 2DS. The strategy of using the Brachypodium distachyon genome, wheat expressed sequence tags and a draft DNA sequences (scaffolds) of the D-genome (Aegilops tauschii Coss.) for the development of simple sequence repeat (SSR) markers was successfully used to identify 147 SSRs in hexaploid wheat. Of the 19 polymorphic SSRs in the RI population, 17 SSRs were mapped in the homeologous group 2 chromosomes near Yrq1 region and eight SSRs were genetically mapped in the 2.7 cM region of Yrq1, providing abundant DNA markers for fine-mapping of Yrq1 and marker-assisted selection in wheat breeding program. The effectiveness of Yrq1 was validated in an independent population, indicating that this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass-pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F(2) population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F(2), resistance was quantified in F(2)-derived F(3) families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet × Pastor wheat population

Leaf rust and stripe rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar 'Pastor' originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf rust and stripe rust pressures. As a consequence, Pastor has good resistance to both rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible 'Avocet'. All 148 F(5) recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf rust (3 environments) and stripe rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for stripe rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf rust resistance were located on 1B, 2A and 2D and for stripe rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for stripe rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.

QTL for fibre-related traits in grain × sweet sorghum as a tool for the enhancement of sorghum as a biomass crop

Compared to maize and temperate grasses, sorghum has received less attention in terms of improving cell wall components. The objectives of this study were to identify quantitative trait loci (QTL) with main effects, epistatic and pleiotropic effects along with QTL × environment (QE) interactions controlling fibre-related traits in sorghum. Neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent lignin (ADL), cellulose, hemicellulose, fresh leaf mass, stripped stalk mass, dry stalk mass, fresh biomass and dry biomass were analysed from a population of 188 grain × sweet sorghum recombinant inbred lines. A genetic map consisting of 157 DNA markers was constructed, and QTL were detected using composite interval mapping (CIM). CIM detected more than 5 additive QTL per trait explaining 7.1-24.7% of the phenotypic variation. Abundant co-localization of these QTL was observed across all chromosomes, and the highest cluster was identified on chromosome 6. Searching for candidate genes using the confidence interval of our QTL clusters reveals that these clusters might comprise a set of genes that are tightly linked. Some QTL showed multiple effects; however, the allele for each trait was favouring the parent with the increasing effect. QE interactions were observed for QTL showing multiple effects. Additive × additive interaction was observed for 7 out of 10 traits, indicating the importance of epistatic analysis. However, the phenotypic variation explained by digenic interactions was lower compared to the individual QTL. Our results indicate that various genetic components contribute to fibre-related traits and should be considered during the enhancement of sorghum for lignocellulosic biomass.

Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench

The productivity of sorghum is mainly determined by quantitative traits such as grain yield and stem sugar-related characteristics. Substantial crop improvement has been achieved by breeding in the last decades. Today, genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement. We have investigated QTL associated with the sugar components (Brix, glucose, sucrose, and total sugar content) and sugar-related agronomic traits (flowering date, plant height, stem diameter, tiller number per plant, fresh panicle weight, and estimated juice weight) in four different environments (two locations) using a population of 188 recombinant inbred lines (RILs) from a cross between grain (M71) and sweet sorghum (SS79). A genetic map with 157 AFLP, SSR, and EST-SSR markers was constructed, and several QTLs were detected using composite interval mapping (CIM). Further, additive x additive interaction and QTL x environmental interaction were estimated. CIM identified more than five additive QTLs in most traits explaining a range of 6.0-26.1% of the phenotypic variation. A total of 24 digenic epistatic locus pairs were identified in seven traits, supporting the hypothesis that QTL analysis without considering epistasis can result in biased estimates. QTLs showing multiple effects were identified, where the major QTL on SBI-06 was significantly associated with most of the traits, i.e., flowering date, plant height, Brix, sucrose, and sugar content. Four out of ten traits studied showed a significant QTL x environmental interaction. Our results are an important step toward marker-assisted selection for sugar-related traits and biofuel yield in sorghum.

Genetic loci in the photoperiod pathway interactively modulate reproductive development of winter wheat

Responses to photoperiod and low temperature are the two primary adaptive mechanisms which enable wheat plants to synchronize developmental processes with changes in seasonal climate. In this study, the developmental process was characterized at two stages: stem length during the onset of stem elongation and heading date. These two developmental events were monitored and mapped in recombinant inbred lines (RILs) of a population generated from a cross between two complementary and locally adapted hard winter wheat cultivars. 'Intrada' undergoes stem elongation earlier but reaches heading later, whereas 'Cimarron' undergoes stem elongation later but reaches heading earlier. Variation in the developmental process in this population was associated with three major QTLs centered on Xbarc200 on chromosome 2B, PPD-D1 on chromosome 2D, and Xcfd14 on chromosome 7D. The Intrada Xbarc200 and Xcfd14 alleles and the Cimarron PPD-D1 allele accelerated both stem elongation and heading stages, or the Cimarron Xbarc200 and Xcfd14 alleles and the Intrada PPD-D1 allele delayed both stem elongation and heading stages. Integrative effects of the three QTLs accounted for 43% (initial stem length) and 68% (heading date) of the overall phenotypic variation in this population. PPD-D1 is a reasonable candidate gene for the QTL on chromosome 2D, PPD-B1 could be associated with the QTL on chromosome 2B, but VRN-D3 (=FT-D1) was not linked with the QTL on chromosome 7D, suggesting that this is a novel locus involved in winter wheat development. Because the PPD-D1 QTL was observed to interact with other two QTLs, all of these QTLs could play a role in the same pathway as involved in photoperiod response of winter wheat.

Quantitative trait loci for slow-rusting resistance in wheat to leaf rust and stripe rust identified with multi-environment analysis

Rust diseases are a major cause of yield loss in wheat worldwide, and are often controlled through the incorporation of resistance genes using conventional phenotypic selection methods. Slow-rusting resistance genes are expressed quantitatively and are typically small in genetic effect thereby requiring multiple genes to provide adequate protection against pathogens. These effects are valuable and are generally considered to confer durable resistance. Therefore an understanding of the chromosomal locations of such genes and their biological effects are important in order to ensure they are suitably deployed in elite germplasm. Attila is an important wheat grown throughout the world and is used as a slow-rusting donor in international spring wheat breeding programs. This study identified chromosomal regions associated with leaf rust and stripe rust resistances in a cross between Attila and a susceptible parent, Avocet-S, evaluated over 3 years in the field. Genotypic variation for both rusts was large and repeatable with line-mean heritabilities of 94% for leaf rust resistance and 87% for stripe rust. Three loci, including Lr46/Yr29 on chromosome 1BL, were shown to provide resistance to leaf rust whereas six loci with small effects conferred stripe rust resistance, with a seventh locus having an effect only by epistasis. Disease scoring over three different years enabled inferences to be made relating to stripe rust pathogen strains that predominated in different years.

Association of gene-linked SSR markers to seed glucosinolate content in oilseed rape (Brassica napus ssp. napus)

Breeding of oilseed rape (Brassica napus ssp. napus) has evoked a strong bottleneck selection towards double-low (00) seed quality with zero erucic acid and low seed glucosinolate content. The resulting reduction of genetic variability in elite 00-quality oilseed rape is particularly relevant with regard to the development of genetically diverse heterotic pools for hybrid breeding. In contrast, B. napus genotypes containing high levels of erucic acid and seed glucosinolates (++ quality) represent a comparatively genetically divergent source of germplasm. Seed glucosinolate content is a complex quantitative trait, however, meaning that the introgression of novel germplasm from this gene pool requires recurrent backcrossing to avoid linkage drag for high glucosinolate content. Molecular markers for key low-glucosinolate alleles could potentially improve the selection process. The aim of this study was to identify potentially gene-linked markers for important seed glucosinolate loci via structure-based allele-trait association studies in genetically diverse B. napus genotypes. The analyses included a set of new simple-sequence repeat (SSR) markers whose orthologs in Arabidopsis thaliana are physically closely linked to promising candidate genes for glucosinolate biosynthesis. We found evidence that four genes involved in the biosynthesis of indole, aliphatic and aromatic glucosinolates might be associated with known quantitative trait loci for total seed glucosinolate content in B. napus. Markers linked to homoeologous loci of these genes in the paleopolyploid B. napus genome were found to be associated with a significant effect on the seed glucosinolate content. This example shows the potential of Arabidopsis-Brassica comparative genome analysis for synteny-based identification of gene-linked SSR markers that can potentially be used in marker-assisted selection for an important trait in oilseed rape.

Molecular characterization of a powdery mildew resistance gene in wheat cultivar suwon 92

ABSTRACT Powdery mildew, caused by Blumeria graminis f. sp tritici, is an important foliar disease of wheat worldwide. Pyramiding race-specific genes into a single cultivar and combining race-specific resistance genes with durable resistance genes are the preferred strategies to improve the durability of powdery mildew resistance. The objectives of this study were to characterize a powdery mildew resistance gene in Suwon 92 and identify gene-specific or tightly linked molecular markers for marker-assisted selection (MAS). A population of recombinant inbred lines (RILs) was derived by single seed descent from a cross between Suwon 92 and a susceptible cultivar, CI 13227. The RILs were screened for adult-plant infection type of powdery mildew and characterized with amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. The linked markers explained 41.3 to 69.2% of the phenotypic variances measured in 2 years. A morphological marker, hairy glume, was also associated with powdery mildew resistance in Suwon 92, and explained 43 to 51% of the phenotypic variance. The powdery mildew resistance gene in Suwon 92 was located on the short arm of chromosome 1A where Pm3 was located. Two gene-specific markers were developed based on the sequence of the cloned Pm3b gene. These two markers, which were mapped at the same locus in the peak region of the LOD score for the RIL population, explained most of the phenotypic variance for powdery mildew resistance in the RIL population. The powdery mildew resistance in Suwon 92 is most likely conditioned by the Pm3 locus. The gene markers developed herein can be directly used for MAS of some of the Pm3 alleles in breeding programs.