Molecular characterization of durum and common wheat recombinant lines carrying leaf rust resistance (Lr19) and yellow pigment (Y) genes from Lophopyrum ponticum

Exploitation of the genetic potential of Thinopyrum and Agropyron genera to protect wheat from diseases and environmental stresses

Common wheat is one of the most important food crops in the world. Grain harvests can be increased by reducing losses from diseases and environmental stresses. The tertiary gene pool, including Thinopyrum spp., is a valuable resource for increasing genetic diversity and wheat resistance to fungal diseases and abiotic stresses. Distant hybridization between wheat and Thinopyrum spp. began in the 1920s in Russia, and later continued in different countries. The main results were obtained using the species Th. ponticum and Th. intermedium. Additionally, introgression material was created based on Th. elongatum, Th. bessarabicum, Th. junceiforme, Agropyron cristatum. The results of introgression for resistance to diseases (leaf, stem, and stripe rusts; powdery mildew; Fusarium head blight; and Septoria blotch) and abiotic stresses (drought, extreme temperatures, and salinity) to wheat was reviewed. Approaches to improving the agronomic properties of introgression breeding material (the use of irradiation, ph-mutants and compensating Robertsonian translocations) were described. The experience of long-term use in the world of a number of genes from the tertiary gene pool in protecting wheat from leaf and stem rust was observed. Th. ponticum is a nonhost for Puccinia triticina (Ptr) and P. graminis f. sp. tritici (Pgt) and suppresses the development of rust fungi on the plant surface. Wheat samples with the tall wheatgrass genes Lr19, Lr38, Sr24, Sr25 and Sr26 showed defence mechanisms similar to nonhosts resistance. Their influence led to disruption of the development of surface infection structures and fungal death when trying to penetrate the stomata (prehaustorial resistance or stomatal immunity). Obviously, a change in the chemical properties of fungal surface structures of races virulent to Lr19, Lr24, Sr24, Sr25, and Sr26 leads to a decrease in their adaptability to the environment. This possibly determined the durable resistance of cultivars to leaf and stem rusts in different regions. Alien genes with a similar effect are of interest for breeding cultivars with durable resistance to rust diseases and engineering crops with the help of molecular technologies.

Genetic mapping of the wheat leaf rust resistance gene Lr19 and development of translocation lines to break its linkage with yellow pigment

KEY MESSAGE

The leaf rust resistance gene Lr19, which is present on the long arm of chromosome 7E1 in Thinopyrum ponticum, was mapped within a 0.3-cM genetic interval, and translocation lines were developed to break its linkage with yellow pigmentation The leaf rust resistance locus Lr19, which was transferred to wheat (Triticum aestivum) from its relative Thinopyrum ponticum in 1966, still confers broad resistance to most known races of the leaf rust pathogen Puccinia triticina (Pt) worldwide. However, this gene has not previously been fine-mapped, and its tight linkage with a gene causing yellow pigmentation has limited its application in bread wheat breeding. In this study, we genetically mapped Lr19 using a bi-parental population from a cross of two wheat-Th. ponticum substitution lines, the Lr19-carrying line 7E1(7D) and the leaf rust-susceptible line 7E2(7D). Genetic analysis of the F2 population and the F2:3 families showed that Lr19 was a single dominant gene. Genetic markers allowed the gene to be mapped within a 0.3-cM interval on the long arm of Th. ponticum chromosome 7E1, flanked by markers XsdauK3734 and XsdauK2839. To reduce the size of the Th. ponticum chromosome segment carrying Lr19, the Chinese Spring Ph1b mutant was employed to promote recombination between the homoeologous chromosomes of the wheat chromosome 7D and the Th. ponticum chromosome 7E1. Two translocation lines with short Th. ponticum chromosome fragments carrying Lr19 were identified using the genetic markers closely linked to Lr19. Both translocation lines were resistant to 16 Pt races collected throughout China. Importantly, the linkage between Lr19 and yellow pigment content was broken in one of the lines. Thus, the Lr19 linked markers and translocation lines developed in this study are valuable resources in marker-assisted selection as part of common wheat breeding programs.

Combining high carotenoid, grain protein content and rust resistance in wheat for food and nutritional security

Globally, malnutrition has given birth to an alarming predicament, especially in developing countries, and has extensively shifted consumer preferences from conventional high-energy diets to a nutritionally balanced, cost-effective, sustainable, and healthy lifestyle. In keeping with this view and the mandate for developing high-yielding, disease-resistant biofortified staple food (wheat) for catering to the demand-driven market, the current research aimed at stacking together the enhanced grain protein content, carotenoid content, and disease resistance in an elite bread wheat background. The Y gene (PsyE1) and the GpcB1 gene were used as novel sources for enhancing the grain carotenoid and protein content in the commercial elite bread wheat cultivar HD2967. The combination also led to the stacking of resistance against all three foliar rusts owing to linked resistance genes. A stepwise hybridization using Parent 1 (HD2967 + PsyE1/Lr19/Sr25) with Parent 2 (PBW550 + GpcB1/Yr36+ Yr15), coupled with a phenotypic-biochemical selection, narrowed down 2748 F2 individuals to a subset of 649 F2 plants for molecular screening. The gene-specific markers PsyE1, PsyD1, Xucw108, and Xbarc8 for the genes PsyE1, PsyD1, GpcB1, and Yr15, respectively, were employed for forward selection. Four bread wheat lines positive for all the desired genes with high carotenoid (>8ppm) and protein (>13%) content were raised to the F5 generation and will be evaluated for yield potential after bulking. These improved advanced breeding lines developed following multipronged efforts should prove a valuable and unique source for the development of cultivars with improved nutritional quality and rust resistance in wheat breeding programs.

Cytogenetic and genomic characterization of a novel tall wheatgrass-derived Fhb7 allele integrated into wheat B genome

We identified and integrated the novel FHB-resistant Fhb7^The2 allele into wheat B genome and made it usable in both common and durum wheat breeding programs without yellow flour linkage drag. A novel tall wheatgrass-derived (Thinopyrum elongatum, genome EE) Fhb7 allele, designated Fhb7^The2, was identified and integrated into the wheat B genome through a small 7B-7E translocation (7BS·7BL-7EL) involving the terminal regions of the long arms. Fhb7^The2 conditions significant Type II resistance to Fusarium head blight (FHB) in wheat. Integration of Fhb7^The2 into the wheat B genome makes this wild species-derived FHB resistance gene usable for breeding in both common and durum wheat. By contrast, other Fhb7 introgression lines involving wheat chromosome 7D can be utilized only in common wheat breeding programs, not in durum wheat. Additionally, we found that Fhb7^The2 does not have the linkage drag of the yellow flour pigment gene that is tightly linked to the decaploid Th. ponticum-derived Fhb7 allele Fhb7^Thp. This will further improve the utility of Fhb7^The2 in wheat breeding. DNA sequence analysis identified 12 single nucleotide polymorphisms (SNPs) in Fhb7^The2, Fhb7^Thp, and another Th. elongatum-derived Fhb7 allele Fhb7^The1, which led to seven amino acid conversions in Fhb7^The2, Fhb7^Thp, and Fhb7^The1, respectively. However, no significant variation was observed in their predicted protein configuration as a glutathione transferase. Diagnostic DNA markers were developed specifically for Fhb7^The2. The 7EL segment containing Fhb7^The2 in the translocation chromosome 7BS·7BL-7EL exhibited a monogenic inheritance pattern in the wheat genetic background. This will enhance the efficacy of marker-assisted selection for Fhb7^The2 introgression, pyramiding, and deployment in wheat germplasm and varieties.

Bread wheat with enhanced grain carotenoid content: a novel option for wheat biofortification

Colored wheat has piqued the interest of breeders and consumers alike. The chromosomal segment from 7E of Thinopyrum ponticum, which carries a leaf rust resistant gene, Lr19, has been rarely employed in wheat breeding operations due to its association with the Y gene, which gives a yellow tint to the flour. By prioritizing nutritional content over color preferences, consumer acceptance has undergone a paradigm change. Through marker-assisted backcross breeding, we introduced an alien segment harboring the Y (PsyE1) gene into a high yielding commercial bread wheat (HD 2967) background to generate rust resistant carotenoid biofortified bread wheat. Agro-morphological characterization was also performed on a subset of developed 70 lines having enhanced grain carotene content. In the introgression lines, carotenoid profiling using HPLC analysis demonstrated a considerable increase in β-carotene levels (up to 12 ppm). Thus, the developed germplasm caters the threat to nutritional security and can be utilized to produce carotenoid fortified wheat.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01338-0.

Wheat Genes Associated with Different Types of Resistance against Stem Rust (Puccinia graminis Pers.)

Stem rust is one wheat's most dangerous fungal diseases. Yield losses caused by stem rust have been significant enough to cause famine in the past. Some races of stem rust are considered to be a threat to food security even nowadays. Resistance genes are considered to be the most rational environment-friendly and widely used way to control the spread of stem rust and prevent yield losses. More than 60 genes conferring resistance against stem rust have been discovered so far (so-called Sr genes). The majority of the Sr genes discovered have lost their effectiveness due to the emergence of new races of stem rust. There are some known resistance genes that have been used for over 50 years and are still effective against most known races of stem rust. The goal of this article is to outline the different types of resistance against stem rust as well as the effective and noneffective genes, conferring each type of resistance with a brief overview of their origin and usage.

Colored wheat and derived products: key to global nutritional security

Ensuring food and nutritional security of fast-growing population will pose a huge challenge in future. An estimated one-half population who does not go hungry, nonetheless suffers the debilitating effects of unhealthy diets. In view of the nutritional awareness, when the major wheat breeding programs have started shifting to quality, instead of quantity in wheat, the colored wheats give a novel twist of targeting the malnutrition by enhancing the antioxidants such as anthocyanin, carotenoids, flavonoids, polyphenols etc. Moreover, changing consumer demands have picked the trend to prefer a nutritionally balanced diet over the conventional high energy diets and thus, colored wheat has opened up a hidden avenue for providing additional value to the wheat-based products. Besides providing nutrition, these pigments have the potential to replace the synthetic dyes and food colorants prevalent in the market. The review summarizes the genetics and biochemistry of the pigments of colored wheat along with their product development, nutritional status and consumer preference. The review also sheds light on the environmental effect on color accumulation and the effect of increased colorants on other quality traits of wheat.

Wheat speciation and adaptation: perspectives from reticulate evolution

Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.

Introgression of Thinopyrum elongatum DNA fragments carrying resistance to fusarium head blight into Triticum aestivum cultivar Chinese Spring is associated with alteration of gene expression

The tall wheatgrass species Thinopyrum elongatum carries on the long arm of chromosome 7E, a locus that contributes strongly to resistance to fusarium head blight (FHB), a devastating fungal disease affecting wheat crops in all temperate areas of the world. Introgression of Th. elongatum 7E chromatin into chromosome 7D of wheat was induced by the ph1b mutant of CS. Recombinants between chromosome 7E and wheat chromosome 7D, induced by the ph1b mutation, were monitored by a combination of molecular markers and phenotyping for FHB resistance. Progeny of up to five subsequent generations derived from two lineages, 64-8 and 32-5, were phenotyped for FHB symptoms and genotyped using published and novel 7D- and 7E-specific markers. Fragments from the distal end of 7EL, still carrying FHB resistance and estimated to be less than 114 and 66 Mbp, were identified as introgressed into wheat chromosome arm 7DL of progeny derived from 64-8 and 32-5, respectively. Gene expression analysis revealed variation in the expression levels of genes from the distal ends of 7EL and 7DL in the introgressed progeny. The 7EL introgressed material will facilitate the use of the 7EL FHB resistance locus in wheat breeding programs.

Challenges and prospects for developing genetic resistance in common wheat against stem rust in Western Siberia

Современные исследования проблемы устойчивости мягкой пшеницы к стеблевой ржавчине включают два основных направления: оценку устойчивости коллекций мягкой пшеницы к заболеванию с помощью молекулярных маркеров к известным генам устойчивости в дополнение к полевому скринингу материала и лабораторным тестам к образцам различных популяций гриба; поиск источников и доноров новых генов и генных локусов, в том числе среди культурных и дикорастущих родичей пшеницы. Для достижения адекватного генетического контроля заболевания важен интегральный подход, включающий как данные об источниках устойчивости, так и актуальные сведения о действующих в регионе патогенных популяциях, их расовом составе и динамике генов вирулентности. Результаты анализа экспериментальных данных полевого скрининга устойчивости к стеблевой ржавчине сортов мягкой пшеницы из коллекции питомников CIMMYT в условиях Омской и Новосибирской областей, а также лабораторного тестирования образцов инфекции на международном наборе пшеничных линий-дифференциаторов позволяют предполагать, что на территории Западной Сибири и Алтайского края существует обособленная, «азиатская», популяция Puccinia graminis f. sp. tritici. При этом практический интерес для современных программ опережающей селекции пшеницы на иммунитет к стеблевой ржавчине в условиях Западной Сибири представляют гены устойчивости Sr2, Sr6Ai#2, Sr24, Sr25, Sr26, Sr31, Sr39, Sr40, Sr44 и Sr57. В настоящем обзоре проанализированы источники генов, сохраняющих эффективность к западносибирской популяции P. graminis, с целью упрощения первичного этапа отбора селекционного материала для создания устойчивого генотипа путем пирамидирования генов. Описаны основные требования, предъявляемые к фитопатологическому тестированию селекционного материала. Составлен список молекулярных маркеров к указанным генам устойчивости – как широко применяющихся в маркер-ориентированной селекции, так и требующих верификации.

Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population

Comprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome-wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits in a soft red winter wheat population. The study of linkage disequilibrium (LD) revealed that the extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LD with slow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for selection signatures using F_ST and hapFLK identified 13 genomic regions under selection, of which five loci (LT, Fr-A2, Vrn-A1, Vrn-B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1). Genome-wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, major loci with effects sizes of 2.2 days and 5 cm were identified on chromosomes 7B and 6A respectively. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for yield alone, no major loci were detected. A combination of selection for large effect loci for yield components and genomic selection could be a promising approach for yield improvement.

The Resurgence of Introgression Breeding, as Exemplified in Wheat Improvement

Breeding progress in most crops has relied heavily on the exploitation of variation within the species' primary gene pool, a process which is destined to fail once the supply of novel variants has been exhausted. Accessing a crop's secondary gene pool, as represented by its wild relatives, has the potential to greatly expand the supply of usable genetic variation. The crop in which this approach has been most strongly championed is bread wheat (Triticum aestivum), a species which is particularly tolerant of the introduction of chromosomal segments of exotic origin thanks to the genetic buffering afforded by its polyploid status. While the process of introgression can be in itself cumbersome, a larger problem is that linkage drag and/or imperfect complementation frequently impose a yield and/or quality penalty, which explains the reluctance of breeders to introduce such materials into their breeding populations. Thanks to the development of novel strategies to induce introgression and of genomic tools to facilitate the selection of desirable genotypes, introgression breeding is returning as a mainstream activity, at least in wheat. Accessing variation present in progenitor species has even been able to drive genetic advance in grain yield. The current resurgence of interest in introgression breeding can be expected to result in an increased deployment of exotic genes in commercial wheat cultivars.

Evaluation and identification of stem rust resistance genes Sr2, Sr24, Sr25, Sr26, Sr31 and Sr38 in wheat lines from Gansu Province in China

Wheat stem rust, caused by Puccinia granimis f. sp. tritici, severely affects wheat production, but it has been effectively controlled in China since the 1970s. However, the appearance and spread of wheat stem rust races Ug99 (TTKSK, virulence to Sr31), TKTTF (virulence to SrTmp) and TTTTF (virulence to the cultivars carrying Sr9e and Sr13) have received attention. It is important to clarify the effectiveness of resistance genes in a timely manner, especially for the purpose of using new resistance genes in wheat cultivars for durable-resistance. However, little is known about the stem rust resistance genes present in widely used wheat cultivars from Gansu. This study aimed to determine the resistance level at the seedling stage of the main wheat cultivars in Gansu Province. A secondary objective was to assess the prevalence of Sr2, Sr24, Sr25, Sr26, Sr31, and Sr38 using molecular markers. The results of the present study indicated that 38 (50.7%) wheat varieties displayed resistance to all the tested races of Puccinia graminis f. sp. tritici. The molecular marker analysis showed that 13 out of 75 major wheat cultivars likely carried Sr2; 25 wheat cultivars likely carried Sr31; and nine wheat cultivars likely carried Sr38. No cultivar was found to have Sr25 and Sr26, as expected. Surprisingly, no wheat cultivars carried Sr24. The wheat lines with known stem rust resistance genes could be used as donor parent for further breeding programs.

A New Map Location of Gene Stb3 for Resistance to Septoria Tritici Blotch in Wheat

Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (synonym: Zymoseptoria tritici; asexual stage: Septoria tritici), is an important disease of wheat worldwide. Management of the disease usually is by host resistance or fungicides. However, M. graminicola has developed insensitivity to most commonly applied fungicides so there is a continuing need for well-characterized sources of host resistance to accelerate the development of improved wheat cultivars. Gene Stb3 has been a useful source of major resistance, but its mapping location has not been well characterized. Based on linkage to a single marker, a previous study assigned Stb3 to a location on the short arm of chromosome 6D. However, the results from the present study show that this reported location is incorrect. Instead, linkage analysis revealed that Stb3 is located on the short arm of wheat chromosome 7A, completely linked to microsatellite (SSR) locus Xwmc83 and flanked by loci Xcfa2028 (12.4 cM distal) and Xbarc222 (2.1 cM proximal). Linkage between Stb3 and Xwmc83 was validated in BC₁F₃ progeny of other crosses, and analyses of the flanking markers with deletion stocks showed that the gene is located on 7AS between fraction lengths 0.73 and 0.83. This revised location of Stb3 is different from those for other STB resistance genes previously mapped in hexaploid wheat but is approximately 20 cM proximal to an STB resistance gene mapped on the short arm of chromosome 7A^m in Triticum monococcum. The markers described in this study are useful for accelerating the deployment of Stb3 in wheat breeding programs.

Development and characterization of a Psathyrostachys huashanica Keng 7Ns chromosome addition line with leaf rust resistance

The aim of this study was to characterize a Triticum aestivum-Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) disomic addition line 2-1-6-3. Individual line 2-1-6-3 plants were analyzed using cytological, genomic in situ hybridization (GISH), EST-SSR, and EST-STS techniques. The alien addition line 2-1-6-3 was shown to have two P. huashanica chromosomes, with a meiotic configuration of 2n = 44 = 22 II. We tested 55 EST-SSR and 336 EST-STS primer pairs that mapped onto seven different wheat chromosomes using DNA from parents and the P. huashanica addition line. One EST-SSR and nine EST-STS primer pairs indicated that the additional chromosome of P. huashanica belonged to homoeologous group 7, the diagnostic fragments of five EST-STS markers (BE404955, BE591127, BE637663, BF482781 and CD452422) were cloned, sequenced and compared. The results showed that the amplified polymorphic bands of P. huashanica and disomic addition line 2-1-6-3 shared 100% sequence identity, which was designated as the 7Ns disomic addition line. Disomic addition line 2-1-6-3 was evaluated to test the leaf rust resistance of adult stages in the field. We found that one pair of the 7Ns genome chromosomes carried new leaf rust resistance gene(s). Moreover, wheat line 2-1-6-3 had a superior numbers of florets and grains per spike, which were associated with the introgression of the paired P. huashanica chromosomes. These high levels of disease resistance and stable, excellent agronomic traits suggest that this line could be utilized as a novel donor in wheat breeding programs.

Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat

Root architecture traits are an important component for improving water stress adaptation. However, selection for aboveground traits under favorable environments in modern cultivars may have led to an inadvertent loss of genes and novel alleles beneficial for adapting to environments with limited water. In this study, we elucidate the physiological and molecular consequences of introgressing an alien chromosome segment (7DL) from a wild wheat relative species (Agropyron elongatum) into cultivated wheat (Triticum aestivum). The wheat translocation line had improved water stress adaptation and higher root and shoot biomass compared with the control genotypes, which showed significant drops in root and shoot biomass during stress. Enhanced access to water due to higher root biomass enabled the translocation line to maintain more favorable gas-exchange and carbon assimilation levels relative to the wild-type wheat genotypes during water stress. Transcriptome analysis identified candidate genes associated with root development. Two of these candidate genes mapped to the site of translocation on chromosome 7DL based on single-feature polymorphism analysis. A brassinosteroid signaling pathway was predicted to be involved in the novel root responses observed in the A. elongatum translocation line, based on the coexpression-based gene network generated by seeding the network with the candidate genes. We present an effective and highly integrated approach that combines root phenotyping, whole-plant physiology, and functional genomics to discover novel root traits and the underlying genes from a wild related species to improve drought adaptation in cultivated wheat.

A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat

Lr19, one of the few widely effective genes conferring resistance to leaf rust in wheat, was transferred from the wild relative Thinopyrum ponticum to durum wheat. Since Lr19 confers a hypersensitive response to the pathogen, it was considered likely that the gene would be a member of the major nucleotide-binding site (NBS)-leucine-rich repeat (LRR) plant R gene family. NBS profiling, based on PCR amplification of conserved NBS motifs, was applied to durum wheat-Th. ponticum recombinant lines involving different segments of the alien 7AgL chromosome arm, carrying or lacking Lr19. Differential PCR products were isolated and sequenced. From one such sequence (AG15), tightly linked to Lr19, a 4,121-bp full-length cDNA was obtained. Its deduced 1,258 amino acid sequence has the characteristic NBS-LRR domains of plant R gene products and includes a coiled-coil (CC) region typical of monocots. The genomic DNA sequence showed the presence of two exons and a short intron upstream of the predicted stop codon. Homology searches revealed considerable identity of AG15 with the cloned wheat resistance gene Pm3a and a lower similarity with wheat Lr1, Lr21, and Lr10. Quantitative PCR on leaf-rust-infected and non-infected Lr19 carriers proved AG15 to be constitutively expressed, as is common for R genes.

QTL analysis of pasta quality using a composite microsatellite and SNP map of durum wheat

Bright yellow color, firmness and low cooking loss are important factors for the production of good-quality pasta products. However, the genetic factors underlying those traits are still poorly understood. To fill this gap we developed a population of 93 recombinant inbred lines (RIL) from the cross between experimental line UC1113 (intermediate pasta quality) with the cultivar Kofa (excellent pasta quality). A total of 269 markers, including 23 SNP markers, were arranged on 14 linkage groups covering a total length of 2,140 cM. Samples from each RIL from five different environments were used for complete pasta quality testing and the results from each year were used for QTL analyses. The combined effect of different loci, environment and their interactions were analyzed using factorial ANOVAs for each trait. We identified major QTLs for pasta color on chromosomes 1B, 4B, 6A, 7A and 7B. The 4B QTL was linked to a polymorphic deletion in the Lpx-B1.1 lipoxygenase locus, suggesting that it was associated with pigment degradation during pasta processing. The 7B QTL for pasta color was linked to the Phytoene synthase 1 (Psy-B1) locus suggesting difference in pigment biosynthesis. QTLs affecting pasta firmness and cooking loss were detected on chromosomes 5A and 7B, and in both cases they were overlapping with QTL for grain protein content and wet gluten content. These last two parameters were highly correlated with pasta firmness (R > 0.71) and inversely correlated to cooking loss (R < -0.37). The location and effect of other QTLs affecting grain size and weight, gluten strength, mixing properties, and ash content are also discussed.

A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL

A recombinant inbred line (RIL) population and a set of advanced lines from multiple crosses were used to investigate the leaf rust (Puccinia triticina Eriks.) resistance carried by the durum wheat cultivar Creso and its derivatives (Colosseo and Plinio). One hundred seventy-six RILs from the cross Colosseo x Lloyd were tested under artificial rust inoculation in the field. The response at the seedling stage was also investigated. A major QTL (QLr.ubo-7B.2) for leaf rust resistance controlling both the seedling and the adult open field based-response was mapped on 7BL, with the favourable allele inherited from Colosseo. QLr.ubo-7B.2 showed R2 and LOD peak values for the area under disease progress curve (AUDPC) equal to 72.9% and 44.5, respectively. The presence and location of QLr.ubo-7B.2 was validated by a linkage disequilibrium-based test using two-year field data of 62 advanced lines from 21 crosses with Creso, Colosseo or Plinio as resistance donors. QLr.ubo-7B.2 maps in a gene-dense region (7BL10-0.78-1.00) carrying several genes/QTLs in wheat and barley for resistance to rusts and other fungal diseases.

Association between allelic variation at the Phytoene synthase 1 gene and yellow pigment content in the wheat grain

A better understanding of the genetic factors controlling grain yellow pigment content (GYPC) is important for both pasta (high GYPC) and bread wheat (low GYPC) quality improvement. Quantitative trait loci (QTL) for GYPC have been mapped repeatedly on the distal regions of chromosome arms 7AL and 7BL in wheat, and the Phytoene synthase 1 (PSY-1) gene located in this region has been proposed as a candidate gene. We show here that PSY-E1, the tall wheatgrass orthologue, is completely linked to differences in GYPC, and that selection for white endosperm mutants in recombinant lines carrying this gene resulted in the identification of a mutation in a conserved amino acid of PSY-E1. These results, together with the association between GYPC and allelic differences in PSY-1 in hexaploid wheat, suggest that this gene plays an important role in the determination of GYPC. However, a second white endosperm mutant previously mapped to chromosome arm 7EL showed no mutations in PSY-E1 suggesting the existence of additional gene(s) affecting GYPC in this chromosome region. This hypothesis was further supported by the mapping of QTL for GYPC on 7AL proximal to PSY-1 in a cross between pasta wheat varieties UC1113 and Kofa. Interestingly, the Kofa PSY-B1 allele showed unusually high levels of polymorphisms as a result of a conversion event involving the PSY-A1 allele. In summary, our results support the hypothesis that allelic differences in PSY-1 and at least one additional gene in the distal region of the long arm of homoeologous group 7L are associated with differences in GYPC.

The effects on grain quality traits of a grain serpin protein and the VPM1 segment in southern Australian wheat breeding

Production of wheat of sufficient quality to meet market demands is an ongoing agricultural challenge. Identification and evaluation of alleles of genes affecting quality parameters enables breeders to improve their germplasm by active selection towards specific allele combinations. Using a large dataset obtained from southern Australian wheat breeding programs, and including a relationship matrix in the analysis to minimise bias, we re-evaluated the effects of high- and low-molecular-weight glutenin alleles and puroindoline alleles on the grain quality parameters Rmax, dough extensibility, dough development time, flour water absorption, and milling yield and found that estimated effects were in close agreement with those from earlier analyses without a relationship matrix. We also evaluated, for the first time, the effects on the same quality parameters of 2 alleles (wild-type and null) of a defence grain protein, a serpin located on chromosome 5B. In addition, we assessed the effect of the VPM1 alien segment. The serpin null allele significantly reduced milling yield by ~0.4 g of flour per 100 g of grain milled across different germplasm sources and flour protein levels. In Australian germplasm, the origin of this allele was traced to a 19th Century introduction from India by William Farrer; however other sources, of significance in international breeding programs, were also identified. Our analysis of the effect of the VPM1 segment on quality traits revealed no detrimental effects of its presence on the traits we measured.

Trigenomic chromosomes by recombination of Thinopyrum intermedium and Th. ponticum translocations in wheat

Rusts and barley yellow dwarf virus (BYDV) are among the main diseases affecting wheat production world wide for which wild relatives have been the source of a number of translocations carrying resistance genes. Nevertheless, along with desirable traits, alien translocations often carry deleterious genes. We have generated recombinants in a bread wheat background between two alien translocations: TC5, ex-Thinopyrum (Th) intermedium, carrying BYDV resistance gene Bdv2; and T4m, ex-Th. ponticum, carrying rust resistance genes Lr19 and Sr25. Because both these translocations are on the wheat chromosome arm 7DL, homoeologous recombination was attempted in the double hemizygote (TC5/T4m) in a background homozygous for the ph1b mutation. The identification of recombinants was facilitated by the use of newly developed molecular markers for each of the alien genomes represented in the two translocations and by studying derived F(2), F(3) and doubled haploid populations. The occurrence of recombination was confirmed with molecular markers and bioassays on families of testcrosses between putative recombinants and bread wheat, and in F(2) populations derived from the testcrosses. As a consequence it has been possible to derive a genetic map of markers and resistance genes on these previously fixed alien linkage blocks. We have obtained fertile progeny carrying new tri-genomic recombinant chromosomes. Furthermore we have demonstrated that some of the recombinants carried resistance genes Lr19 and Bdv2 yet lacked the self-elimination trait associated with shortened T4 segments. We have also shown that the recombinant translocations are fixed and stable once removed from the influence of the ph1b. The molecular markers developed in this study will facilitate selection of individuals carrying recombinant Th. intermedium-Th. ponticum translocations (Pontin series) in breeding programs.

Genetic variability of carotenoid concentration and degree of esterification among tritordeum (xTritordeum Ascherson et Graebner) and durum wheat accessions

The higher carotenoid content (commonly referred as "yellow pigment content") of tritordeum seeds as compared to wheat and the potential of this species as a donor of useful traits to wheat led us to investigate the detailed carotenoid composition of 53 accessions of hexaploid tritordeums originating from different stages of the tritordeum breeding program developed at IAS-CSIC. In addition, seven durum wheat accessions were also studied for comparison. Lutein was the unique carotenoid detected, either free or esterified with fatty acids. On average, tritordeum had 5.2 times more carotenoids than durum wheat, which suggests a high potential of this species to become a functional food. In addition, the most outstanding result of this work is the high esterification degree of lutein found in tritordeums as compared to durum wheat. This difference may indicate the differential esterification ability between tritordeum and durum wheat species. The implications of this high level of lutein esterification on both carotenoid accumulation and stability are discussed.

Escherichia coli as a platform for functional expression of plant P450 carotene hydroxylases

Carotenoids and their derivatives are essential for growth, development, and signaling in plants and have an added benefit as nutraceuticals in food crops. Despite the importance of the biosynthetic pathway, there remain open questions regarding some of the later enzymes in the pathway. The CYP97 family of P450 enzymes was predicted to function in carotene ring hydroxylation, to convert provitamin A carotenes to non-provitamin A xanthophylls. However, substrate specificity was difficult to investigate directly in plants, which mask enzyme activities by a complex and dynamic metabolic network. To characterize the enzymes more directly, we amplified cDNAs from a model crop, Oryza sativa, and used functional complementation in Escherichia coli to test activity and specificity of members of Clans A and C. This heterologous system will be valuable for further study of enzyme interactions and substrate utilization needed to understand better the role of CYP97 hydroxylases in plant carotenoid biosynthesis.

New sources of rust resistance from alien species: meliorating linked defects and discovery

This paper presents a review of projects undertaken over the past 2 decades aimed at improving the yield and/or quality attributes of translocation lines carrying rust resistance genes from species related to wheat, so as to make these lines more suitable for use in breeding programs. Homeologous recombination between the alien chromosome segments and normal wheat chromosomes was induced in a ph1bph1b background. Lines with shortened alien chromatin were selected using dissociation patterns of molecular-based markers. A new line of bread wheat was developed containing a shortened chromosome 1RS segment carrying rust resistance gene SrR (Secale cereale L.), in which a defect affecting dough-quality appears to have been deleted. In addition, several advanced lines were produced with modified 6Ae#1L chromosome segments with Sr26 (Thinopyrum ponticum), 2S#1 chromosome segments with Sr32, and a previously unnamed gene, a 2S#2 chromosome segment with Sr39 (Triticum speltoides), 4G#1 chromosome segments with Sr37, and 2G#2 chromosome segments with Sr40 (T. timopheevii).

Cytogenetics in the age of molecular genetics

From the beginning of the 20th Century, we have seen tremendous advances in knowledge and understanding in almost all biological disciplines, including genetics, molecular biology, structural and functional genomics, and biochemistry. Among these advances, cytogenetics has played an important role. This paper details some of the important milestones of modern cytogenetics. Included are the historical role of cytogenetics in genetic studies in general and the genetics stocks produced using cytogenetic techniques. The basic biological questions cytogenetics can address and the important role and practical applications of cytogenetics in applied sciences, such as in agriculture and in breeding for disease resistance in cereals, are also discussed. The goal of this paper is to show that cytogenetics remains important in the age of molecular genetics, because it is inseparable from overall genome analysis. Cytogenetics complements studies in other disciplines within the field of biology and provides the basis for linking genetics, molecular biology and genomics research.

Challenges for sustainable cereal rust control in South Africa

The cultivation of small grain cereals was introduced to South Africa by Dutch settlers in the 17th Century. According to historical records the first documented epidemic of wheat stem rust occurred in the south-western parts of the current Western Cape in 1726. Recurring stem and leaf rust epidemics were associated with expanding wheat production and became particularly severe in the winter-rainfall regions of the Western and Eastern Cape, as well as in the summer-rainfall regions of the Free State. The wheat stripe rust pathogen was first detected in South Africa in 1996. Due to susceptibility of cultivars at the time of this exotic introduction, stripe rust has caused significant losses in commercial wheat production over the past 10 years. Pathotype surveys of Puccinia graminis and P. triticina were initiated in the 1920s, but were discontinued until research on wheat stem rust was resumed in the 1960s. Recent evidence has shown that P. graminis f. sp. tritici continues to evolve. In addition, the annual number of wheat stem rust collections is increasing, emphasising the sustained threat of this damaging pathogen. A stem rust pathotype first detected in 2000, with newly acquired virulence for Sr8b and Sr38, currently constitutes more than 80% of all collections. Leaf and stem rust diseases also occur on barley, oat, triticale, and rye and are important production constraints in several regions. Some studies have described variability in these pathogens but long-term records of pathogenicity changes in barley and oat rust are not available. Cereal rust diseases have clearly played an important role in South African agriculture and many production regions remain favourable for rust development. Current expertise in cereal rusts covers most technologies necessary to study the respective host–pathogen systems. However, a general lack of capacity and fragmentation of research groups prevent a unified approach and remain a challenge for sustainable cereal rust control in South Africa. A national strategy for cereal rust control, with particular emphasis on pathogen and host resources, and breeding for resistance, is urgently needed.

The development of a PCR-based marker for PSY1 from Hordeum chilense, a candidate gene for carotenoid content accumulation in tritordeum seeds

Hexaploid tritordeums are the amphiploids derived from the cross between the wild barley Hordeum chilense and durum wheat. Tritordeums are characterised by higher yellow pigment content in their seeds than their durum wheat progenitors due to certain H. chilense genes located on the α arm of chromosome 7Hch. In this work a candidate gene approach based on the phytoene synthase gene (PSY) was followed to investigate whether PSY1 may be responsible for the high carotenoid content in tritordeum and to develop a diagnostic marker for H. chilense PSY. This gene codes for the first step in the carotenoid biosynthetic pathway. It was first demonstrated that PSY is duplicated in H. chilense, Triticum urartu, and durum wheat (PSY1 and PSY2), and subsequently a diagnostic cleaved amplified polymorphism (CAP) marker able to differentiate between H. chilense and durum wheat PSY1 was developed. Using this CAP marker and a set of H. chilense-common wheat addition lines it was found that PSY1 is located on the α arm of chromosome 7Hch, where the gene(s) for yellow pigment content are located. PSY1 is located on chromosomes 7A and 7B of durum wheat as demonstrated using Langdon substitution lines. Furthermore, synteny between rice and wheat indicates that PSY1 should be located on the long arms of chromosomes 7A and 7B, in agreement with QTL data for yellow pigment content. Together, these results suggest that PSY1 may be a good candidate gene for further work with yellow pigment content in both durum wheat and tritordeum. In addition, the diagnostic CAP marker developed will be used in our breeding program to transfer H. chilense genes to durum wheat, to evaluate their potential for durum wheat improvement.