Identification of a microsatellite on chromosome 7B showing a strong linkage with yellow pigment in durum wheat (Triticum turgidum L. var. durum)

The Combining Ability and Heterosis Analysis of Sweet-Waxy Corn Hybrids for Yield-Related Traits and Carotenoids

Improving sweet-waxy corn hybrids enriched in carotenoids via a hybrid breeding approach may provide an alternative cash crop for growers and provide health benefits for consumers. This study estimates the combining ability and heterosis of sweet-waxy corn hybrids for yield-related traits and carotenoids. Eight super sweet corn and three waxy corn lines were crossed to generate 24 F1 hybrids according to the North Carolina Design II scheme, and these hybrids were evaluated across two seasons of 2021/22. The results showed that both additive and non-additive genetic effects were involved in expressing the traits, but the additive genetic effect was more predominant. Most observed traits exhibited moderate to high narrow-sense heritability. Three parental lines, namely the ILS2 and ILS7 females and the ILW1 male, showed the highest positive GCA effects on yield-related traits, making them desirable for developing high-yielding hybrids. Meanwhile, five parental lines, namely the ILS3, ILS5, and ILS7 females and the ILW1 and ILW2 males, were favorable general combiners for high carotenoids. A tested hybrid, ILS2 × ILW1, was a candidate biofortified sweet-waxy corn hybrid possessing high yields and carotenoids. Heterosis and per se performance were more positively correlated with GCAsum than SCA, indicating that GCAsum can predict heterosis for improving biofortified sweet-waxy corn hybrid enriched in carotenoids. The breeding strategies of biofortified sweet-waxy corn hybrids with high yield and carotenoid content are discussed.

Development, results and prospects of the spring durum wheat breeding in Russia (post-Soviet states)

The article outlines a brief historical background on the introduction to cultivation, distribution and breeding of spring durum wheat in the steppe and forest-steppe regions of Eurasia (the countries of the former USSR: Russia, Ukraine, and Kazakhstan). The approaches and methodology for improving durum wheat during certain scientific selection periods are given. The features of the selection program implementation and the breeding scale expansion during the creation of breeding stations at the beginning of the XX century, after the end of the Great Patriotic War, in the second half of the XX century, and at present are considered. A characteristic according to the main features and properties of varieties created in different periods is given. The achievements of the classical breeding method by comparing old and new varieties are analyzed. The efficiency and rate of wheat selection by periods in different regions of Russia is estimated. The results and methods of breeding for yield, resistance to drought, leaf diseases (Stagonospora nodorum Berk., Septoria tritici (Roeb. et Desm.), Bipolaris sorokiniana (Sacc.) Shoemaker, Pyrenophora tritici repentis (Died.) Drechs., Fusarium sp., Puccinia titicina Eriks., Puccinia graminis Pers. f. sp. tritici Eriks., Blumeria graminis (DC.) f. sp. tritici Em. Marchal), grain pathogens Ustilago tritici (Pers.) Rostr.) and pathogens causing darkening of the corcule and endosperm (Bipolaris sorokiniana (Sacc.) Shoemaker, Alternaria tenuis (Nees et Fr.), Аlternaria triticina (Prasada & Prabhu)), pests (Cephus pygmeus Lens, Osinosoma frit L., Mayetiola destructor (Say)), grain quality (protein content, amount of yellow pigments, dough rheology, sprouting resistance) and end products are presented. The prospects for the molecular marker application for a number of traits in breeding in the near future are given.

Bread Wheat Biofortification for Grain Carotenoid Content by Inter-Specific Breeding

Bread wheat has traditionally been selected for whitish derived flours. As a consequence, the current varieties carry carotenogenic alleles associated with low grain carotenoid. In contrast, high grain yellow pigment content (YPC) has been a major target in durum wheat programs since yellow colour is an important aesthetic factor for pasta production. Phytoene synthase 1 (Psy1) genes have an important role in the determination of the carotenoid content in wheat. In this work, we have transferred the genes Psy1-A1 and Psy1-B1 from durum to bread wheat by inter-specific hybridization in order to evaluate the combined effect of these genes for the improvement of grain carotenoid content, as well as the development of carotenoid-enriched bread wheat lines. Inter-specific breeding coupled with a MAS approach based on Psy1-A1 and Psy1-B1 alleles has allowed the development of bread wheat pre-breeding lines with enhanced grain carotenoid content (16-23% mean). These biofortified lines have the potential to become new varieties or to be used as recurrent parents in bread wheat breeding programs.

Marker-Trait Associations for Total Carotenoid Content and Individual Carotenoids in Durum Wheat Identified by Genome-Wide Association Analysis

Yellow pigment content is one of the main traits considered for grain quality in durum wheat (Triticum turgidum L.). The yellow color is mostly determined by carotenoid pigments, lutein being the most abundant in wheat endosperm, although zeaxanthin, α-carotene and β-carotene are present in minor quantities. Due to the importance of carotenoids in human health and grain quality, modifying the carotenoid content and profile has been a classic target. Landraces are then a potential source for the variability needed for wheat breeding. In this work, 158 accessions of the Spanish durum wheat collection were characterized for carotenoid content and profile and genotyped using the DArTSeq platform for association analysis. A total of 28 marker-trait associations were identified and their co-location with previously described QTLs and candidate genes was studied. The results obtained confirm the importance of the widely described QTL in 7B and validate the QTL regions recently identified by haplotype analysis for the semolina pigment. Additionally, copies of the Zds and Psy genes on chromosomes 7B and 5B, respectively, may have a putative role in determining zeaxanthin content. Finally, genes for the methylerythritol 4-phosphate (MEP) and isopentenyl diphosphate (IPPI) carotenoid precursor pathways were revealed as additional sources of untapped variation for carotenoid improvement.

A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.)

The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.

Tritordeum: Creating a New Crop Species-The Successful Use of Plant Genetic Resources

Hexaploid tritordeum is the amphiploid derived from the cross between the wild barley Hordeum chilense and durum wheat. This paper reviews the main advances and achievements in the last two decades that led to the successful development of tritordeum as a new crop. In particular, we summarize the progress in breeding for agronomic performance, including the potential of tritordeum as a genetic bridge for wheat breeding; the impact of molecular markers in genetic studies and breeding; and the progress in quality and development of innovative food products. The success of tritordeum as a crop shows the importance of the effective utilization of plant genetic resources for the development of new innovative products for agriculture and industry. Considering that wild plant genetic resources have made possible the development of this new crop, the huge potential of more accessible resources, such as landraces conserved in gene banks, goes beyond being sources of resistance to biotic and abiotic stresses. In addition, the positive result of tritordeum also shows the importance of adequate commercialization strategies and demonstrative experiences aimed to integrate the whole food chain, from producers to end-point sellers, in order to develop new products for consumers.

[The content of yellow pigments in durum wheat (Titicum durum Desf.) grains: biosynthesis, genetic control, marker selection]

Зерно с высоким содержанием каротиноидных пигментов ценится за ярко-желтый цвет пасты, производимой из него, и провитаминную (витамин А) и антиоксидантную активность пигментов. Цель настоя- щего обзора – обобщение современных знаний о биосинтезе и генетическом контроле накопления пигментов в зерне твердой пшеницы и оценка основных результатов исследований и селекции за последние двадцать лет за рубежом и в России. Признак «концентрация каротиноидных пигментов в зерне» (Ypc) относится к раз- ряду количественных. Тем не менее превалирование сильных аддитивных эффектов генов и высокая насле- дуемость способствовали значительному прогрессу в селекции по этому признаку. Методами молекулярного маркирования локусов количественных признаков (QTL), контролирующих синтез каротиноидных пигментов и значения индекса желтизны (IY), установлено их распределение по всем хромосомам генома твердой пшеницы. Основные генетические локусы, определяющие более 60 % варьирования признака, были картированы в хромосомах 7AL и 7BL. Вклад этих локусов связан с аллельными вариациями, влияющими на активность фермента фитоенсинтетазы (PSY). В других хромосомах были локализованы минорные генетические факторы, из которых наиболее значимы QTL, расположенные в хромосомах 3AS (ассоциирован с геном LCYE-ликопин- ε-циклаза) и 4ВS (аллель Lpx-B1.1c). При этом показано, что аллель Lpx-B1.1c вносит вклад в снижение актив- ности липоксигеназы, окисляющей каротиноиды в процессе изготовления конечных продуктов. Рассмотрены и обсуждены проблемы использования молекулярных маркеров в селекционных программах, нацеленных на увеличение концентрации пигментов в зерне и улучшение цветовых характеристик пасты.

Genomics-Integrated Breeding for Carotenoids and Folates in Staple Cereal Grains to Reduce Malnutrition

Globally, two billion people suffer from micronutrient deficiencies. Cereal grains provide more than 50% of the daily requirement of calories in human diets, but they often fail to provide adequate essential minerals and vitamins. Cereal crop production in developing countries achieved remarkable yield gains through the efforts of the Green Revolution (117% in rice, 30% in wheat, 530% in maize, and 188% in pearl millet). However, modern varieties are often deficient in essential micronutrients compared to traditional varieties and land races. Breeding for nutritional quality in staple cereals is a challenging task; however, biofortification initiatives combined with genomic tools increase the feasibility. Current biofortification breeding activities include improving rice (for zinc), wheat (for zinc), maize (for provitamin A), and pearl millet (for iron and zinc). Biofortification is a sustainable approach to enrich staple cereals with provitamin A, carotenoids, and folates. Significant genetic variation has been found for provitamin A (96-850 μg and 12-1780 μg in 100 g in wheat and maize, respectively), carotenoids (558-6730 μg in maize), and folates in rice (11-51 μg) and wheat (32.3-89.1 μg) in 100 g. This indicates the prospects for biofortification breeding. Several QTLs associated with carotenoids and folates have been identified in major cereals, and the most promising of these are presented here. Breeding for essential nutrition should be a core objective of next-generation crop breeding. This review synthesizes the available literature on folates, provitamin A, and carotenoids in rice, wheat, maize, and pearl millet, including genetic variation, trait discovery, QTL identification, gene introgressions, and the strategy of genomics-assisted biofortification for these traits. Recent evidence shows that genomics-assisted breeding for grain nutrition in rice, wheat, maize, and pearl millet crops have good potential to aid in the alleviation of micronutrient malnutrition in many developing countries.

Carotenoid Pigment Content in Durum Wheat (Triticum turgidum L. var durum): An Overview of Quantitative Trait Loci and Candidate Genes

Carotenoid pigment content is an important quality trait as it confers a natural bright yellow color to pasta preferred by consumers (whiteness vs. yellowness) and nutrients, such as provitamin A and antioxidants, essential for human diet. The main goal of the present review is to summarize the knowledge about the genetic regulation of the accumulation of pigment content in durum wheat grain and describe the genetic improvements obtained by using breeding approaches in the last two decades. Although carotenoid pigment content is a quantitative character regulated by various genes with additive effects, its high heritability has facilitated the durum breeding progress for this quality trait. Mapping research for yellow index and yellow pigment content has identified quantitative trait loci (QTL) on all wheat chromosomes. The major QTL, accounting for up to 60%, were mapped on 7L homoeologous chromosome arms, and they are explained by allelic variations of the phytoene synthase (PSY) genes. Minor QTL were detected on all chromosomes and associated to significant molecular markers, indicating the complexity of the trait. Despite there being currently a better knowledge of the mechanisms controlling carotenoid content and composition, there are gaps that require further investigation and bridging to better understand the genetic architecture of this important trait. The development and the utilization of molecular markers in marker-assisted selection (MAS) programs for improving grain quality have been reviewed and discussed.

Pasta-Making Quality QTLome From Mediterranean Durum Wheat Landraces

In order to identify genome regions related to pasta-making quality traits, association mapping (AM) was performed in a set of 165 durum wheat landraces from 21 Mediterranean countries. The collection was genotyped using 1149 DArT markers and 872 of them with a known genetic position were used for AM. The collection was grown in north-east Spain during 3 years. Results of ANOVA showed that trait variation for quality traits, except for grain protein content (GPC), was mainly explained by genetic effects. Landraces showed higher GPC than modern cultivars but lower gluten strength (GS). Modern and eastern landraces showed the highest yellow color index (YI). Balkan landraces showed the lowest test weight (TW). A total of 92 marker-trait associations were detected, 20 corresponding to GS, 21 to GPC, 21 to YI and 30 to TW. With the aim of detecting new genomic regions involved in grain quality, the position of the associations was compared with previously mapped QTL by a meta-QTL analysis. A total of 249 QTLs were projected onto the same map used for AM, identifying 45 meta-QTL (MQTL) regions and the remaining 15 QTLs as singletons. The position of known genes involved in grain quality was also included, and gene annotation within the most significant regions detected by AM was carried out using the wheat genome sequence.

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.

Evaluation of 19,460 Wheat Accessions Conserved in the Indian National Genebank to Identify New Sources of Resistance to Rust and Spot Blotch Diseases

A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat-Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011-14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.

Carotenoids in Staple Cereals: Metabolism, Regulation, and Genetic Manipulation

Carotenoids play a critical role in animal and human health. Animals and humans are unable to synthesize carotenoids de novo, and therefore rely upon diet as sources of these compounds. However, major staple cereals often contain only small amounts of carotenoids in their grains. Consequently, there is considerable interest in genetic manipulation of carotenoid content in cereal grain. In this review, we focus on carotenoid metabolism and regulation in non-green plant tissues, as well as genetic manipulation in staple cereals such as rice, maize, and wheat. Significant progress has been made in three aspects: (1) seven carotenogenes play vital roles in carotenoid regulation in non-green plant tissues, including 1-deoxyxylulose-5-phosphate synthase influencing isoprenoid precursor supply, phytoene synthase, β-cyclase, and ε-cyclase controlling biosynthesis, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase and carotenoid cleavage dioxygenases responsible for degradation, and orange gene conditioning sequestration sink; (2) provitamin A-biofortified crops, such as rice and maize, were developed by either metabolic engineering or marker-assisted breeding; (3) quantitative trait loci for carotenoid content on chromosomes 3B, 7A, and 7B were consistently identified, eight carotenogenes including 23 loci were detected, and 10 gene-specific markers for carotenoid accumulation were developed and applied in wheat improvement. A comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops will be beneficial in improving our precision in improving carotenoid contents. Genomic selection and gene editing are emerging as transformative technologies for provitamin A biofortification.

Genome-wide linkage mapping of flour color-related traits and polyphenol oxidase activity in common wheat

KEY MESSAGE

Fifty-six QTL for flour color-related traits and polyphenol oxidase activity were identified using a genome-wide linkage mapping of data from a RIL population derived from a Gaocheng 8901/Zhoumai 16 cross.

ABSTRACT

Flour color-related traits, including L*, a*, b*, yellow pigment content (YPC), and polyphenol oxidase (PPO) activity are important parameters influencing the quality of wheat end-use products. Mapping quantitative trait loci (QTL) for these traits and characterization of candidate genes are important for improving wheat quality. The aims of this study were to identify QTL for flour color-related traits and PPO activity and to characterize candidate genes using a high-density genetic linkage map in a common wheat recombinant inbred line (RIL) population derived from a cross between Gaocheng 8901 and Zhoumai 16. A linkage map was constructed by genotyping the RILs with the wheat 90 K iSelect array. Fifty-six QTL were mapped on 35 chromosome regions on homoeologous groups 1, 2, 5 and 7 chromosomes, and chromosomes 3B, 4A, 4B and 6B. Four QTL were for PPO activity, and the others were for flour color-related traits. Compared with previous studies, five QTL for a*, two for b*, one for L*, one for YPC and one for PPO activity were new. The new QTL on chromosome 2DL was involved in both a* and YPC, and another on chromosome 7DS affected both a* and L*. The scan for SNP sequences tightly linked to QTL for flour color-related traits against the wheat and/or related cereals genomes identified six candidate genes significantly related to these traits, and five of them were associated with the terpenoid backbone biosynthesis pathway. The high-density genetic linkage map of Gaocheng 8901/Zhoumai 16 represents a useful tool to identify QTL for important quality traits and candidate genes.

Screening of SSR markers associated with scale cover pattern and mapped to a genetic linkage map of common carp (Cyprinus carpio L.)

Fish scale is an attractive model in bone physiology research and is also a crucial character for breeding new varieties. Thus, it is important to identify loci in the genome associated with scale formation. In this study, 290 microsatellite markers in common carp (Cyprinus carpio L.) were selected and tested for their segregation in a full-sib mapping panel containing 96 individuals (population 1). Association analysis identified seven simple sequence repeats (SSRs) (HLJ2509, HLJ3227, HLJ3675, HLJ3766, HLJ3863, FGFR1, FGFR7) that showed significant correlation with scale cover pattern in population 1. When the seven SSRs were investigated in two other populations, seven and five SSRs were significantly correlated with scale cover pattern in population 2 (116 individuals) and population 3 (57 individuals), respectively. The exceptions were FGFR1 and HLJ3227. A genetic linkage map was constructed using the 290 SSRs and 241 SSRs were mapped into 47 linkage groups (LGs), with 2-15 markers per LG. The map spanned 2,241.7 cM, with LG sizes that varied from 1.1 to 124.9 cM. All seven markers associated with scale cover mapped into LG3. We considered that a gene cluster that affected the scale cover pattern possibly existed in LG3. By aligning the seven markers with the zebrafish (Danio rerio) genome, we identified six candidate genes (atoh1a, ptch1, bmp1a, fgfr1a, fgf17, wnt5a) that may be associated with scale formation. We propose that the seven markers could be used with marker-assisted selection to breed a new variety of common carp, and the six candidate genes could help in understanding the scale cover mechanism.

Genetic variability in anthocyanin composition and nutritional properties of blue, purple, and red bread (Triticum aestivum L.) and durum (Triticum turgidum L. ssp. turgidum convar. durum) wheats

Renewed interest in breeding for high anthocyanins in wheat (Triticum ssp.) is due to their antioxidant potential. A collection of different pigmented wheats was used to investigate the stability of anthocyanins over three crop years. The data show higher anthocyanins in blue-aleurone bread wheat (Triticum aestivum L.), followed by purple- and red-pericarp durum wheat (Triticum turgidum L. ssp. turgidum convar. durum), using cyanidin 3-O-glucoside as standard. HPLC of the anthocyanin components shows five to eight major anthocyanins for blue wheat extracts, compared to three anthocyanins for purple and red wheats. Delphinidin 3-O-rutinoside, delphinidin 3-O-glucoside, and malvidin 3-O-glucoside are predominant in blue wheat, with cyanidin 3-O-glucoside, peonidin 3-O-galactoside, and malvidin 3-O-glucoside in purple wheat. Of the total anthocyanins, 40-70% remain to be structurally identified. The findings confirm the high heritability for anthocyanins, with small genotype × year effects, which will be useful for breeding purposes, to improve the antioxidant potential of cereal-based foods.

Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses

BACKGROUND

Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3) that have been widely characterized in rice, maize and sorghum.

RESULTS

In wheat, for which yellow pigment content is extremely important for flour colour, only PSY1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY2 has been partially characterized. Here, we report the isolation of bread wheat PSY3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing. Wheat PSY3 homoeologous genes were sequenced and annotated, unravelling their novel structure associated with intron-loss events and consequent exonic fusions. A wheat PSY3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid (ABA), since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses. Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY3 during abiotic stress.

CONCLUSIONS

We investigated the structural and functional determinisms of PSY genes in wheat. More generally, among eudicots and monocots, the PSY gene family was found to be associated with differences in gene copy numbers, allowing us to propose an evolutionary model for the entire PSY gene family in Grasses.

Functional relationships of phytoene synthase 1 alleles on chromosome 7A controlling flour colour variation in selected Australian wheat genotypes

Flour colour measured as a Commission Internationale de l'Eclairage (CIE) b* value is an important wheat quality attribute for a range of end-products, with genes and enzymes of the xanthophyll biosynthesis pathway providing potential sources of trait variation. In particular, the phytoene synthase 1 (Psy1) gene has been associated with quantitative trait loci (QTL) for flour b* colour variation. Several Psy1 alleles on chromosome 7A (Psy-A1) have been described, along with proposed mechanisms for influencing flour b* colour. This study sought to identify evolutionary relationships among known Psy-A1 alleles, to establish which Psy-A1 alleles are present in selected Australian wheat genotypes and establish their role in controlling variation for flour b* colour via QTL analysis. Phylogenetic analyses showed seven of eight known Psy-A1 alleles clustered with sequences from T. urartu, indicating the majority of alleles in Australian germplasm share a common evolutionary lineage. In this regard, Psy-A1a, Psy-A1c, Psy-A1e and Psy-A1p were common in Australian genotypes with flour b* colour ranging from white to yellow. In contrast Psy-A1s was found to be related to A. speltoides, indicating a possible A-B genome translocation during wheat polyploidisation. A new allele Psy-A1t (similar to Psy-A1s) was discovered in genotypes with yellow flour, with QTL analyses indicating Psy-A1t strongly influences flour b* colour in Australian germplasm. QTL LOD value maxima did not coincide with Psy-A1 gene locus in two of three populations and, therefore, Psy-A1a and Psy-A1p may not be involved in flour colour. Instead two other QTL were identified, one proximal and one distal to Psy-A1 in Australian wheat lines. Comparison of Psy-A1t and Psy-A1p predicted protein sequences suggests differences in putative sites for post-translational modification may influence enzyme activity and subsequent xanthophyll accumulation in the wheat endosperm. Psy-A1a and Psy-A1p were not involved in flour b* colour variation, indicating other genes control variation on chromosome 7A in some wheat genotypes.

Insight into durum wheat Lpx-B1: a small gene family coding for the lipoxygenase responsible for carotenoid bleaching in mature grains

BACKGROUND

The yellow colour of pasta products is one of the main criteria used by consumers to assess pasta quality. This character is due to the presence of carotenoid pigments in semolina. During pasta processing, oxidative degradation of carotenoid pigments occurs mainly due to lipoxygenase (LOX). In durum wheat (Triticum durum Desf.), two Lpx-1 genes have been identified on chromosome 4B, Lpx-B1.1 and Lpx-B1.2, and evidences have been reported that the deletion of Lpx-B1.1 is associated with a strong reduction in LOX activity in semolina. In the present study, we characterised the Lpx-B1 gene family identified in a durum wheat germplasm collection and related the distribution and expression of the Lpx-B1 genes and alleles to variations in LOX activity in the mature grains.

RESULTS

In addition to the already known Lpx-B1.1 and Lpx-B1.2 genes, a new gene was identified, Lpx-B1.3, along with three different Lpx-B1.1 alleles, Lpx-B1.1a, Lpx-B1.1b and the partially deleted Lpx-B1.1c. Screening of the germplasm collection showed that all of the genotypes have one of the three Lpx-B1.1 alleles, associated with either Lpx-B1.2 or Lpx-B1.3, thus showing that in this collection the two genes are alternatives. Therefore, based on Lpx-B1 distribution, three different haplotypes were distinguished: haplotype I, carrying Lpx-B1.3 and the Lpx-B1.1b allele; haplotype II carrying Lpx-B1.2 and the Lpx-B1.1a allele; and haplotype III carrying Lpx-B1.2 and the Lpx-B1.1c allele. Determination of Lpx-B1 transcript abundance and total LOX activity in mature grains revealed differences among these three haplotypes: haplotypes I, II and III showed high, intermediate and low levels, respectively, of functional Lpx-B1 transcripts and enzymatic activity.

CONCLUSIONS

In this germplasm collection, the Lpx-B1 gene family accounts for most of the total LOX activity in the mature grains. Information on these Lpx-B1 haplotypes provides significant improvement for prediction of LOX-1 activity levels in mature grains, and will therefore help in breeding programmes aimed at selection of new durum wheat genotypes with higher carotenoid contents in their end products.

cDNA cloning and expression analysis of wheat (Triticum aestivum L.) phytoene and ζ-carotene desaturase genes

Carotene desaturation, an essential step in the carotenoid biosynthesis pathway, is catalyzed by two carotene desaturases, phytoene desaturase (PDS) and ζ-carotene desaturase (ζ-carotene desaturase, ZDS). Full-length cDNAs designated TaPDS and TaZDS were cloned from wheat (Triticum aestivum cv. Chinese Spring) respectively, using the rapid amplification of cDNA ends (RACE) approach. The cDNA of TaPDS sequence was 2076 bp long, containing a 1731 bp open reading frame (ORF) which deduced protein having 576 amino acid residues with predicted molecular mass of 64.3 kDa and having a putative transit sequence for plastid targeting in the N-terminal region. While the cDNA sequence of TaZDS was 2150 bp long, contained an ORF sequence of 1707 bp, and encoded a putative protein of 568 amino acid residues with an estimated molecular mass of 62.5 kDa. Phylogenetic analysis demonstrated that TaPDS and TaZDS showed high homology with other PDSs and ZDSs in higher plant species, respectively. Moreover, sequences analysis also showed a high degree of conservation among plant PDSs and ZDSs. The deduced TaPDS and TaZDS protein both have the dinucleotide binding domain and conserved regions characteristic of other carotene desaturases. Analysis of the expression pattern of wheat TaPDS and TaZDS in different tissues revealed that the transcripts levels were higher in leaves and flowers petals, followed by in inflorescences, and were nearly absent in the roots and seeds. Southern analysis of genomic DNA indicated that the wheat TaPDS and TaZDS probably belong to a low-copy-number gene family.

Chromosomal location of the cadmium uptake gene (Cdu1) in durum wheat

Levels of the heavy metal cadmium (Cd) in food products are a food safety concern. Grain Cd is higher in durum (Triticum turgidum L. var. durum) than in common wheat, so reduction of Cd in durum grain is a priority of breeding programs. Previous research demonstrated that a single dominant gene, Cdu1, confers the low grain Cd phenotype, but the map location of the gene is not known. A doubled haploid population segregating for Cd concentration, developed from the cross of W9262-260D3 (a Kyle*2/Biodur inbred selection with low Cd uptake) and Kofa (high Cd uptake) and mapped with microsatellite markers, was used to locate Cdu1. Grain Cd concentration was determined by standard laboratory methods on field grain samples in 2000 and 2001. The Cd concentration segregated bimodally, allowing Cdu1 to be mapped qualitatively as well as quantitatively with quantitative trait locus analysis. The Cdu1 gene mapped to the long arm of chromosome 5B.

Allelic variation at Psy1-A1 and association with yellow pigment in durum wheat grain

The yellow pigment (YP) of durum wheat (Triticum turgidum L. var durum) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait. Phytoene synthase (Psy) is considered a rate-limiting enzyme in the carotenoid biosynthetic pathway and in this study, three alleles of Psy1-A1 were sequenced from four durum wheat cultivars and a co-dominant marker was developed for genetic mapping. Psy1-A1 mapped to chromosome 7AL near Xwmc809 in three durum mapping populations and was significantly associated with a pigment quantitative trait loci (QTL) identified on that chromosome. A second QTL localized 25 cM proximal to Psy1-A1 in two populations, and the interaction between the two QTL was not significant. Consistent with QTL mapping data, the Psy1-A1o allele was associated with elevated pigment in a validation population comprising 93 diverse cultivars and breeding lines. These results confirm an earlier hypothesis that Psy1, and at least one additional gene in the distal region of 7AL, are associated with grain YP differences in durum wheat. The functional co-dominant marker developed in this study differentiates the Psy1-A1 alleles reported here and could be used as a target to enhance YP selection in durum wheat breeding programs.

Association mapping of yellow pigment in an elite collection of durum wheat cultivars and breeding lines

Association mapping (AM) is an alternative or complementary strategy to QTL mapping for describing associations between genotype and phenotype based on linkage disequilibrium (LD). Yellow pigment (YP), an important end-use quality trait in durum wheat (Triticum turgidum L. var. durum), was evaluated to determine the ability of AM to identify previously published QTL and to identify genomic regions for further genetic dissection. The YP concentration was determined for 93 durum wheat accessions sampled from a variety of geographic origins. Analysis of population structure using distance- and model-based estimates indicated the presence of five subpopulations. Using subpopulation assignments as covariates, significant (P < 0.05) marker-trait associations for YP were detected on all chromosomes of the durum genome. Using AM, genomic regions housing known YP QTL were confirmed, most notably the group 7 chromosomes. In addition, several markers on the group 1, 2, and 3 chromosomes were identified where QTL have yet to be reported. A phytoene synthase gene, Psy1-B1, a potential candidate gene for YP, was significantly associated with YP and was in strong LD with microsatellite markers on the distal end of 7BL. Our results demonstrated that AM complemented traditional QTL mapping techniques and identified novel QTL that should be the target of further genetic dissection.

Alternative splicing, activation of cryptic exons and amino acid substitutions in carotenoid biosynthetic genes are associated with lutein accumulation in wheat endosperm

Endosperm carotenoid content in wheat is a primary determinant of flour colour and this affects both the nutritional value of the grain and its utility for different applications. Utilising wheat rice synteny two genes, epsilon-cyclase (epsilon-LCY) and phytoene synthase (Psy-A1), were identified as candidate genes for two of the QTL affecting lutein content in wheat endosperm. Analysis of the sequence changes in epsilon-LCY and Psy-A1 revealed possible causal mechanisms for both QTL. A point mutation in epsilon-LCY results in the substitution of a conserved amino acid in the high lutein allele. This substitution has been observed in high lutein-accumulating species from the Gentiales order. In Psy-A1, a sequence duplication at the end of exon 2 creates a new splice site and causes alternative splicing of the transcript and activation of a cryptic exon, resulting in four different transcripts: a wild-type transcript, two transcripts with early terminations and a transcript that would produce an in-frame, albeit longer protein. Only the wild-type splice variant produced an enzymatically active protein and its mRNA abundance was reduced by titration with the other splice variants. This reduction in wild-type mRNA is argued to result in a reduction in PSY protein and thus carotenoid content in wheat.

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.

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.

Identification and Molecular Characterization of Leaf Rust Resistance Gene Lr14a in Durum Wheat

Leaf rust, caused by Puccinia triticina, is an important disease of durum wheat (Triticum turgidum subsp. durum) and only a few designated resistance genes are known to occur in this crop. A dominant leaf rust resistance gene in the Chilean durum cv. Llareta INIA was mapped to chromosome arm 7BL through bulked segregant analysis using the amplified fragment length polymorphism (AFLP) technique, and by mapping three polymorphic markers in the common wheat (T. aestivum) International Triticeae Mapping Initiative population. Several simple sequence repeat (SSR) markers, including Xgwm344-7B and Xgwm146-7B, were associated with the leaf rust resistance gene. Resistance response and chromosomal position indicated that this gene is likely to be Lr14a. The SSR markers Xgwm344-7B and Xgwm146-7B and one AFLP marker also differentiated common wheat cv. Thatcher from the near-isogenic line with Lr14a, as well as durum 'Altar C84' from durum wheat with Lr14a. This is the first report of the presence of Lr14a in durum wheat, although the gene originally was transferred from emmer wheat 'Yaroslav' to common wheat. Lr14a is also present in CIMMYT-derived durum 'Somateria' and effective against Mexican and other P. triticina races of durum origin. Lr14a should be deployed in combination with other effective leaf rust resistance genes to prolong its effectiveness in durum wheat.

Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker

Phytoene synthase (Psy), a critical enzyme in the carotenoid biosynthetic pathway, demonstrated high association with the yellow pigment (YP) content in wheat grain. Characterization of Psy genes and the development of functional markers for them are of importance for marker-assisted selection in wheat breeding. In this study, the full-length genomic DNA sequence of a Psy gene (Psy-A1) located on chromosome 7A, was characterized by in silico cloning and experimental validation. The cloned Psy-A1 comprises six exons and five introns, 4,175 bp in total, and an ORF of 1,284 bp. A co-dominant marker, YP7A, was developed based on polymorphisms of two haplotypes of Psy-A1, yielding 194 and 231-bp fragments in cultivars with high and low YP content, respectively. The marker YP7A was mapped on chromosome 7AL using an RIL population from cross PH82-2/Neixing 188, and a set of Chinese Spring nullisomic-tetrasomic lines and ditelosomic line 7AS. Psy-A1, co-segregating with the STS marker YP7A, was linked to SSR marker Xwmc809 on chromosome 7AL with a genetic distance of 5.8 cM, and explained 20-28% of the phenotypic variance for YP content across three environments. A total of 217 Chinese wheat cultivars and advanced lines were used to validate the association between the polymorphic band pattern and grain YP content. The results showed that the functional marker YP7A was closely related to grain YP content and, therefore, could be used in wheat breeding programs targeting of YP content for various wheat-based products.

Identification of QTL and association of a phytoene synthase gene with endosperm colour in durum wheat

The yellow colour of durum wheat (Triticum turgidum L. var durum) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait. We hypothesized that variation in the genes coding for phytoene synthase (Psy), a critical enzyme in carotenoid biosynthesis, may partially explain the phenotypic variation in endosperm colour observed among durum cultivars. Using rice sequence information, primers were designed to PCR clone and sequence the Psy genes from Kofa (high colour) and W9262-260D3 (medium colour) durum cultivars. Sequencing confirmed the presence of four Psy genes in each parent, corresponding to a two member gene family designated as Psy1-1, Psy1-2 and Psy2-1 and Psy2-2. A genetic map was constructed using 155 F1-derived doubled haploid lines from the cross W9262-260D3/Kofa with 194 simple sequence repeat and DArT markers. Using Psy1-1 and Psy2-1 allele-specific markers and chromosome mapping, the Psy1 and Psy2 genes were located to the group 7 and 5 chromosomes, respectively. Four quantitative trait loci (QTL) underlying phenotypic variation in endosperm colour were identified on chromosomes 2A, 4B, 6B, and 7B. The Psy1-1 locus co-segregated with the 7B QTL, demonstrating an association of this gene with phenotypic variation for endosperm colour. This work is the first report of mapping Psy genes and supports the role of Psy1-1 in elevated levels of endosperm colour in durum wheat. This gene is a target for the further development of a molecular marker to enhance selection for endosperm colour in durum wheat breeding programs.

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.

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

Chromosome 7E from Lophopyrum ponticum carries a valuable leaf rust resistant gene designated Lr19. This gene has not been widely used in common wheat breeding because of linkage with the yellow pigment gene Y. This gene tints flour yellow, reducing its appeal in bread making. However, a high level of yellow pigment is desirable in durum wheat breeding. We produced 97 recombinant chromosomes between L. ponticum transfer 7D.7E#1 and its wheat homoeologues, using the ph1b mutation that promotes homoeologous pairing. We characterized a subset of 37 of these lines with 11 molecular markers and evaluated their resistance to leaf rust and the abundance of yellow pigment. The Lr19 gene was mapped between loci Xwg420 and Xmwg2062, whereas Y was mapped distal to Xpsr687, the most distal marker on the long arm of chromosome 7. A short terminal 7EL segment translocated to 7A, including Lr19 and Y (line 1-23), has been transferred to durum wheat by backcrossing. The presence of this alien segment significantly increased the abundance of yellow pigment. The Lr19 also conferred resistance to a new durum leaf rust race from California and Mexico that is virulent on most durum wheat cultivars. The new durum lines with the recombinant 7E segment will be useful parents to increase yellow pigment and leaf rust resistance in durum wheat breeding programs. For the common wheat breeding programs, we selected the recombinant line 1-96, which has an interstitial 7E segment carrying Lr19 but not Y. This recombinant line can be used to improve leaf rust resistance without affecting flour color. The 7EL/7DL 1-96 recombinant chromosome did not show the meiotic self-elimination previously reported for a 7EL/7BL translocation.

PCR identification of durum wheat BAC clones containing genes coding for carotenoid biosynthesis enzymes and their chromosome localization

Carotenoids are essential components in all plants. Their accumulation in wheat seed determines the endosperm colour, which is an important quality trait in wheat. In this study, we report the isolation of BAC clones containing genes coding for three different enzymes of the carotenoid biosynthesis pathway: phytoene synthase (PSY), phytoene desaturase (PDS), and zeta-carotene desaturase (ZDS). Primers were designed on the basis of wheat ESTs similar to the sequences of these three genes in other species, and used to screen a BAC library from Triticum turgidum var. durum (2n = 28, genomes AABB). Eight, six, and nine 384-well plates containing at least one positive clone were found for PSY, PDS, and ZDS, respectively. BACs selected for each of these genes were then divided in two groups corresponding to the A and B genomes of tetraploid wheat, based on differences in the length of the PCR amplification products, conformation-sensitive gel electrophoresis (CSGE), or cleavage amplification polymorphisms. Positive clones were then assigned to chromosomes using a set of D genome substitution lines in T. turgidum var. durum 'Langdon'. PSY clones were localized on chromosomes 5A and 5B, PDS on chromosomes 4A and 4B, and ZDS on chromosomes 2A and 2B. The strategies used for the PCR screening of large BAC libraries and for the differentiation of BAC clones from different genomes in a polyploid species are discussed.

A genetic linkage map of the Durum x Triticum dicoccoides backcross population based on SSRs and AFLP markers, and QTL analysis for milling traits

Durum wheat ( Triticum turgidum L. var durum) is mainly produced and consumed in the Mediterranean region; it is used to produce several specific end-products; such as local pasta, couscous and burghul. To study the genetics of grain-milling quality traits, chromosomal locations, and interaction with the environment, a genetic linkage map of durum was constructed and the quantitative trait loci QTLs for the milling-related traits, test weight (TW) and thousand-kernel weight (TKW), were identified. The population constituted 114 recombinant inbred lines derived from the cross: Omrabi 5 /Triticum dicoccoides 600545// Omrabi 5. TW and TKW were analyzed over 18 environments (sites x years). Single-sequence-repeat markers (SSRs), Amplified-fragment-length-polymorphism markers (AFLPs), and seed storage proteins (SSPs) showed a high level of polymorphism (>60%). The map was constructed with 124 SSRs, 149 AFLPs and 6 SSPs; its length covered 2,288.8 cM (8.2 cM/marker). The map showed high synteny with previous wheat maps, and both SSRs and AFLPs mapped evenly across the genome, with more markers in the B genome. However, some rearrangements were observed. For TW, a high genotypic effect was detected and two QTLs with epistasic effect were identified on 7AS and 6BS, explaining 30% of the total variation. The TKW showed a significant transgressive inheritance and five QTLs were identified, explaining 32% of the total variation, out of which 25% was of a genetic nature, and showing QTLxE interaction. The major TKW-QTLs were around the centromere region of 6B. For both traits, Omrabi 5 alleles had a significant positive effect. This population will be used to determine other QTLs of interest, as its parents are likely to harbor different genes for diseases and drought tolerance.