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

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.

Phenotyping and Identification of Molecular Markers Associated with Leaf Rust Resistance in the Wheat Germplasm from Kazakhstan, CIMMYT and ICARDA

Leaf rust (LR) is the most widespread disease of common wheat worldwide. In order to evaluate leaf rust resistance, 70 uncharacterized wheat cultivars and promising lines with unknown leaf rust resistance genes (Lr genes) were exposed to Kazakhstani Puccinia triticina (Pt) races at the seedling stage. Field tests were performed to characterize leaf rust responses at the adult plant growth stage in the 2020-2021 and 2021-2022 cropping seasons. The wheat collection showed phenotypic diversity when tested with two virulent races of Pt. Thirteen wheat genotypes (18.6%) showed high resistance at both seedling and adult plant stages. In most cases, breeding material originating from international nurseries showed higher resistance to LR. Nine Lr genes, viz. Lr9, Lr10, Lr19, Lr26, Lr28, Lr34, Lr37, Lr46, and Lr68, either singly or in combination, were identified in 47 genotypes. Known Lr genes were not detected in the remaining 23 genotypes. The most commonly identified resistance genes were Lr37 (17 cultivars), Lr34 (16 cultivars), and Lr46 (10 cultivars), while Lr19, Lr68, Lr26, and Lr28 were the least frequent. Four Lr genes were identified in Keremet and Hisorok, followed by three Lr genes in Aliya, Rasad, Reke, Mataj, Egana and Almaly/Obri. The molecular screening revealed twenty-nine carriers of a single Lr gene, ten carriers of two genes, six carriers of three genes, and two carriers of four genes. Most of these accessions showed a high and moderate level of APR (Adult plant resistance) and may be utilized for the incorporation of Lr genes in well-adapted wheat cultivars. The most effective combination was Lr37, Lr34, and Lr68, the carriers of which were characterized by a low disease susceptibility index. The obtained results will facilitate breeding programs for wheat resistance in Kazakhstan.

Conservatively transmitted alleles of key agronomic genes provide insights into the genetic basis of founder parents in bread wheat (Triticum aestivum L.)

BACKGROUND

Founder parents play extremely important roles in wheat breeding. Studies into the genetic basis of founder parents and the transmission rules of favorable alleles are of great significance in improving agronomically important traits in wheat.

RESULTS

Here, a total of 366 founder parents, widely grown cultivars, and derivatives of four representative founder parents were genotyped based on efficient kompetitive allele-specific PCR (KASP) markers in 87 agronomically important genes controlling yield, quality, adaptability, and stress resistance. Genetic composition analysis of founder parents and widely grown cultivars showed a consistently high frequency of favorable alleles for yield-related genes. This analysis further showed that other alleles favorable for resistance, strong gluten, dwarf size, and early heading date were also subject to selective pressure over time. By comparing the transmission of alleles from four representative founder parents to their derivatives during different breeding periods, it was found that the genetic composition of the representative founder parents was optimized as breeding progressed over time, with the number and types of favorable alleles carried gradually increasing and becoming enriched. There are still a large number of favorable alleles in wheat founder parents that have not been fully utilized in breeding selection. Eighty-seven agronomically important genes were used to construct an enrichment map that shows favorable alleles of four founder parents, providing an important theoretical foundation for future identification of candidate wheat founder parents.

CONCLUSIONS

These results reveal the genetic basis of founder parents and allele transmission for 87 agronomically important genes and shed light on breeding strategies for the next generation of elite founder parents in wheat.

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.

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.

Genome-wide association mapping of bread wheat genotypes for sustainable food security and yield potential under limited water conditions

Determining the genetic basis of yield and water deficient tolerance in wheat is vital for wheat breeding programs. Herein, a genome-wide association study (GWAS) was performed for water deficient and yield-related attributes on wheat genotypes with high-density Illumina 90K Infinium SNP array. Major yield and drought-related attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water deficient stressed environments during two crop cycles. Among all accessions, highly significant variations were shown in studied environments for examined characters. Water deficient conditions, reduced the wheat yield and had strong and positive correlation among relative water content and grain yield per plant. Population structure analyses based on 90,000 SNP data, classify the accessions into 4 sub-populations. Marker-trait association analyses (MTA) revealed that 134 significant SNPs were linked with yield and drought tolerance attributes. Pleotropic loci RAC875_s117925_244 and RAC875_c16333_340 located on chromosome 5A and 2A respectively, were significantly linked with relative water contents (RWC), cell membrane thermo-stability (CMT), grain per spike (GPS), spikelet per spike (SPS) and grain yield per plant (GYP). The markers Ra_c58279_684, BobWhite_c23828_341 and IAAV3414 located on chromosomes 2A, 6B and 7B respectively, showed pleotropic effects for RWC, GPS and GYP under both environments. The current experiment not only validated several MTAs reported in other studies but also discovered novel MTAs which significant under drought-stressed conditions. A total of 171 candidate genes were recognized that could be cloned and functionally characterized for the respective associated traits. For RWC and CMT, total 11 and 3 associated SNPs were mapped on coding DNA sequence (CDS) of the identified candidate genes. Isolation and characterization of the candidate genes herein mapped SNPs will be useful in discovering novel genes underpinning drought tolerance in bread wheat to fulfill the wheat demand and sustainable food security under limited water conditions.

Mutant combinations of lycopene ɛ-cyclase and β-carotene hydroxylase 2 homoeologs increased β-carotene accumulation in endosperm of tetraploid wheat (Triticum turgidum L.) grains

Grains of tetraploid wheat (Triticum turgidum L.) mainly accumulate the non-provitamin A carotenoid lutein-with low natural variation in provitamin A β-carotene in wheat accessions necessitating alternative strategies for provitamin A biofortification. Lycopene ɛ-cyclase (LCYe) and β-carotene hydroxylase (HYD) function in diverting carbons from β-carotene to lutein biosynthesis and catalyzing the turnover of β-carotene to xanthophylls, respectively. However, the contribution of LCYe and HYD gene homoeologs to carotenoid metabolism and how they can be manipulated to increase β-carotene in tetraploid wheat endosperm (flour) is currently unclear. We isolated loss-of-function Targeting Induced Local Lesions in Genomes (TILLING) mutants of LCYe and HYD2 homoeologs and generated higher order mutant combinations of lcye-A, lcye-B, hyd-A2, and hyd-B2. Hyd-A2 hyd-B2, lcye-A hyd-A2 hyd-B2, lcye-B hyd-A2 hyd-B2, and lcye-A lcye-B hyd-A2 hyd-B2 achieved significantly increased β-carotene in endosperm, with lcye-A hyd-A2 hyd-B2 exhibiting comparable photosynthetic performance and light response to control plants. Comparative analysis of carotenoid profiles suggests that eliminating HYD2 homoeologs is sufficient to prevent β-carotene conversion to xanthophylls in the endosperm without compromising xanthophyll production in leaves, and that β-carotene and its derived xanthophylls are likely subject to differential catalysis mechanisms in vegetative tissues and grains. Carotenoid and gene expression analyses also suggest that the very low LCYe-B expression in endosperm is adequate for lutein production in the absence of LCYe-A. These results demonstrate the success of provitamin A biofortification using TILLING mutants while also providing a roadmap for guiding a gene editing-based approach in hexaploid wheat.

Genome-wide association mapping for high temperature tolerance in wheat through 90k SNP array using physiological and yield traits

Dissecting the genetic basis of physiological and yield traits against tolerance to heat stress is an essential in wheat breeding programs to boost up the wheat yield for sustainable food security. Herein, a genome-wide association study (GWAS) was performed to reveal the genetic basis of heat tolerance using high-density Illumina 90K Infinium SNPs array through physiological and yield indices. These indices were phenotyped on a diverse panel of foreign and domestic genotypes of Pakistan, grown in normal and heat-stressed environments. Based on STRUCTURE analysis, the studied germplasm clustered into four sub-population. Highly significant variations with a range of moderate (58.3%) to high (77.8%) heritability was observed under both conditions. Strong positive correlation existed among physiological and yield related attributes. A total of 320 significant (-log10 P ≥ 3) marker-trait associations (MTAs) were identified for the observed characters. Out of them 169 and 151 MTAs were recorded in normal and heat stress environments, respectively. Among the MTA loci, three (RAC875_c103017_302, Tdurum_contig42087_1199, and Tdurum_contig46877_488 on chromosomes 4B, 6B, and 7B respectively), two (BobWhite_c836_422 and BS00010616_51) and three (Kukri_rep_c87210_361, D_GA8KES401BNLTU_253 and Tdurum_contig1015_131) on chromosomes 5A, 1B, and 3D at the positions 243.59cM, 77.82cM and 292.51cM) showed pleiotropic effects in studied traits under normal, heat-stressed and both conditions respectively. The present study not only authenticated the numerous previously reported MTAs for examined attributes but also revealed novel MTAs under heat-stressed conditions. Identified SNPs will be beneficial in determining the novel genes in wheat to develop the heat tolerant and best yielded genotypes to fulfill the wheat requirement for the growing population.

Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

BACKGROUND

Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat.

RESULTS

Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59-12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000.

CONCLUSIONS

To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

Evaluation of Wheat Germplasm for Resistance to Leaf Rust (Puccinia triticina) and Identification of the Sources of Lr Resistance Genes Using Molecular Markers

Leaf rust, caused by Puccinia triticina (Ptr), is a significant disease of spring wheat spread in Kazakhstan. The development of resistant cultivars importantly requires the effective use of leaf rust resistance genes. This study aims to: (i) determine variation in Ptr population using races from the East Kazakhstan, Akmola, and Almaty regions of Kazakhstan; (ii) examine resistance during seedling and adult plant stages; and (iii) identify the sources of Lr resistance genes among the spring wheat collection using molecular markers. Analysis of a mixed population of Ptr identified 25 distinct pathotypes. Analysis of these pathotypes using 16 Thatcher lines that are near-isogenic for leaf rust resistance genes (Lr) showed different virulence patterns, ranging from least virulent “CJF/B” and “JCL/G” to highly virulent “TKT/Q”. Most of the pathotypes were avirulent to Lr9, Lr19, Lr24, and Lr25 and virulent to Lr1, Lr2a, Lr3ka, Lr11, and Lr30. The Ptr population in Kazakhstan is diverse, as indicated by the range of virulence observed in five different races analyzed in this study. The number of genotypes showed high levels of seedling resistance to each of the five Ptr races, thus confirming genotypic diversity. Two genotypes, Stepnaya 62 and Omskaya 37, were highly resistant to almost all five tested Ptr pathotypes. Stepnaya 62, Omskaya 37, Avangard, Kazakhstanskaya rannespelaya, and Kazakhstanskaya 25 were identified as the most stable genotypes for seedling resistance. However, most of the varieties from Kazakhstan were susceptible in the seedling stage. Molecular screening of these genotypes showed contrasting differences in the genes frequencies. Among the 30 entries, 22 carried leaf rust resistance gene Lr1, and two had Lr9 and Lr68. Lr10 and Lr28 were found in three and four cultivars, respectively. Lr19 was detected in Omskaya 37. Two single cultivars separately carried Lr26 and Lr34, while Lr37 was not detected in any genotypes within this study. Field evaluation demonstrated that the most frequent Lr1 gene is ineffective. Kazakhstanskaya 19 and Omskaya 37 had the highest number of resistance genes: three and four Lr genes, respectively. Two gene combinations (Lr1, Lr68) were detected in Erythrospermum 35 and Astana. The result obtained may assist breeders in incorporating effective Lr genes into new cultivars and developing cultivars resistant to leaf rust.

Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

The genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

[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.

From Genetic Maps to QTL Cloning: An Overview for Durum Wheat

Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.

Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population

To enrich carotenoids, especially β-cryptoxanthin, in juice sac tissues of fruits via molecular breeding in citrus, allele mining was utilized to dissect allelic variation of carotenoid metabolic genes and identify an optimum allele on the target loci characterized by expression quantitative trait (eQTL) analysis. SNPs of target carotenoid metabolic genes in 13 founders of the Japanese citrus breeding population were explored using the SureSelect target enrichment method. An independent allele was determined based on the presence or absence of reliable SNPs, using trio analysis to confirm inheritability between parent and offspring. Among the 13 founders, there were 7 PSY alleles, 7 HYb alleles, 11 ZEP alleles, 5 NCED alleles, and 4 alleles for the eQTL that control the transcription levels of PDS and ZDS among the ancestral species, indicating that some founders acquired those alleles from them. The carotenoid composition data of 263 breeding pedigrees in juice sac tissues revealed that the phenotypic variance of carotenoid composition was similar to that in the 13 founders, whereas the mean of total carotenoid content increased. This increase in total carotenoid content correlated with the increase in either or both β-cryptoxanthin and violaxanthin in juice sac tissues. Bayesian statistical analysis between allelic composition of target genes and carotenoid composition in 263 breeding pedigrees indicated that PSY-a and ZEP-e alleles at PSY and ZEP loci had strong positive effects on increasing the total carotenoid content, including β-cryptoxanthin and violaxanthin, in juice sac tissues. Moreover, the pyramiding of these alleles also increased the β-cryptoxanthin content. Interestingly, the offset interaction between the alleles with increasing and decreasing effects on carotenoid content and the epistatic interaction among carotenoid metabolic genes were observed and these interactions complexed carotenoid profiles in breeding population. These results revealed that allele composition would highly influence the carotenoid composition in citrus fruits. The allelic genotype information for the examined carotenoid metabolic genes in major citrus varieties and the trio-tagged SNPs to discriminate the optimum alleles (PSY-a and ZEP-e) from the rest would promise citrus breeders carotenoid enrichment in fruit via molecular breeding.

Effect of cultivation system on quality changes in durum wheat grain and flour produced in North-Eastern Europe

Grain of the highest hardness was produced from durum wheat grown without the use of growth regulator, at the lowest sowing density (350 seeds m-2) and nitrogen fertilization dose of 80 kg ha-1. The highest values L* and b* were determined in the grain of wheat cultivated without additional agrotechnical measures (growth regulator and nitrogen fertilization). Study results, supported by correlation analysis, indicated that high-quality grain with desired flour quality parameters (level of: FER ≈ 64%; FPS ≈ 98%; L* ≈ 92) can be produced from spring durum wheat grown without the growth regulator and at 80 kg·ha-1 nitrogen fertilization. Additionally, this variant of applied cultivation system can reduce costs of durum wheat production and contamination of the natural environment.

Differential Regulation of Phytoene Synthase PSY1 During Fruit Carotenogenesis in Cultivated and Wild Tomato Species (Solanum section Lycopersicon)

In plants, carotenoids define fruit pigmentation and are involved in the processes of photo-oxidative stress defense and phytohormone production; a key enzyme responsible for carotene synthesis in fruit is phytoene synthase 1 (PSY1). Tomatoes (Solanum section Lycopersicon) comprise cultivated (Solanum lycopersicum) as well as wild species with different fruit color and are a good model to study carotenogenesis in fleshy fruit. In this study, we identified homologous PSY1 genes in five Solanum section Lycopersicon species, including domesticated red-fruited S. lycopersicum and wild yellow-fruited S. cheesmaniae and green-fruited S. chilense, S. habrochaites and S. pennellii. PSY1 homologs had a highly conserved structure, including key motifs in the active and catalytic sites, suggesting that PSY1 enzymatic function is similar in green-fruited wild tomato species and preserved in red-fruited S. lycopersicum. PSY1 mRNA expression directly correlated with carotenoid content in ripe fruit of the analyzed tomato species, indicating differential transcriptional regulation. Analysis of the PSY1 promoter and 5′-UTR sequence revealed over 30 regulatory elements involved in response to light, abiotic stresses, plant hormones, and parasites, suggesting that the regulation of PSY1 expression may affect the processes of fruit senescence, seed maturation and dormancy, and pathogen resistance. The revealed differences between green-fruited and red-fruited Solanum species in the structure of the PSY1 promoter/5′-UTR, such as the acquisition of ethylene-responsive element by S. lycopersicum, could reflect the effects of domestication on the transcriptional mechanisms regulating PSY1 expression, including induction of carotenogenesis during fruit ripening, which would contribute to red coloration in mature fruit.

Phytoene synthase 1 (Psy-1) and lipoxygenase 1 (Lpx-1) Genes Influence on Semolina Yellowness in Wheat Mediterranean Germplasm

Phytoene synthase 1 (Psy1) and lipoxygenase 1 (Lpx-1) are key genes involved in the synthesis and catalysis of carotenoid pigments in durum wheat, regulating the increase and decrease in these compounds, respectively, resulting in the distinct yellow color of semolina and pasta. Here, we reported new haplotype variants and/or allele combinations of these two genes significantly affecting yellow pigment content in grain and semolina through their effect on carotenoid pigments. To reach the purpose of this work, three complementary approaches were undertaken: the identification of QTLs associated to carotenoid content on a recombinant inbred line (RIL) population, the characterization of a Mediterranean panel of accessions for Psy1 and Lpx-1 genes, and monitoring the expression of Psy1 and Lpx-1 genes during grain filling on two genotypes with contrasting yellow pigments. Our data suggest that Psy1 plays a major role during grain development, contributing to semolina yellowness, and Lpx-1 appears to be more predominant at post-harvest stages and during pasta making.

In Vitro Bioaccessibility of Carotenoids and Chlorophylls in a Diverse Collection of Spinach Accessions and Commercial Cultivars

Spinach, a nutrient-dense, green-leafy vegetable, is a rich source of carotenoid and chlorophyll bioactives. While the content of bioactives is known to vary with the genotype, variation in bioaccessibility is unknown. Bioaccessibility was explored in 71 greenhouse-grown spinach genotypes in fall and spring 2018/2019. Spinach was phenotyped for its greenness, leaf texture, leaf shape, and SPAD chlorophyll content. Postharvest, spinach was washed, blanched, and homogenized prior to assessment of bioactive bioaccessibility using a novel high-throughput in vitro digestion model followed by high-performance liquid chromatography with a photodiode array detector analysis. There was a significant variation in the bioaccessible content for all bioactives (p < 0.05), except for chlorophyll b (p = 0.063) in spring-grown spinach. The correlation coefficients of bioaccessible contents between seasons reveal that lutein (r = 0.52) and β-carotene (r = 0.55) were correlated to a greater extent than chlorophyll a (r = 0.38) and chlorophyll b (r = 0.19). The results suggest that carotenoid and chlorophyll bioaccessible contents may vary based on spinach genotypes and may be stable across seasons.

Multifamily QTL analysis and comprehensive design of genotypes for high-quality soft wheat

Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.

Expression Analysis, Functional Marker Development and Verification of AgFNSI in Celery

Apigenin is one of the primary flavonoids in celery, which has a high medicinal value. Flavone synthase I (FNSI) is the last step enzyme in apigenin biosynthesis. In this study, the 1492 bp promoter sequence before AgFNSI initiation codon (ATG) of celery was obtained, which included methyl jasmonate (MeJA) responsive elements, light responsive elements, anaerobic induction elements and five MYB binding sites. AgFNSI was sensitive to temperature, UV-B, water deficit and MeJA. Comparative analysis of AgFNSI genome and promoter sequences among celery accessions with different apigenin content showed that there were four allelic variations in AgFNSI, and four accessions with high apigenin content belonged to AgFNSIa, and five accessions with low apigenin content belonged to AgFNSIc. Three pairs of dominant complementary markers were designed based on the single-nucleotile polymorphisms (SNPs) of the AgFNSIa and AgFNSIc genomes and promoter sequences. Three pairs of functional markers were validated by 112 celery accessions. The results showed that AFPA1/AFPB1 detected significant differences in apigenin content between different genotypes. Therefore, marker AFPA1/AFPB1 is associated with apigenin content in celery and could be used for the genetic improvement of apigenin content in celery.

Carotenoids in Cereal Food Crops: Composition and Retention throughout Grain Storage and Food Processing

Carotenoids are C40 isoprenoids synthesized by plants, as well as some bacteria, fungi and algae, that have been reported to be responsible for a number of benefits conferred on human health. The inability of animals and humans to synthesize de novo these compounds is the reason why they must be introduced from dietary sources. In cereal grains, carotenoids are important phytochemicals responsible for the characteristic yellow colour of the endosperm, which confers nutritional and aesthetic quality to cereal-based products. Cereals are staple foods for a large portion of the world population, and the biofortification of cereal grains with carotenoids may represent a simple way to prevent many human diseases and disorders. Unfortunately, evidence exists that the storage and processing of cereal grains into food products may negatively impact their carotenoid content; so, this loss should be taken into consideration when analysing the potential health benefits of the cereal-based products. Focusing on the recent updates, this review summarizes the chemical composition of the carotenoids in the grains of staple cereals, including wheat, maize, rice and sorghum, the main factors that affect their carotenoid content during storage and processing and the most fruitful strategies used improve the grain carotenoid content and limit the carotenoid post-harvest losses.

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.

Genome-wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour colour in Chinese bread wheat

Flour colour, kernel hardness, grain protein content and wet gluten content are important quality properties that determine end use in bread wheat. Here, a wheat 90K genotyping assay was used for a genome-wide association study (GWAS) of the six quality-related traits in Chinese wheat cultivars in eight environments over four years. A total of 846 significant single nucleotide polymorphisms (SNPs) were identified, explaining approximately 30% of the phenotypic variation on average, and 103 multienvironment-significant SNPs were detected in more than four environments. Quantitative trait loci (QTL) mapping in the biparent population confirmed some important SNP loci. Moreover, it was determined that some important genes were associated with the six quality traits, including some known functional genes and annotated unknown functional genes. Of the annotated unknown functional genes, it was verified that TaRPP13L1 was associated with flour colour. Wheat cultivars or lines with TaRPP13L1-B1a showed extremely significantly higher flour redness and lower yellowness than those with TaRPP13L1-B1b in the Chinese wheat natural population and the doubled haploid (DH) population. Two tetraploid wheat lines with premature stop codons of the TaRPP13L1 gene mutagenized by ethyl methanesulfonate (EMS) showed extremely significantly higher flour redness and lower yellowness than wild type. Our data suggest that the TaRPP13L1 gene plays an important role in modulating wheat flour colour. This study provides useful information for further dissection of the genetic basis of flour colour and also provides valuable genes or genetic loci for marker-assisted selection to improve the process of breeding quality wheat in China.

Association Mapping for 24 Traits Related to Protein Content, Gluten Strength, Color, Cooking, and Milling Quality Using Balanced and Unbalanced Data in Durum Wheat [Triticum turgidum L. var. durum (Desf).]

Durum wheat [Triticum durum (Desf).] is mostly used to produce pasta, couscous, and bulgur. The quality of the grain and end-use products determine its market value. However, quality tests are highly resource intensive and almost impossible to conduct in the early generations in the breeding program. Modern genomics-based tools provide an excellent opportunity to genetically dissect complex quality traits to expedite cultivar development using molecular breeding approaches. This study used a panel of 243 cultivars and advanced breeding lines developed during the last 20 years to identify SNPs associated with 24 traits related to nutritional value and quality. Genome-wide association study (GWAS) identified a total of 179 marker-trait associations (MTAs), located in 95 genomic regions belonging to all 14 durum wheat chromosomes. Major and stable QTLs were identified for gluten strength on chromosomes 1A and 1B, and for PPO activity on chromosomes 1A, 2B, 3A, and 3B. As a large amount of unbalance phenotypic data are generated every year on advanced lines in all the breeding programs, the applicability of such a dataset for identification of MTAs remains unclear. We observed that ∼84% of the MTAs identified using a historic unbalanced dataset (belonging to a total of 80 environments collected over a period of 16 years) were also identified in a balanced dataset. This suggests the suitability of historic unbalanced phenotypic data to identify beneficial MTAs to facilitate local-knowledge-based breeding. In addition to providing extensive knowledge about the genetics of quality traits, association mapping identified several candidate markers to assist durum wheat quality improvement through molecular breeding. The molecular markers associated with important traits could be extremely useful in the development of improved quality durum wheat cultivars using marker-assisted selection (MAS).

Genome-wide association analyses for yield and yield-related traits in bread wheat (Triticum aestivum L.) under pre-anthesis combined heat and drought stress in field conditions

Understanding the genetic basis of heat and drought stress tolerance in wheat is prerequisite for wheat breeding program. In the present study, a wheat panel comprising of 192 elite bread wheat genotypes was phenotyped in eight environments for yield and related traits in field conditions. Four stress environments were created by implying four different treatments differing in sowing date and water availability, panel was evaluated for two years in field conditions. The panel was genotyped with 15K Illumina chip and 9236 polymorphic markers concentrated on B genome were employed in GWAS analysis. Consistent, fast LD decay was observed on D genome and structure analysis germplasm divided panel into three major populations. GWAS was performed using BLUEs values of combined environment data in R package GAPIT using log10(P) = 3.96 as significance threshold. The significance of association was further checked using FDR<0.05 threshold. The GWAS identified 487 loci associated with the traits and were significant at log10(p) threshold out of these 350 loci were significant at FDR threshold. For two stress indices 108 associations were significant at FDR threshold. Nine genomic regions were shared among all treatment, while multiple pleiotropic regions were present on chromosome 7D followed by unmapped chromosome. The present study validated many marker trait associations for yield and other traits, MTAs significant under combined drought and heat stress were novel. These regions are important and can be used for fine mapping and marker assisted selection to discover new genes responsible for heat and drought tolerance in wheat.

Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height

Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.

Genome-wide association mapping in bread wheat subjected to independent and combined high temperature and drought stress

Most investigations to date aiming to identify the genetic basis of the stress response of wheat (Triticum aestivum L.) have focused on the response to single stress agents such as high temperature or drought, even though in the natural situation, these stresses tend often to occur together. Here, a panel of 108 spring type bread wheat cultivars was phenotyped for 15 yield and yield related traits for two years (2014/15 and 2015/16) under non-stressed conditions, under high temperature stress, under drought and under a combined high temperature and drought regime. The mean loss in grain yield caused by all stress regimes was 51.33%. Analysis of variance (ANOVA) of yield trait showed significant differences among genotypes environments and their interactions (G×E). All the studied traits had higher heritability values which ranged from 0.35-0.94 under [C], 0.58-0.95 under [D], 0.62-0.93 under [H] and 0.60-0.95 under [HD]. GWAS was performed by using 9,646 informative SNP markers and based on these polymorphic SNPs population structure analysis divided whole germplasm into five major sub-populations. Mixed model association analysis detected 503 marker-trait associations (MTAs) at P ≤0.001 while 329 MTAs crossed FDR ≤ 0.05 for all traits with phenotypic variances (R2) ranged from 24.83% to 12.51%. Seven new pleiotropic SNPs on chromosome 7D and IAAV8258 (86.91cM) and wsnp_Ex_c7168_12311649 (57.93cM) on chromosome 5A were most stable association in present study. Furthermore, candidate genes Psy and Sr25 (TG0040) were also significant in present study, these genes were previously mapped on 7A and 7D. The region on 7D was assiociated with 7DL.7Ag translocation from Lophopyrum carring rust resistance Yr16 and many other genes. Similarly region on chromosome 7A which was associated with Psy gene was linked with grain yellow pigment content QTLs. Favourable alleles controlling grain yield were of vital importance and incorporation of these alleles after validation through marker assisted selection and fine mapping could be helpful in wheat yield improvement stress and non-stress conditions.

Significance of Genetic, Environmental, and Pre- and Postharvest Factors Affecting Carotenoid Contents in Crops: A Review

Carotenoids are a diverse group of tetraterpenoid pigments that play indispensable roles in plants and animals. The biosynthesis of carotenoids in plants is strictly regulated at the transcriptional and post-transcriptional levels in accordance with inherited genetic signals and developmental requirements and in response to external environmental stimulants. The alteration in the biosynthesis of carotenoids under the influence of external environmental stimulants, such as high light, drought, salinity, and chilling stresses, has been shown to significantly influence the nutritional value of crop plants. In addition to these stimulants, several pre- and postharvesting cultivation practices significantly influence carotenoid compositions and contents. Thus, this review discusses how various environmental stimulants and pre- and postharvesting factors can be positively modulated for the enhanced biosynthesis and accumulation of carotenoids in the edible parts of crop plants, such as the leaves, roots, tubers, flowers, fruit, and seeds. In addition, future research directions in this context are identified.

Breeding Major Cereal Grains through the Lens of Nutrition Sensitivity

Cereal grains are the common food staples that collectively provide over 50% of dietary calories and proteins for the world's population. Although the Green Revolution has greatly increased the yield of commercial cereal crops, they often lack nutrients essential for human health in the edible tissues. In developing nutrition-sensitive agriculture, the nutritional quality of cereal grains has been a major target for improvement using breeding and biotechnology approaches. This review examines recent progress on biofortification of micronutrients (provitamin A and folates) and an essential amino acid (lysine) in three major cereal grains, wheat, rice, and maize, through plant breeding. In addition, how natural variations, induced mutations, and the advanced genome-editing technologies can be applied to improving the nutrient content and stability in these cereal grains are discussed. High-yield cereal crops pyramided with improved (micro)nutrient contents hold great promise to meet the increasing demand of nutritionally limited populations and to contribute to achieving sustainable nutrition security.

A Genome-Wide Association Study Reveals a Rich Genetic Architecture of Flour Color-Related Traits in Bread Wheat

Flour color-related traits, including brightness (L^*), redness (a^*), yellowness (b^*) and yellow pigment content (YPC), are very important for end-use quality of wheat. Uncovering the genetic architecture of these traits is necessary for improving wheat quality by marker-assisted selection (MAS). In the present study, a genome-wide association study (GWAS) was performed on a collection of 166 bread wheat cultivars to better understand the genetic architecture of flour color-related traits using the wheat 90 and 660 K SNP arrays, and 10 allele-specific markers for known genes influencing these traits. Fifteen, 28, 25, and 32 marker-trait associations (MTAs) for L^*, a^*, b^*, and YPC, respectively, were detected, explaining 6.5-20.9% phenotypic variation. Seventy-eight loci were consistent across all four environments. Compared with previous studies, Psy-A1, Psy-B1, Pinb-D1, and the 1B•1R translocation controlling flour color-related traits were confirmed, and four loci were novel. Two and 11 loci explained much more phenotypic variation of a^* and YPC than phytoene synthase 1 gene (Psy1), respectively. Sixteen candidate genes were predicted based on biochemical information and bioinformatics analyses, mainly related to carotenoid biosynthesis and degradation, terpenoid backbone biosynthesis and glycolysis/gluconeogenesis. The results largely enrich our knowledge of the genetic basis of flour color-related traits in bread wheat and provide valuable markers for wheat quality improvement. The study also indicated that GWAS was a powerful strategy for dissecting flour color-related traits and identifying candidate genes based on diverse genotypes and high-throughput SNP arrays.

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.

Cytogenetic mapping of a major locus for resistance to Fusarium head blight and crown rot of wheat on Thinopyrum elongatum 7EL and its pyramiding with valuable genes from a Th. ponticum homoeologous arm onto bread wheat 7DL

A major locus for resistance to different Fusarium diseases was mapped to the most distal end of Th. elongatum 7EL and pyramided with Th. ponticum beneficial genes onto wheat 7DL. Perennial Triticeae species of the Thinopyrum genus are among the richest sources of valuable genes/QTL for wheat improvement. One notable and yet unexploited attribute is the exceptionally effective resistance to a major wheat disease worldwide, Fusarium head blight, associated with the long arm of Thinopyrum elongatum chromosome 7E (7EL). We targeted the transfer of the temporarily designated Fhb-7EL locus into bread wheat, pyramiding it with a Th. ponticum 7el₁L segment stably inserted into the 7DL arm of wheat line T4. Desirable genes/QTL mapped along the T4 7el₁L segment determine resistance to wheat rusts (Lr19, Sr25) and enhancement of yield-related traits. Mapping of the Fhb-7EL QTL, prerequisite for successful pyramiding, was established here on the basis of a bioassay with Fusarium graminearum of different 7EL-7el₁L bread wheat recombinant lines. These were obtained without resorting to any genetic pairing promotion, but relying on the close 7EL-7el₁L homoeology, resulting in 20% pairing frequency between the two arms. Fhb-7EL resided in the telomeric portion and resistant recombinants could be isolated with useful combinations of more proximally located 7el₁L genes/QTL. The transferred Fhb-7EL locus was shown to reduce disease severity and fungal biomass in grains of infected recombinants by over 95%. The same Fhb-7EL was, for the first time, proved to be effective also against F. culmorum and F. pseudograminearum, predominant agents of crown rot. Prebreeding lines possessing a suitable 7EL-7el₁L gene/QTL assembly showed very promising yield performance in preliminary field tests.

Allelic diversity of phytoene synthase gene influences the transcription level in citrus fruit among a citrus F1 hybrid population

Phytoene synthase (PSY) is one of the key regulatory enzyme on the biosynthesis and accumulation of carotenoid in citrus fruits. The transcriptional diversity of PSY is mainly attributed to the structural variation in promoter region among PSY alleles. In aim to clarify how this transcriptional diversity is regulated among them, PSY alleles responsible for carotenoid biosynthesis in the fruits are characterized and their promoter sequences were compared. Based on gene structure and expression pattern of PSY homologues on the clementine mandarin genome sequence, PSY alleles responsible for carotenoid biosynthesis are derived from a single locus in the scaffold 6. AG mapping population possessed four PSY alleles derived from parent lines of A255 and G434, and their F₁ individuals with PSY-g2 allele tended to have low transcription level. From sequence comparison of their promoter regions, the cis-motif alternation from MYBPZM to RAV1AAT might be a candidate to influence the transcription level. Among the ancestral pedigree varieties of AG mapping population, the transcription level of PSY correlated with genotypes of MYBPZM and RAV1AAT motifs in the promoter region of PSY alleles, so that homozygous genotype of MYBPZM showed higher transcription level while heterozygous genotype of MYBPZM and RAV1AAT showed lower transcription level.

Characterization of Aldehyde Oxidase (AO) Genes Involved in the Accumulation of Carotenoid Pigments in Wheat Grain

Aldehyde Oxidase (AO) enzyme (EC 1.2.3.1) catalyzes the final steps of carotenoid catabolism and it is a key enzyme in the abscisic acid (ABA) biosynthesis. AO isoforms are located in the cytosolic compartment of tissues in many plants, where induce the oxidation of aldehydes into carboxylic acid, and in addition, catalyze the hydroxylation of some heterocycles. The goal of the present study was to characterize the AO genes involved in the accumulation of carotenoid pigments in wheat grain, an important quantitative trait controlled by multiple genes. The cDNAs corresponding to the four AO isoforms from Arabidopsis thaliana and five AO isoforms from Brachypodium distachyon were used as query in 454 sequence assemblies data for Triticum aestivum cv. Chinese Spring (https://urgi.versailles.inra.fr/blast/blast.php) to obtain the partial or whole orthologous wheat AO sequences. Three wheat isoforms, designated AO1, AO2, and AO3 were located on the chromosome groups 2, 5, and 7, respectively, and mapped on two consensus wheat maps by SNP markers located within the AO gene sequences. To validate the possible relationships between AO3 genes and carotenoid accumulation in wheat, the expression levels of AO-A3 and AO-B3 gene were determined during the kernel maturation stage of two durum wheat cultivars, Ciccio and Svevo, characterized by a low and high carotenoid content, respectively. Different AO-A3 gene expression values were observed between the two cultivars indicating that the AO-A3 allele present in Ciccio was more active in carotenoid degradation. A gene marker was developed and can be used for marker-assisted selection in wheat breeding programs.

The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments

BACKGROUND

In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they influence the colour (whiteness vs. yellowness) of the grain. Understanding the genetic basis of grain yellow pigments, and identifying associated markers provide the basis for improving wheat quality by molecular breeding.

RESULTS

Twenty-four candidate genes involved in the biosynthesis and catabolism of carotenoid compounds have been identified in wheat by comparative genomics. Single nucleotide polymorphisms (SNPs) found in the coding sequences of 19 candidate genes allowed their chromosomal location and accurate map position on two reference consensus maps to be determined. The genome-wide association study based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs validated quantitative trait loci (QTLs) previously detected in biparental populations and discovered new QTLs for grain colour-related traits. Ten carotenoid genes mapped in chromosome regions underlying pigment content QTLs indicating possible functional relationships between candidate genes and the trait.

CONCLUSIONS

The availability of linked, candidate gene-based markers can facilitate breeding wheat cultivars with desirable levels of carotenoids. Identifying QTLs linked to carotenoid pigmentation can contribute to understanding genes underlying carotenoid accumulation in the wheat kernels. Together these outputs can be combined to exploit the genetic variability of colour-related traits for the nutritional and commercial improvement of wheat products.

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.

Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat

BACKGROUND

Phytoene synthase 1 (PSY1) is the most important regulatory enzyme in carotenoid biosynthesis, whereas its function is hardly known in common wheat. The aims of the present study were to investigate Psy1 function and genetic regulation using reverse genetics approaches.

RESULTS

Transcript levels of Psy1 in RNAi transgenic lines were decreased by 54-76 % and yellow pigment content (YPC) was reduced by 26-35 % compared with controls, confirming the impact of Psy1 on carotenoid accumulation. A series of candidate genes involved in secondary metabolic pathways and core metabolic processes responded to Psy1 down-regulation. The aspartate rich domain (DXXXD) was important for PSY1 function, and conserved nucleotides adjacent to the domain influenced YPC by regulating gene expression, enzyme activity or alternative splicing. Compensatory responses analysis indicated that three Psy1 homoeologs may be coordinately regulated under normal conditions, but separately regulated under stress. The period 14 days post anthesis (DPA) was found to be a key regulation node during grain development.

CONCLUSION

The findings define key aspects of flour color regulation in wheat and facilitate the genetic improvement of wheat quality targeting color/nutritional specifications required for specific end products.

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.

Distinct expression and function of carotenoid metabolic genes and homoeologs in developing wheat grains

BACKGROUND

β-carotene, the most active provitamin A molecule produced by plants, plays important roles in human nutrition and health. β-carotene does not usually accumulate in the endosperm (i.e. flour) of mature wheat grains, which is a major food source of calories for humans. Therefore, enriching β-carotene accumulation in wheat grain endosperm will enable a sustainable dietary supplementation of provitamin A. Several metabolic genes affecting β-carotene accumulation have already been isolated from wheat, including phytoene synthase 1 (PSY1), lycopene ε-cyclase (LCYe) and carotenoid β-ring hydroxylase1/2 (HYD1/2).

RESULTS

In this work, we cloned and biochemically characterized two carotenoid cleavage dioxygenases (CCDs), CCD1 and CCD4, from wheat. While CCD1 homoeologs cleaved β-apo-8'-carotenal, β-carotene, lutein and zeaxanthin into apocarotenoid products, CCD4 homoeologs were inactive towards these substrates in in vitro assays. When analyzed by real-time qPCR, PSY1, LCYe, HYD1/2 and CCD1/4 homoeologs showed distinct expression patterns in vegetative tissues and sections of developing tetraploid and hexaploid wheat grains, suggesting that carotenoid metabolic genes and homoeologs are differentially regulated at the transcriptional level in wheat.

CONCLUSIONS

The CCD1/4 enzyme activity and the spatial-temporal gene expression data provide critical insights into the specific carotenoid metabolic gene homoeologs that control β-carotene accumulation in wheat grain endosperm, thus establishing the knowledge base for generation of wheat varieties with enhanced β-carotene in the endosperm through breeding and genome editing approaches.

Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust

KEY MESSAGE

Barley resistance to wheat stripe rust has remained effective for a long time and, therefore, the genes underlying this resistance can be a valuable tool to engineer durable resistance in wheat. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major disease of wheat that is causing large economic losses in many wheat-growing regions of the world. Deployment of Pst resistance genes has been an effective strategy for controlling this pathogen, but many of these genes have been defeated by new Pst races. In contrast, genes providing resistance to this wheat pathogen in other grass species (nonhost resistance) have been more durable. Barley varieties (Hordeum vulgare ssp. vulgare) are predominately immune to wheat Pst, but we identified three accessions of wild barley (Hordeum vulgare ssp. spontaneum) that are susceptible to Pst. Using these accessions, we mapped a barley locus conferring resistance to Pst on the distal region of chromosome arm 7HL and designated it as Rps6. The detection of the same locus in the cultivated barley 'Tamalpais' and in the Chinese barley 'Y12' by an allelism test suggests that Rps6 may be a frequent component of barley intermediate host resistance to Pst. Using a high-density mapping population (>10,000 gametes) we precisely mapped Rps6 within a 0.14 cM region (~500 kb contig) that is colinear to regions in Brachypodium (<94 kb) and rice (<9 kb). Since no strong candidate gene was identified in these colinear regions, a dedicated positional cloning effort in barley will be required to identify Rps6. The identification of this and other barley genes conferring resistance to Pst can contribute to our understanding of the mechanisms for durable resistance against this devastating wheat pathogen.

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.