Gene-based high-density mapping of the gene rym7 conferring resistance to Barley mild mosaic virus (BaMMV)

For genetic analysis of Ppd-1 homoeologs controlling photoperiodic response of wheat (Triticum aestivum L.), bulk segregant analysis was performed using a doubled haploid (DH) population derived from a cross of Japanese wheat genotypes Winter-Abukumawase and Chihokukomugi. Based on the segregation of simple sequence repeat markers linked to the Ppd-1 homoeologs, Winter-Abukumawase carried insensitive alleles Ppd-B1a and Ppd-D1a and Chihokukomugi carried a single insensitive allele (Ppd-A1a) that was first found in common wheat. The genomic sequence of Ppd-1 homoeologs including the 5′ upstream region was determined and compared between the two genotypes. Ppd-D1a of Winter-Abukumawase had a deletion of 2,089 bp that was already reported for Ciano 67. Critical sequence polymorphism causing photoperiod insensitivity was not detected from the translation start codon to the 3′ untranslated region of Ppd-A1 and Ppd-B1. However, novel mutations were found in the 5′ upstream region. Ppd-A1a of Chihokukomugi had a deletion of 1,085 bp and Ppd-B1a of Winter-Abukumawase had an insertion of 308 bp. A total of 80 DH lines were classified into eight genotypes by PCR-based genotyping using specific primer sets to detect the In/Dels in the 5′ upstream region of three Ppd-1 genes. The heading dates of the DH lines differed significantly between the eight genotypes, showing that each of the three insensitive alleles accelerates heading by 7–9 days compared with the photoperiod-sensitive genotype. Interaction between the three genes was also significant.     

Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat

The introgression of Reduced height (Rht)-B1b and Rht-D1b into bread wheat (Triticum aestivum) varieties beginning in the 1960s led to improved lodging resistance and yield, providing a major contribution to the ‘green revolution’. Although wheat Rht-1 and surrounding sequence is available, the genetic composition of this region has not been examined in a homoeologous series. To determine this, three Rht-1-containing bacterial artificial chromosome (BAC) sequences derived from the A, B, and D genomes of the bread wheat variety Chinese Spring (CS) were fully assembled and analyzed. This revealed that Rht-1 and two upstream genes were highly conserved among the homoeologs. In contrast, transposable elements (TEs) were not conserved among homoeologs with the exception of intronic miniature inverted-repeat TEs (MITEs). In relation to the Triticum urartu ancestral line, CS-A genic sequences were highly conserved and several colinear TEs were present. Comparative analysis of the CS wheat BAC sequences with assembled Poaceae genomes showed gene synteny and amino acid sequences were well preserved. Further 5′ and 3′ of the wheat BAC sequences, a high degree of gene colinearity is present among the assembled Poaceae genomes. In the 20 kb of sequence flanking Rht-1, five conserved non-coding sequences (CNSs) were present among the CS wheat homoeologs and among all the Poaceae members examined. Rht-A1 was mapped to the long arm of chromosome 4 and three closely flanking genetic markers were identified. The tools developed herein will enable detailed studies of Rht-1 and linked genes that affect abiotic and biotic stress response in wheat.     

Single nucleotide polymorphism tightly linked to a major QTL on chromosome 7A for both kernel length and kernel weight in wheat

Thousand-kernel weight (TKW) is one of the major components of grain yield in wheat (Triticum aestivum). Identifying major quantitative trait loci (QTLs) for TKW and developing effective markers are prerequisite for success in marker-assisted selection (MAS) to improve wheat yield through breeding. This study mapped a major QTL, designated as TaTKW-7AL, for increasing TKW on the long arm of chromosome 7A of ‘Clark’ to a 1.3-cM interval between single nucleotide polymorphism (SNP) markers IWB13913 and IWA5913. This QTL explained 19.7 % of the phenotypic variation for TKW. A QTL for increasing kernel length (KL), one of the major components of TKW, was mapped in the same interval as TaTKW-7AL, suggesting that increased TKW by the QTL in ‘Clark’ is most likely due to the increased KL. Association analysis on a diversity panel of 200 US winter wheat accessions also identified a haplotype of three SNP markers (IWB13913, IWB6693 and IWA5913) that were tightly associated with the both KL and TKW. The analysis of allele frequencies of the haplotype in the diversity panel suggested that the favorable allele of TaTKW-7AL has not been strongly selected for in practice and has potential to be used to improve grain yield in US hard winter wheat breeding. Two user-friendly flanking KASPar markers, IWB13913 and IWA5913, were developed for MAS of TaTKW-7AL.     

Recent emergence of the wheat Lr34 multi-pathogen resistance: insights from haplotype analysis in wheat, rice, sorghum and Aegilops tauschii

Spontaneous sequence changes and the selection of beneficial mutations are driving forces of gene diversification and key factors of evolution. In highly dynamic co-evolutionary processes such as plant-pathogen interactions, the plant’s ability to rapidly adapt to newly emerging pathogens is paramount. The hexaploid wheat gene Lr34, which encodes an ATP-binding cassette (ABC) transporter, confers durable field resistance against four fungal diseases. Despite its extensive use in breeding and agriculture, no increase in virulence towards Lr34 has been described over the last century. The wheat genepool contains two predominant Lr34 alleles of which only one confers disease resistance. The two alleles, located on chromosome 7DS, differ by only two exon-polymorphisms. Putatively functional homoeologs and orthologs of Lr34 are found on the B-genome of wheat and in rice and sorghum, but not in maize, barley and Brachypodium. In this study we present a detailed haplotype analysis of homoeologous and orthologous Lr34 genes in genetically and geographically diverse selections of wheat, rice and sorghum accessions. We found that the resistant Lr34 haplotype is unique to the wheat D-genome and is not found in the B-genome of wheat or in rice and sorghum. Furthermore, we only found the susceptible Lr34 allele in a set of 252 Ae. tauschii genotypes, the progenitor of the wheat D-genome. These data provide compelling evidence that the Lr34 multi-pathogen resistance is the result of recent gene diversification occurring after the formation of hexaploid wheat about 8,000 years ago.     

Characterization of grain protein content gene (<Emphasis Type="Italic">GPC</Emphasis>-<Emphasis Type="Italic">B1</Emphasis>) introgression lines and its potential use in breeding for enhanced grain zinc and iron concentration in spring wheat

At least two billion people around the world suffer from micronutrient deficiency, or hidden hunger, which is characterized by iron-deficiency anemia, vitamin A and zinc deficiency. As a key staple food crop, wheat provides 20% of the world’s dietary energy and protein, therefore wheat is an ideal vehicle for biofortification. Developing biofortified wheat varieties with genetically enhanced levels of grain zinc (Zn) and iron (Fe) concentrations, and protein content provides a cost-effective and sustainable solution to the resource-poor wheat consumers. Large genetic variation for Fe and Zn were found in the primitive and wild relatives of wheat, the potential high Zn and Fe containing genetic resources were used as progenitors to breed high-yielding biofortified wheat varieties with 30–40% higher Zn content. Grain protein content (GPC) determines processing and end-use quality of wheat for making diverse food products. The GPC-B1 allele from Triticum turgidum L. var. dicoccoides have been well characterized for the increase in GPC and the associated pleiotropic effect on grain Zn and Fe concentrations in wheat. In this study effect of GPC-B1 allele on grain Zn and Fe concentrations in wheat were measured in different genetic backgrounds and two different agronomic management practices (with- and without foliar Zn fertilization). Six pairs of near-isogenic lines differing for GPC-B1 gene evaluated at CIMMYT, Mexico showed that GPC-B1 influenced marginal increase for grain Zn, Fe concentrations, grain protein content and slight reduction in kernel weight and grain yield. However, the magnitude of GPC and grain Zn and Fe reductions varied depending on the genetic background. Introgression of GPC-B1 functional allele in combination with normal or delayed maturity alleles in the CIMMYT elite wheat germplasm has the potential to improve GPC and grain Zn and Fe concentrations without the negative effect on grain yield due to early senescence and accelerated maturity.     

Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments

Key message

We identified 27 stable loci associated with agronomic traits in spring wheat using genome-wide association analysis, some of which confirmed previously reported studies. GWAS peaks identified in regions where no QTL for grain yield per se has been mapped to date, provide new opportunities for gene discovery and creation of new cultivars with desirable alleles for improving yield and yield stability in wheat.

Abstract

We undertook large-scale genetic analysis to determine marker-trait associations (MTAs) underlying agronomic and physiological performance in spring wheat using genome-wide association studies (GWAS). Field trials were conducted at seven sites in three countries (Sudan, Egypt, and Syria) over 2–3 years in each country. Twenty-five agronomic and physiological traits were measured on 188 wheat genotypes. After correcting for population structure and relatedness, a total of 245 MTAs distributed over 66 loci were associated with agronomic traits in individual and mean performance across environments respectively; some of which confirmed previously reported loci. Of these, 27 loci were significantly associated with days to heading, thousand kernel weight, grain yield, spike length, and leaf rolling for mean performance across environments. Despite strong QTL by environment interactions, eight of the loci on chromosomes 1A, 1D, 5A, 5D, 6B, 7A, and 7B had pleiotropic effects on days to heading and yield components (TKW, SM^?2, and SNS). The winter-type alleles at the homoeologous VRN1 loci significantly increased days to heading and grain yield in optimal environments, but decreased grain yield in heat prone environments. Top 20 high-yielding genotypes, ranked by additive main effects and multiplicative interaction (AMMI), had low kinship relationship and possessed 4–5 favorable alleles for GY MTAs except two genotypes, Shadi-4 and Qafzah-11/Bashiq-1–2. This indicated different yield stability mechanisms due to potentially favorable rare alleles that are uncharacterized. Our results will enable wheat breeders to effectively introgress several desirable alleles into locally adapted germplasm in developing wheat varieties with high yield stability and enhanced heat tolerance.

     

Chromosomal location of wheat genes of the carotenoid biosynthetic pathway and evidence for a catalase gene on chromosome 7A functionally associated with flour b* colour variation

Knowledge of molecular and genetic mechanisms controlling wheat grain quality characteristics is significant for improving flour for end-product functionality. Flour b* colour is an important quality trait for breeding wheat varieties to produce grain for specific market requirements. The degree of flour yellowness is due to the accumulation of carotenoids in grain, particularly lutein. Flour b* is under polygenic control and quantitative trait loci (QTL) have frequently been reported on chromosome 7AL. Analysis of carotenoid genes showed that phytoene synthase (PSY) co-located to the QTL on 7AL but other genes at this locus are also thought to contribute flour b* colour variation. This study used the wheat genome survey sequence and identified the chromosomal location of all wheat carotenoid genes, but none other than PSY were located on 7AL and, therefore, other genes may control flour b* colour variation including oxidative genes that degrade carotenoids. An investigation of EST bin mapped to 7AL identified a gene encoding a catalase enzyme (Cat3-A1) that was phylogenetically related to other plant class III enzymes, co-located to the QTL for flour b* colour variation on 7AL in three mapping populations and expressed during seed development. Therefore, Cat3-A1 was functionally associated with flour b* colour variation. Catalase acts upon hydrogen peroxide as a substrate and it was postulated that Cat3-A1 alleles control varying degrees of bleaching action on lutein in developing wheat grain. Markers for Cat3-A1 developed in this study can be used in conjunction with other candidate gene markers including phytoene synthase and lycopene-ε-cylase to develop a molecular signature for selecting lines with specific flour b* colour values in wheat breeding.     

Gene editing of the wheat homologs of TONNEAU1‐recruiting motif encoding gene affects grain shape and weight in wheat

Grain size and weight are important components of a suite of yield‐related traits in crops. Here, we showed that the CRISPR‐Cas9 gene editing of TaGW7, a homolog of rice OsGW7 encoding a TONNEAU1‐recruiting motif (TRM) protein, affects grain shape and weight in allohexaploid wheat. By editing the TaGW7 homoeologs in the B and D genomes, we showed that mutations in either of the two or both genomes increased the grain width and weight but reduced the grain length. The effect sizes of mutations in the TaGW7 gene homoeologs coincided with the relative levels of their expression in the B and D genomes. The effects of gene editing on grain morphology and weight traits were dosage dependent with the double‐copy mutant showing larger effect than the respective single copy mutants. The TaGW7‐centered gene co‐expression network indicated that this gene is involved in the pathways regulating cell division and organ growth, also confirmed by the cellular co‐localization of TaGW7 with α‐ and β‐tubulin proteins, the building blocks of microtubule arrays. The analyses of exome capture data in tetraploid domesticated and wild emmer, and hexaploid wheat revealed the loss of diversity around TaGW7‐associated with domestication selection, suggesting that TaGW7 is likely to play an important role in the evolution of yield component traits in wheat. Our study showed how integrating CRISPR‐Cas9 system with cross‐species comparison can help to uncover the function of a gene fixed in wheat for allelic variants targeted by domestication selection and select targets for engineering new gene variants for crop improvement.     

Cloning of <Emphasis Type="Italic">TaTPP-6AL1</Emphasis> associated with grain weight in bread wheat and development of functional marker

Trehalose 6-phosphate phosphatase (TPP) dephosphorylates trehalose 6-phosphate to trehalose, an important growth regulator, and is involved in starch accumulation and grain yield. In this study, wheat TPP homologs were isolated from chromosomes 6AL, 6BL, and 6DL, designated as TaTPP-6AL1, TaTPP-6BL1, and TaTPP-6DL1, respectively. Sequence alignment showed a single-nucleotide polymorphism (SNP) at TaTPP-6AL1 locus between cultivars with contrasting thousand grain weight (TGW), forming alleles TaTPP-6AL1a and TaTPP-6AL1b, respectively. A cleaved amplified polymorphic sequence (CAPS) marker, TaTPP-6AL1-CAPS, was developed to differentiate the two alleles. TaTPP-6AL1 was mapped within the interval of IWB65749 and IWB60449 in a recombinant inbred line (RIL) population derived from Zhou8425B/Chinese Spring using the wheat 90K SNP assay. A QTL for TGW identified in the interval explained 12.1–19.1% of the phenotypic variance across five environments. Association analysis on 141 Chinese wheat cultivars also indicated a significant correlation of TaTPP-6AL1 with TGW. In conclusion, TaTPP-6AL1 and its functional marker are valuable to improve grain yield in wheat breeding.     

Improving the yellow pigment content of bread wheat flour by selecting the three homoeologous copies of Psy1

The yellow pigment content (YPC) of endosperm affects the quality and nutritional value of wheat grain products. Major quantitative trait loci (QTL) for endosperm YPC have been repeatedly mapped on chromosomes 7A and 7B in durum and bread wheats. The genes coding for phytoene synthase (PSY1), which is involved in the biosynthesis of carotenoids, generally co-segregate with these QTL, indicating their role in determining YPC. Here, to study the genetic factors underlying endosperm YPC in bread wheat, the sequence polymorphism of the homoeologous A, B and D copies of genes coding for PSY1, Psy-A1, Psy-B1, and Psy-D1, was studied in a worldwide core collection, which was also phenotyped for flour YPC. Seven novel alleles of Psy-A1 and two novel alleles of Psy-B1 were detected, which confirms the high level of polymorphism of these genes. Two major QTL with respective candidate genes Psy-A1 and Psy-B1 were identified in the distal region of chromosomes 7A and 7B using progeny of a cross between Apache and Ornicar, high and low YPC cultivars, respectively. Association mapping confirms the role of these genes in YPC and shows that the D copy also significantly influences this trait. These results indicate that breeders need to consider all three Psy1 copies when seeking to improve the YPC of wheat endosperm.     

Development of a complete set of wheat–barley group-7 Robertsonian translocation chromosomes conferring an increased content of β-glucan

Key message

A complete set of six compensating Robertsonian translocation chromosomes involving barley chromosome 7H and three chromosomes of hexaploid wheat was produced. Grain β-glucan content increased in lines containing 7HL.

Abstract

Many valuable genes for agronomic performance, disease resistance and increased yield have been transferred from relative species to wheat (Triticum aestivum L.) through whole-arm Robertsonian translocations (RobT). Although of a great value, the sets of available translocations from barley (Hordeum vulgare L.) are limited. Here, we present the production of a complete set of six compensating RobT chromosomes involving barley chromosome 7H and three group-7 chromosomes of wheat. The barley group-7 long-arm RobTs had a higher grain β-glucan content compared to the wheat control. The β-glucan levels varied depending on the temperature and were higher under hot conditions. Implicated in this increase, the barley cellulose synthase-like F6 gene (CslF6) responsible for β-glucan synthesis was physically mapped near the centromere in the long arm of barley chromosome 7H. Likewise, wheat CslF6 homoeologs were mapped near the centromere in the long arms of all group-7 wheat chromosomes. With the set of novel wheat–barley translocations, we demonstrate a valuable increase of β-glucan, along with a resource of genetic stocks that are likely to carry many other important genes from barley into wheat.

     

Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population

Key message

Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields.

Abstract

Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur?×?Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity (QG_(1–5).asl-7A), one for leaf Na⁺ exclusion (QNa.asl-7A) and four for leaf K⁺ accumulation (QK.asl-2B.1, QK.asl-2B.2, QK.asl-5A and QK:Na.asl-6A). The beneficial allele for QG_(1–5).asl-7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na⁺ exclusion and/or K⁺ maintenance at three QTL (QNa.asl-7A, QK.asl-2B.2 and QK:Na.asl-6A) excluded more Na⁺ or accumulated more K⁺ compared to lines without these alleles. Importantly, the QK.asl-2B.2 allele for higher K⁺ accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.

     

Sequence diversity, haplotype analysis, association mapping and functional marker development in the waxy and starch synthase IIa genes for grain-yield-related traits in hexaploid wheat (Triticum aestivum L.)

Development of high-yielding cereal crops could meet increasing global demands for food, feed and bio-fuels. Wheat is one of the world??s most important cereal crops. The biosynthesis of starch is the major determinant of yield in wheat. Two starch biosynthesis genes, the waxy (Wx) genes and the starch synthase IIa (SSIIa) genes, were amplified and sequenced in 92 diverse wheat genotypes using genome-specific primers. Nucleotide diversity, haplotype analysis and association mapping were performed. The first exon (5??-UTR) and the first intron of the three homoeologous Wx genes were isolated using expressed sequence tag sequences. The Wx genes contained 12 exons separated by 11 introns. SNP (single nucleotide polymorphism) frequency ranged from 1 SNP/3,648?bp for Wx-D1 to 1 SNP/135?bp for SSIIa-A1, with an average of 1 SNP/230?bp. The average SNP frequencies in exon and intron regions were 1 SNP/322?bp and 1 SNP/228?bp, respectively. Thirty, 23 and 5 SNPs were identified and formed five, six and five haplotypes for SSIIa-A1, SSIIa-B1 and SSIIa-D1, respectively. However, no association was found between these SNPs and seven yield-related traits. Twenty-two, 15 and 1 SNPs were detected and formed nine, five and two haplotypes for Wx-A1, Wx-B1 and Wx-D1, respectively. Three unique nucleotides C+A+T at SNP5, SNP6 and SNP12 formed Wx-B1-H3, which was significantly associated with increased grain weight, thousand kernel weight, and total starch content in three spring wheat genotypes and five winter wheat genotypes. Cost-effective and co-dominant SNP markers were developed using temperature-switch (TS)-PCR and are being used for marker-assisted selection of doubled haploid lines with enhanced grain yield and starch content in winter wheat breeding programs.     

Identification and characterization of <Emphasis Type="Italic">Rht25</Emphasis>, a locus on chromosome arm 6AS affecting wheat plant height,heading time,and spike development

Key message

This study identified Rht25, a new plant height locus on wheat chromosome arm 6AS, and characterized its pleiotropic effects on important agronomic traits.

Abstract

Understanding genes regulating wheat plant height is important to optimize harvest index and maximize grain yield. In modern wheat varieties grown under high-input conditions, the gibberellin-insensitive semi-dwarfing alleles Rht-B1b and Rht-D1b have been used extensively to confer lodging tolerance and improve harvest index. However, negative pleiotropic effects of these alleles (e.g., poor seedling emergence and reduced biomass) can cause yield losses in hot and dry environments. As part of current efforts to diversify the dwarfing alleles used in wheat breeding, we identified a quantitative trait locus (QHt.ucw-6AS) affecting plant height in the proximal region of chromosome arm 6AS (<?0.4 cM from the centromere). Using a large segregating population (~?2800 gametes) and extensive progeny tests (70–93 plants per recombinant family), we mapped QHt.ucw-6AS as a Mendelian locus to a 0.2 cM interval (144.0–148.3 Mb, IWGSC Ref Seq v1.0) and show that it is different from Rht18. QHt.ucw-6AS is officially designated as Rht25, with Rht25a representing the height-increasing allele and Rht25b the dwarfing allele. The average dwarfing effect of Rht25b was found to be approximately half of the effect observed for Rht-B1b and Rht-D1b, and the effect is greater in the presence of the height-increasing Rht-B1a and Rht-D1a alleles than in the presence of the dwarfing alleles. Rht25b is gibberellin-sensitive and shows significant pleiotropic effects on coleoptile length, heading date, spike length, spikelet number, spikelet density, and grain weight. Rht25 represents a new alternative dwarfing locus that should be evaluated for its potential to improve wheat yield in different environments.

     

Allelic variation and distribution independence of Puroindoline b-B2 variants and their association with grain texture in wheat

In this study, we identify the allelic variation of the Pinb-B2v3 variant, which could be divided into three different alleles, Pinb-B2v3a, Pinb-B2v3b and Pinb-B2v3c. The result of χ² tests showed that the distribution of Puroindoline b-2 variants has different frequencies in common and durum wheats. Analysis of the association of Pinb-B2v with grain hardness indicated that wheat cultivars with Pinb-B2v3b possessed relatively higher single kernel characterization system (SKCS) hardness indices in soft wheat in the 2006–2007 cropping season. Further analysis of SKCS hardness among different Puroindoline B-b2 variants by an F₈ recombinant inbred line (RIL) population containing 350 RILs indicated that lines with Pinb-2v3b were on average 5.4 SKCS hardness index units harder than those carrying the Pinb-2v2 haplotype. Derived cleaved amplified polymorphic sequence markers were developed for identification of Pinb-B2v3b and Pinb-B2v3c alleles and will be useful for screening early generation materials by marker-assisted selection during wheat breeding. The results of quantitative real-time PCR indicated that the relative expression level of Pinb-B2v3b was significantly higher than those of Pinb-B2v2, Pinb-B2v3a and Pinb-B2v3c, that four Pinb-B2 alleles showed the highest relative expression level on the 14th day after anthesis during grain development, and that relative expression levels of Pinb-B2v3b and Pinb-B2v2 in leaf were significantly higher than those in root, suggesting that PINB-2 are possibly not seed-specific proteins and that the expression level of Pinb-B2v3 was possibly positively correlated with grain hardness.     

Application of gliadin polymorphism for pedigree analysis in common wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) from Northern Kazakhstan

Gliadins, seed storage proteins, are popular markers effectively employed for the analysis of common wheat. Gliadin electrophoretic patterns are genotype-specific, reproducible, not dependent on growing conditions and are suitable for germplasm identification complementary to molecular markers. Gliadins have been identified and used in wheat from various countries, but prior to this study little was known about gliadin polymorphism in wheat from Kazakhstan. In this study, 48 alleles of six gliadin-coding loci were identified in 43 cultivars of spring wheat from Northern Kazakhstan. The alleles Gli-A1 f , Gli-B1 e , Gli-D1 a , Gli-A2 p , Gli-B2 d and Gli-D2 e had maximal frequencies in each of the six loci. Identified Gli alleles in the loci formed ‘Gliadin Genetic Formula’ unique for each studied variety, and these were compared to the published data from previously analyzed wheat varieties. Pedigree analysis of 43 varieties studied for gliadin polymorphisms indicated that some Gli alleles were conserved and inherited from the progenitor cultivar Akmolinka 1. In contrast, other Gli alleles were replaced by those from modern germplasms. It is assumed that a higher frequency of gliadin alleles can be associated with the selection of genotypes with improved traits for yield and seed quality in the studied wheat cultivars from Northern Kazakhstan.     

Lycopene-ε-cyclase (e-LCY3A) is functionally associated with quantitative trait loci for flour b* colour on chromosome 3A in wheat (Triticum aestivum L.)

Flour b* colour is an important grain quality parameter for specific wheat end-products. The genetic control of b* colour in Australian wheat accessions is controlled by quantitative trait loci (QTL) on chromosomes 3A, 3B, 7A and 7B accumulating lutein, a compound of the carotenoid biosynthetic pathway. The relationship between lutein accumulation and flour b* colour provides an opportunity to identify sequence variants of genes encoding enzymes from the biosynthetic pathway that may control trait variation. This study identified a single nucleotide polymorphism (SNP) in the gene encoding lycopene-ε-cylcase on chromosome 3A (e-LYC3A) between two wheat accessions Ajana and WAWHT2074, identifying two alleles, e-LYC3Aa and e-LYC3Ab, respectively. e-LCY3Ab was present in 62.5 % of the wheat accessions analysed. A highly significant (P < 0.01) association with QTL on chromosome 3A in two mapping populations indicated that e-LYC3A is functionally associated with b* colour variation in some Australian wheat accessions. The SNP induced a serine/glycine substitution at amino acid residue 123 and a subtle change in protein folding at amino acid residue 119. The e-LYC3A SNP may be considered along with other alleles and genes on homoeologous group 3 and 7 chromosomes for selecting desirable flour b* colour variation in marker-assisted breeding.