Exploring diverse wheat germplasm for novel alleles in HMW-GS for bread quality improvement

A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew

Crop wild relatives offer natural variations of disease resistance for crop improvement. Here, we report the isolation of broad-spectrum powdery mildew resistance gene Pm36, originated from wild emmer wheat, that encodes a tandem kinase with a transmembrane domain (WTK7-TM) through the combination of map-based cloning, PacBio SMRT long-read genome sequencing, mutagenesis, and transformation. Mutagenesis assay reveals that the two kinase domains and the transmembrane domain of WTK7-TM are critical for the powdery mildew resistance function. Consistently, in vitro phosphorylation assay shows that two kinase domains are indispensable for the kinase activity of WTK7-TM. Haplotype analysis uncovers that Pm36 is an orphan gene only present in a few wild emmer wheat, indicating its single ancient origin and potential contribution to the current wheat gene pool. Overall, our findings not only provide a powdery mildew resistance gene with great potential in wheat breeding but also sheds light into the mechanism underlying broad-spectrum resistance.

Effect of high molecular weight glutenin subunits on wheat quality properties, across a wide range of climates and environments in Iran

High molecular weight glutenin subunits (HMW-GSs) at the Glu-1 loci play an important role in the variation of dough strength, elasticity, and end-use quality of bread wheat. Multilocation trials in a wide range of climatic conditions and crop management practices help explain the role of HMW-GSs in the rheological properties of dough. In the current study, allelic variation of HMWs and quality scores were determined in 28 bread wheat cultivars across a wide range of climates and locations in Iran. Twelve HMW-GSs subunits (3 at Glu-A1, 7 at Glu-B1 and 2 at Glu D-1) in 16 unique combinations were identified in the studied cultivars. In the most rheological properties associated with good bread-making quality, the compositions of 1/17 + 18/5 + 10, 1/13 + 16/5 + 10 and 2*/7 + 9/5 + 10 (all with a quality score of 10) had significantly higher values than the other allelic compositions. While, the lowest values were observed in 1/21 + 19/2 + 12 (quality score of 6). The degree of dough softening was significantly greater in 1/21 + 19/2 + 12 than other allelic combinations. At Glu-A1, Glu-B1 and Glu-D1, 2*, 17 + 18 and 5 + 10 had significantly greater qualitative and rheological properties than the other subunits, which are related to the good quality of wheat flour. While null at Glu-A1, subunits 21 + 19 at Glu-B1 and 2 + 12 at Glu-D1 were associated with weak baking quality. Moreover, the highest dough softening values at Glu-A1, Glu-B1 and Glu-D1 were observed in null, 21 + 19 and 2 + 12 subunits, respectively. A negative and significant correlation (P < 0.05) was observed between the degree of dough softening and other qualitative and rheological properties related to good bread-making performance. The results of this study demonstrated the role of HMW-GSs in determining the end-use quality of bread wheat across a wide range of climates and environments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01324-6.

Multiomics Based Association Mapping in Wheat Reveals Genetic Architecture of Quality and Allergenic Related Proteins

Wheat is an important staple crop since its proteins contribute to human and animal nutrition and are important for its end-use quality. However, wheat proteins can also cause adverse human reactions for a large number of people. We performed a genome wide association study (GWAS) on 114 proteins quantified by LC-MS-based proteomics and expressed in an environmentally stable manner in 148 wheat cultivars with a heritability > 0.6. For 54 proteins, we detected quantitative trait loci (QTL) that exceeded the Bonferroni-corrected significance threshold and explained 17.3−84.5% of the genotypic variance. Proteins in the same family often clustered at a very close chromosomal position or the potential homeolog. Major QTLs were found for four well-known glutenin and gliadin subunits, and the QTL segregation pattern in the protein encoding the high molecular weight glutenin subunit Dx5 could be confirmed by SDS gel-electrophoresis. For nine potential allergenic proteins, large QTLs could be identified, and their measured allele frequencies open the possibility to select for low protein abundance by markers as long as their relevance for human health has been conclusively demonstrated. A potential allergen was introduced in the beginning of 1980s that may be linked to the cluster of resistance genes introgressed on chromosome 2AS from Triticum ventricosum. The reported sequence information for the 54 major QTLs can be used to design efficient markers for future wheat breeding.

Indian Wheat Genomics Initiative for Harnessing the Potential of Wheat Germplasm Resources for Breeding Disease-Resistant, Nutrient-Dense, and Climate-Resilient Cultivars

Wheat is one of the major staple cereal food crops in India. However, most of the wheat-growing areas experience several biotic and abiotic stresses, resulting in poor quality grains and reduced yield. To ensure food security for the growing population in India, there is a compelling need to explore the untapped genetic diversity available in gene banks for the development of stress-resistant/tolerant cultivars. The improvement of any crop lies in exploring and harnessing the genetic diversity available in its genetic resources in the form of cultivated varieties, landraces, wild relatives, and related genera. A huge collection of wheat genetic resources is conserved in various gene banks across the globe. Molecular and phenotypic characterization followed by documentation of conserved genetic resources is a prerequisite for germplasm utilization in crop improvement. The National Genebank of India has an extensive and diverse collection of wheat germplasm, comprising Indian wheat landraces, primitive cultivars, breeding lines, and collection from other countries. The conserved germplasm can contribute immensely to the development of wheat cultivars with high levels of biotic and abiotic stress tolerance. Breeding wheat varieties that can give high yields under different stress environments has not made much headway due to high genotypes and environmental interaction, non-availability of truly resistant/tolerant germplasm, and non-availability of reliable markers linked with the QTL having a significant impact on resistance/tolerance. The development of new breeding technologies like genomic selection (GS), which takes into account the G × E interaction, will facilitate crop improvement through enhanced climate resilience, by combining biotic and abiotic stress resistance/tolerance and maximizing yield potential. In this review article, we have summarized different constraints being faced by Indian wheat-breeding programs, challenges in addressing biotic and abiotic stresses, and improving quality and nutrition. Efforts have been made to highlight the wealth of Indian wheat genetic resources available in our National Genebank and their evaluation for the identification of trait-specific germplasm. Promising genotypes to develop varieties of important targeted traits and the development of different genomics resources have also been highlighted.

Characterization of Glutenin Genes in Bread Wheat by Third-Generation RNA Sequencing and the Development of a Glu-1Dx5 Marker Specific for the Extra Cysteine Residue

High-molecular-weight glutenin subunits (HMW-GS) and low-molecular-weight glutenin subunits (LMW-GS) in a mature grain play important roles in the formation of a glutenin macropolymer and gluten quality. To characterize the expressed glutenin genes of the bread wheat variety Xinmai 26 during seed development, a total of 18 full-length transcripts were obtained by the newly emerged third-generation RNA sequencing of the PacBio Sequel II platform, including 5 transcripts of HMW-GS genes and 13 transcripts of LMW-GS genes (8 intact genes and 5 pseudogenes). Combined with the patterns of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), allelic types of the obtained glutenin genes were, respectively, determined, wherein molecular characterization deduced by transcript1528 (1Dx5) and transcript907 (Glu-A3c) indicated their great influence on dough quality. In addition, a specific functional marker dCAPS5 was developed for the single-nucleotide substitution at position 353 of the 1Dx5 subunit, which was further intensively compared with the other proposed markers to efficiently utilize the 1Dx5 subunit with the extra cysteine residue. This study provides an efficient method to accurately identify and utilize glutenin genes in bread wheat, which is helpful in understanding the contributions of glutenin genes to wheat quality.

Allelic variation and genetic diversity of HMW glutenin subunits in Chinese wheat (Triticum aestivum L.) landraces and commercial cultivars

Wheat landraces have abundant genetic variation at the Glu-1 loci, which is desirable germplasms for genetic enhancement of modern wheat varieties, especially for quality improvement. In the current study, we analyzed the allelic variations of the Glu-1 loci of 597 landraces and 926 commercial wheat varieties from the four major wheat-growing regions in China using SDS-PAGE. As results, alleles Null, 7+8, and 2+12 were the dominant HMW-GSs in wheat landraces. Compared to landraces, the commercial varieties contain higher frequencies of high-quality alleles, including 1, 7+9, 14+15 and 5+10. The genetic diversity of the four commercial wheat populations (alleles per locus (A) = 7.33, percent polymorphic loci (P) = 1.00, effective number of alleles per locus (Ae) = 2.347 and expected heterozygosity (He) = 0.563) was significantly higher than that of the landraces population, with the highest genetic diversity found in the Southwestern Winter Wheat Region population. The genetic diversity of HMW-GS is mainly present within the landraces and commercial wheat populations instead of between populations. The landraces were rich in rare subunits or alleles may provide germplasm resources for improving the quality of modern wheat.

Wheat Proteins: A Valuable Resources to Improve Nutritional Value of Bread

Triticum aestivum, commonly known as bread wheat, is one of the most cultivated crops globally. Due to its increasing demand, wheat is the source of many nutritious products including bread, pasta, and noodles containing different types of seed storage proteins. Wheat seed storage proteins largely control the type and quality of any wheat product. Among various unique wheat products, bread is the most consumed product around the world due to its fast availability as compared to other traditional food commodities. The production of highly nutritious and superior quality bread is always a matter of concern because of its increasing industrial demand. Therefore, new and more advanced technologies are currently being applied to improve and enrich the bread, having increased fortified nutrients, gluten-free, highly stable with enhanced shelf-life, and long-lasting. This review focused on bread proteins with improving wheat qualities and nutritional properties using modern technologies. We also describe the recent innovations in processing technologies to improve various quality traits of wheat bread. We also highlight some modern forms of bread that are utilized in different industries for various purposes and future directions.

Exploring the End-Use Quality Potential of a Collection of Spanish Bread Wheat Landraces

Modern plant-breeding practices have narrowed the genetic base of wheat, such that there is a need to introduce new germplasms with underexploited diversity into breeding programs. Wheat landraces are a very valuable resource when searching for genetic variation, which not only possess increased adaptability, but also quality-related traits. Several studies have shown a wide genetic diversity in Spanish wheat landraces compared to other germplasm collections; therefore, the main objective of this study is to analyze the variability in a collection of 189 landraces from the Spanish National Plant Genetic Resources Centre (Centro de Recursos Fitogenéticos, CRF-INIA, Alcalá de Henares), in relation to end-use quality traits. We characterized the whole collection for high-molecular-weight glutenin and puroindoline allelic composition, and for gluten strength. In addition, grain protein content, grains per spike, and thousand kernel weight were evaluated in samples from four-year field trials. The relationship between glutenin composition and quality was evaluated, and some alleles strongly associated with high quality were identified in the collection, some of them specific for Iberian landraces. The results also show the presence of novel variability within high-molecular-weight glutenin and puroindolines, which needs to be characterized further in order to assess its influence on wheat quality. In addition, a set of landraces showing outstanding values for gluten quality and a good agronomic performance was selected for testing in field trials in order to evaluate the suitability of their direct use in cropping systems.

Characterization of high- and low-molecular-weight glutenin subunits from Chinese Xinjiang wheat landraces and historical varieties

Landraces and historical varieties are necessary germplasms for genetic improvement of modern cereals. Allelic variations at the Glu-1 and Glu-3 loci in 300 common wheat landraces and 43 historical varieties from Xinjiang, China, were evaluated by Sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and allele-specific molecular markers. Among the materials investigated, three, nine, and seven alleles were identified from the Glu-A1, Glu-B1, and Glu-D1 loci, respectively, and a total of 26 high-molecular-weight glutenin subunit (HMW-GS) combinations were found, of which 18 combinations were identified in landraces and historical varieties. Allelic frequency of HMW-GS combinations null, 7 + 8, 2 + 12 was found to be the highest in both the landraces (63.3%) and historical varieties (39.5%). Besides, some distinctive HMW-GS alleles, such as the novel Glu-B1 allele 6.1* + 8.1* and Glu-D1 alleles 2.6 + 12, 2.1 + 10.1, and 5** + 10 were observed in Xinjiang wheat landraces. Among the Glu-A3 and Glu-B3 loci of landraces and historical varieties, a total of eight and nine alleles were found, respectively. At each locus, two novel alleles were identified. A total of 33 low-molecular-weight glutenin subunit (LMW-GS) combinations of Glu-A3 and Glu-B3 were identified, with 31 and 14 combinations occurring in landraces and historical varieties, respectively, but only 10 combinations shared by both of them. As Glu-D1, Glu-A3, and Glu-B3 have highest contribution to the end-use quality and processing properties as compared to Glu-A1, Glu-B1, and Glu-D3 locus, the novel or distinctive HMW-GS and LMW-GS alleles in these loci could potentially be utilized for the improvement in the quality of modern wheat.

Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseq^TM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.

Genebanks hold comprehensive collections of wild species, wild relatives, and landraces that are useful for genetic improvement. Here, the authors report the genotype of nearly 80,000 wheat accessions using DArTseq technology to show the less explored genetic diversity.

Gene-ecology of durum wheat HMW glutenin reflects their diffusion from the center of origin

The production of many food items processed from wheat grain relies on the use of high gluten strength flours. As a result, about 80% of the allelic variability in the genes encoding the glutenin proteins has been lost in the shift from landraces to modern cultivars. Here, the allelic variability in the genes encoding the high molecular weight glutenin subunits (HMW-GSs) has been characterized in 152 durum wheat lines developed from a set of landraces. The allelic composition at the two Glu-1 loci (Glu-A1 and -B1) was obtained at both the protein and the DNA level. The former locus was represented by three alleles, of which the null allele Glu-A1c was the most common. The Glu-B1 locus was more variable, with fifteen alleles represented, of which Glu-B1b (HMW-GSs 7 + 8), -B1d (6 + 8) and -B1e (20 + 20) were the most frequently occurring. The composition of HMW-GSs has been used to make inferences regarding the diffusion and diversification of durum wheat. The relationships of these allelic frequencies with their geographical distribution within the Mediterranean basin is discussed in terms of gene-ecology.