Genetic analysis of kernel texture (grain hardness) in a hard red spring wheat (Triticum aestivum L.) bi-parental population

Dissection of a novel major stable QTL on chromosome 7D for grain hardness and its breeding value estimation in bread wheat

Grain hardness (Gh) is important for wheat processing and end-product quality. Puroindolines polymorphism explains over 60% of Gh variation and the novel genetic factors remain to be exploited. In this study, a total of 153 quantitative trait loci (QTLs), clustered into 12 genomic intervals (C1-C12), for 13 quality-related traits were identified using a recombinant inbred line population derived from the cross of Zhongkemai138 (ZKM138) and Chuanmai44 (CM44). Among them, C7 (harboring eight QTLs for different quality-related traits) and C8 (mainly harboring QGh.cib-5D.1 for Gh) were attributed to the famous genes, Rht-D1 and Pina, respectively, indicating that the correlation of involved traits was supported by the pleotropic or linked genes. Notably, a novel major stable QTL for Gh was detected in the C12, QGh.cib-7D, with ZKM138-derived allele increasing grain hardness, which was simultaneously mapped by the BSE-Seq method. The geographic pattern and transmissibility of this locus revealed that the increasing-Gh allele is highly frequently present in 85.79% of 373 worldwide wheat varieties and presented 99.31% transmissibility in 144 ZKM138-derivatives, indicating the non-negative effect on yield performance and that its indirect passive selection has happened during the actual breeding process. Thus, the contribution of this new Gh-related locus was highlighted in consideration of improving the efficiency and accuracy of the soft/hard material selection in the molecular marker-assisted process. Further, TraesCS7D02G099400, TraesCS7D02G098000, and TraesCS7D02G099500 were initially deduced to be the most potential candidate genes of QGh.cib-7D. Collectively, this study provided valuable information of elucidating the genetic architecture of Gh for wheat quality improvement.

Genetic architecture of end-use quality traits in soft white winter wheat

Background

Genetic improvement of end-use quality is an important objective in wheat breeding programs to meet the requirements of grain markets, millers, and bakers. However, end-use quality phenotyping is expensive and laborious thus, testing is often delayed until advanced generations. To better understand the underlying genetic architecture of end-use quality traits, we investigated the phenotypic and genotypic structure of 14 end-use quality traits in 672 advanced soft white winter wheat breeding lines and cultivars adapted to the Pacific Northwest region of the United States.

Results

This collection of germplasm had continuous distributions for the 14 end-use quality traits with industrially significant differences for all traits. The breeding lines and cultivars were genotyped using genotyping-by-sequencing and 40,518 SNP markers were used for association mapping (GWAS). The GWAS identified 178 marker-trait associations (MTAs) distributed across all wheat chromosomes. A total of 40 MTAs were positioned within genomic regions of previously discovered end-use quality genes/QTL. Among the identified MTAs, 12 markers had large effects and thus could be considered in the larger scheme of selecting and fixing favorable alleles in breeding for end-use quality in soft white wheat germplasm. We also identified 15 loci (two of them with large effects) that can be used for simultaneous breeding of more than a single end-use quality trait. The results highlight the complex nature of the genetic architecture of end-use quality, and the challenges of simultaneously selecting favorable genotypes for a large number of traits. This study also illustrates that some end-use quality traits were mainly controlled by a larger number of small-effect loci and may be more amenable to alternate selection strategies such as genomic selection.

Conclusions

In conclusion, a breeder may be faced with the dilemma of balancing genotypic selection in early generation(s) versus costly phenotyping later on.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08676-5.

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

Bread wheat is a highly adaptable food crop grown extensively around the world and its quality genetic improvement has received wide attention. In this study, the genetic loci associated with five quality traits including protein content (PC), gluten content (GC), baking value (BV), grain hardness (HA), and sedimentation value (SV) in a population of 253 Chinese wheat grown in Inner Mongolia were investigated through genome wide association mapping. A total of 103 QTL containing 556 SNPs were significantly related to the five quality traits based on the phenotypic data collected from three environments and BLUP data. Of these QTL, 32 QTL were continuously detected under at least two experiments. Some QTL such as qBV3D.2/qHA3D.2 on 3D, qPC5A.3/qGC5A on 5A, qBV5D/qHA5D on 5D, qBV6B.2/qHA6B.3 on 6B, and qBV6D/qHA6D.1 on 6D were associated with multiple traits. In addition, distribution of favorable alleles of the stable QTL in the association panel and their effects on five quality traits were validated. Analysis of existing transcriptome data revealed that 34 genes were specifically highly expressed in grains during reproductive growth stages. The functions of these genes will be characterized in future experiments. This study provides novel insights into the genetic basis of quality traits in wheat.

Genome-wide association mapping of the 'super-soft' kernel texture in white winter wheat

The novel super-soft kernel phenotype has the potential to improve wheat processing and flour quality. We identified genomic regions associated with this kernel texture in white winter wheat. Grain hardness is a key determinant of wheat milling and baking quality. The recently discovered 'super-soft' kernel phenotype has the potential to improve wheat processing and flour quality. However, the genetic basis underlying the super-soft trait in wheat is not yet well understood. In this study, we investigated the phenotypic and genotypic structure of the super-soft trait in a collection of 172 advanced soft white winter wheat breeding lines and cultivars adapted to the Pacific Northwest region of the USA. This collection had a continuous distribution for grain hardness index (single-kernel characterization system). Ten super-soft genotypes showed hardness index ≤ 12 including the cultivar Jasper. Over 98,000 SNP markers from genotyping-by-sequencing were used for association mapping (GWAS). The GWAS identified 20 significant markers associated with grain hardness. These significant SNPs corresponded to seven QTL on chromosomes 2B, 3A, 3B, 5A, 6B,7A, and one unaligned chromosome. Two of these QTL, QSKhard.wql-3A and QSKhard.wql-5A, had large effects and distinguished between the normal soft and the super-soft classes. QSKhard.wql-3A and QSKhard.wql-5A reduced the hardness index by 11.7 and 13.1 on average, respectively. The remaining QTL had small effects and reduced grain hardness within the normal soft range. QSKhard.wql-2B, QSKhard.wql-3A, QSKhard.wql-3B, and QSKhard.wql-6B were not previously reported to be in genomic regions of grain hardness-related genes/QTL. The identified super-soft genotypes as well as the SNPs associated with lower grain hardness will be useful to assist breeding for this grain texture trait.

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.

Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat

Kernel hardness is one of the most important single traits of wheat seed. It classifies wheat cultivars, determines milling quality and affects many end-use qualities. Starch granule surfaces, polar lipids, storage protein matrices and Puroindolines potentially form a four-way interaction that controls wheat kernel hardness. As a genetic factor, Puroindoline polymorphism explains over 60% of the variation in kernel hardness. However, genetic factors other than Puroindolines remain to be exploited. Over the past two decades, efforts using population genetics have been increasing, and numerous kernel hardness-associated quantitative trait loci (QTLs) have been identified on almost every chromosome in wheat. Here, we summarize the state of the art for mapping kernel hardness. We emphasize that these steps in progress have benefitted from (1) the standardized methods for measuring kernel hardness, (2) the use of the appropriate germplasm and mapping population, and (3) the improvements in genotyping methods. Recently, abundant genomic resources have become available in wheat and related Triticeae species, including the high-quality reference genomes and advanced genotyping technologies. Finally, we provide perspectives on future research directions that will enhance our understanding of kernel hardness through the identification of multiple QTLs and will address challenges involved in fine-tuning kernel hardness and, consequently, food properties.

Co-expression of high-molecular-weight glutenin subunit 1Ax1 and Puroindoline a (Pina) genes in transgenic durum wheat (Triticum turgidum ssp. durum) improves milling and pasting quality

BACKGROUND

Durum wheat is considered not suitable for making many food products that bread wheat can. This limitation is largely due to: (i) lack of grain-hardness controlling genes (Puroindoline a and b) and consequently extremely-hard kernel; (ii) lack of high- and low-molecular-weight glutenin subunit loci (Glu-D1 and Glu-D3) that contribute to gluten strength. To improve food processing quality of durum wheat, we stacked transgenic Pina and HMW-glutenin subunit 1Ax1 in durum wheat and developed lines with medium-hard kernel texture.

RESULTS

Here, we demonstrated that co-expression of Pina + 1Ax1 in durum wheat did not affect the milling performance that was enhanced by Pina expression. While stacking of Pina + 1Ax1 led to increased flour yield, finer flour particles and decreased starch damage compared to the control lines. Interestingly, Pina and 1Ax1 co-expression showed synergistic effects on the pasting attribute peak viscosity. Moreover, Pina and 1Ax1 co-expression suggests that PINA impacts gluten aggregation via interaction with gluten protein matrix.

CONCLUSIONS

The results herein may fill the gap of grain hardness between extremely-hard durum wheat and the soft kernel durum wheat, the latter of which has been developed recently. Our results may also serve as a proof of concept that stacking Puroindolines and other genes contributing to wheat end-use quality from the A and/or D genomes could improve the above-mentioned bottleneck traits of durum wheat and help to expand its culinary uses.

Sequence Diversity and Identification of Novel Puroindoline and Grain Softness Protein Alleles in Elymus, Agropyron and Related Species

The puroindoline proteins, PINA and PINB, which are encoded by the Pina and Pinb genes located at the Ha locus on chromosome 5D of bread wheat, are considered to be the most important determinants of grain hardness. However, the recent identification of Pinb-2 genes on group 7 chromosomes has stressed the importance of considering the effects of related genes and proteins. Several species related to wheat (two diploid Agropyron spp., four tetraploid Elymus spp. and five hexaploid Elymus and Agropyron spp.) were therefore analyzed to identify novel variation in Pina, Pinb and Pinb-2 genes which could be exploited for the improvement of cultivated wheat. A novel sequence for the Pina gene was detected in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus and Elymus nutans and novel PINB sequences in Elymus burchan-buddae, Elymus dahuricus subsp. excelsus, and Elymus nutans. A novel PINB-2 variant was also detected in Agropyron repens and Elymus repens. The encoded proteins detected all showed changes in the tryptophan-rich domain as well as changes in and/or deletions of basic and hydrophobic residues. In addition, two new AGP sequences were identified in Elymus nutans and Elymus wawawaiensis. The data presented therefore highlight the sequence diversity in this important gene family and the potential to exploit this diversity to modify grain texture and end-use quality in wheat.