High Density Mapping of Quantitative Trait Loci Conferring Gluten Strength in Canadian Durum Wheat

Dissecting Genotype by Environment Interactions in Moroccan Wheat: An Advanced Biplot and Heatmap Analysis Unveiling Agronomic, Quality Traits, and Genotypic Stability for Tailored Breeding Strategies

This five-year study (2016-2021) across diverse Moroccan agro-climatic zones investigated genotype by environment (G × E) interactions in wheat, focusing on variations in agronomic traits and quality attributes such as protein and gluten content. Significant environmental effects were observed on key traits, like yield, thousand kernel weight (TKW), and spikes per square meter (Spk/m2), highlighting environmental factors' role in wheat yield variability. In the Tassaout (TST) location, notable genotypic effects emerged for traits like biomass, underscoring genetic factors' importance in specific contexts, while in Sidi El Aidi (SEA) and Marchouch (MCH), genotypic effects on yield and its components were predominantly absent, indicating a more substantial environmental influence. These findings illustrate the complexity of G × E interactions and the need for breeding strategies considering genetic potential and environmental adaptability, especially given the trade-offs between yield enhancement and quality maintenance. Insights from the biplot and heatmap analyses enhanced the understanding of genotypes' dynamic interactions with environmental factors, establishing a basis for strategic genotype selection and management to optimize wheat yield and quality. This research contributes to sustainable wheat breeding in Morocco, aligning with global efforts to adapt wheat breeding strategies to changing climatic conditions.

Reviving grain quality in wheat through non-destructive phenotyping techniques like hyperspectral imaging

A long-term goal of breeders and researchers is to develop crop varieties that can resist environmental stressors and produce high yields. However, prioritising yield often compromises improvement of other key traits, including grain quality, which is tedious and time-consuming to measure because of the frequent involvement of destructive phenotyping methods. Recently, non-destructive methods such as hyperspectral imaging (HSI) have gained attention in the food industry for studying wheat grain quality. HSI can quantify variations in individual grains, helping to differentiate high-quality grains from those of low quality. In this review, we discuss the reduction of wheat genetic diversity underlying grain quality traits due to modern breeding, key traits for grain quality, traditional methods for studying grain quality and the application of HSI to study grain quality traits in wheat and its scope in breeding. Our critical review of literature on wheat domestication, grain quality traits and innovative technology introduces approaches that could help improve grain quality in wheat.

QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat

BACKGROUND

Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs.

RESULTS

Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation.

CONCLUSIONS

Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.

Multi-omics revolution to promote plant breeding efficiency

Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

Effectiveness of and Perspectives for the Sedimentation Analysis Method in Grain Quality Evaluation in Various Cereal Crops for Breeding Purposes

The existing standardized methods for assessing the quality of marketable grain do not always meet the requirements of the breeding, such as the method’s rapidity, sufficiency of the minimum amount of experimental material, the minimal modifying influence of the external environment on the degree of expression of a criterion, and genetic determination and heritability of the latter. One of the methods that meets these requirements is the sediment volume test. The present study offers an analysis and examples of methodological developments in relation to the assessment of winter bread wheat grain in arid regions of cultivation, as well as of winter triticale. The fluorescent probing method was used as an example for demonstrating the prospects for assessing the swelling of ground grain products of both bread and durum wheat, and for such crops with a less-strong complex of storage polymers as triticale, rye, and millet. A two-stage sedimentation procedure that allows a successful differentiation of samples has been developed for sorghum and maize grain. It is presented here alongside with methodological works on wheat from different countries of the world. Examples of the proven high reproducibility of the sediment volume test in the offspring, and its genetic determination are provided. In general, the data obtained and the material accumulated by various researchers indicate that a modification of the sedimentation method, correctly chosen for specific goals and objectives, solves the problem of assessing grain quality in breeding samples starting from early progenies. All these circumstances make the sedimentation testing the leading or most promising method for assessing grain quality when breeding of a broad range of grain crops is carried out.

Effect of Multi-Year Environmental and Meteorological Factors on the Quality Traits of Winter Durum Wheat

A detailed study was made of the effect of rainfall, average temperature and hot days on the gluten index and Minolta b* value of winter durum wheat sown in the field in 16 consecutive crop years (2005-2020). The joint analysis of these two technological quality traits represented a complex (plant-environment-meteorological factors) approach for the identification of durum wheat cultivars carrying an optimum combination of the two traits and for the determination of quality stability. The results of GGE-biplot analysis indicated that the cultivar that had the most favorable combination of the traits was 'MVP', while cultivar 'GKS' had the best gluten strength and 'MVH' the best yellow pigment content. Correlation analysis and stepwise regression between various meteorological factors (rainfall, mean temperature, number of heat days per 10-day period during grain-filling) and the two technological quality traits indicated that the expected value of the quality traits could be reliably estimated based on meteorological factors, with a generally negative effect on gluten index and a positive one on yellowness in all cultivars.

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

Combining Protein Content and Grain Yield by Genetic Dissection in Bread Wheat under Low-Input Management

The simultaneous improvement of protein content (PC) and grain yield (GY) in bread wheat (Triticum aestivum L.) under low-input management enables the development of resource-use efficient varieties that combine high grain yield potential with desirable end-use quality. However, the complex mechanisms of genotype, management, and growing season, and the negative correlation between PC and GY complicate the simultaneous improvement of PC and GY under low-input management. To identify favorable genotypes for PC and GY under low-input management, this study used 209 wheat varieties, including strong gluten, medium-strong gluten, medium gluten, weak gluten, winter, semi-winter, weak-spring, and spring types, which has been promoted from the 1980s to the 2010s. Allelic genotyping, performed using kompetitive allele-specific polymerase chain reaction (KASP) technology, found 69 types of GY-PC allelic combinations in the tested materials. Field trials were conducted with two growing season treatments (2018–2019 and 2019–2020) and two management treatments (conventional management and low-input management). Multi-environment analysis of variance showed that genotype, management, and growing season had extremely substantial effects on wheat GY and PC, respectively, and the interaction of management × growing season also had extremely significant effects on wheat GY. According to the three-sigma rule of the normal distribution, the GY of wheat varieties Liangxing 66 and Xinmai 18 were stable among the top 15.87% of all tested materials with high GY, and their PC reached mean levels under low-input management, but also stably expressed high GY and high PC under conventional management, which represents a great development potential. These varieties can be used as cultivars of interest for breeding because TaSus1-7A, TaSus1-7B, TaGW2-6A, and TaGW2-6B, which are related to GY, and Glu-B3, which is related to PC, carry favorable alleles, among which Hap-1/2, the allele of TaSus1-7A, and Glu-B3b/d/g/i, the allele of Glu-B3, can be stably expressed. Our results may be used to facilitate the development of high-yielding and high-quality wheat varieties under low-input management, which is critical for sustainable food and nutrition security.

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.

Conditional Mapping Identified Quantitative Trait Loci for Grain Protein Concentration Expressing Independently of Grain Yield in Canadian Durum Wheat

Grain protein concentration (GPC) is an important trait in durum cultivar development as a major determinant of the nutritional value of grain and end-use product quality. However, it is challenging to simultaneously select both GPC and grain yield (GY) due to the negative correlation between them. To characterize quantitative trait loci (QTL) for GPC and understand the genetic relationship between GPC and GY in Canadian durum wheat, we performed both traditional and conditional QTL mapping using a doubled haploid (DH) population of 162 lines derived from Pelissier × Strongfield. The population was grown in the field over 5 years and GPC was measured. QTL contributing to GPC were detected on chromosome 1B, 2B, 3A, 5B, 7A, and 7B using traditional mapping. One major QTL on 3A (QGpc.spa-3A.3) was consistently detected over 3 years accounting for 9.4-18.1% of the phenotypic variance, with the favorable allele derived from Pelissier. Another major QTL on 7A (QGpc.spa-7A) detected in 3 years explained 6.9-14.8% of the phenotypic variance, with the beneficial allele derived from Strongfield. Comparison of the QTL described here with the results previously reported led to the identification of one novel major QTL on 3A (QGpc.spa-3A.3) and five novel minor QTL on 1B, 2B and 3A. Four QTL were common between traditional and conditional mapping, with QGpc.spa-3A.3 and QGpc.spa-7A detected in multiple environments. The QTL identified by conditional mapping were independent or partially independent of GY, making them of great importance for development of high GPC and high yielding durum.

Breeding and biotechnological interventions for trait improvement: status and prospects

Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.