Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Ancient diversity of Triticum aestivum subspecies as source of novel loci for bread wheat improvement

Ancient subspecies of hexaploid wheat, not yet subjected to intensive selection, harbor potentially valuable alternative genetic variability for the genetic improvement of modern cultivated bread wheat. To investigate these hitherto unexplored resources, we established a panel, currently unique, consisting of 190 accessions of Triticum aestivum belonging to five different neglected subspecies, compactum, sphaerococcum, macha, spelta, and vavilovii, with few aestivum references. The panel was genotyped through the iSelect Illumina arrays (20K and 25K) and phenotyped for 25 traits related to phenology, morphology, yield, and physiology for 4 years under field conditions. We found wide variability for all traits analyzed, both within and among subspecies, demonstrating the richness contained therein. Through a genome-wide association study (GWAS), we identified a total of 126 marker-trait associations (MTAs), including 4 for years, 58 for morphological traits, 39 related to yield, and 25 for physiological traits, some of them confirming loci previously published and others being novel. Fourteen MTAs were associated with multiple traits. Among them, one on chromosome 2D at 360.2 Mb was associated with spike density, length, and shape, and thus is of particular interest because it may underlie the compactum (C) gene, until now considered difficult to clone because of its centromeric position. The physical distance defined by this MTA is considerably smaller (1.7 Mb) than what is reported so far in the literature, paving the way toward physical mapping of the C gene. A potential candidate gene has been identified for the trait grain number per spike. This is TraesCS6A03G0476500, coding for a monosaccharide-sensing protein 2, located on chromosome 6A at 233 Mb and identified through an MTA that segregates exclusively in compactum accessions. The results obtained confirm the remarkable potential present in the panel of wheat subspecies analyzed in this study, which, being characterized by a very short linkage disequilibrium (LD) decay, allowed the definition of rather narrow ranges around key traits, such as those related to yield, providing new perspectives on transferring genes across subspecies for wheat improvement.

Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects

The advancement of multi-omics tools has revolutionized the study of complex biological systems, providing comprehensive insights into the molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify and characterize biological elements that contribute to phenotypic traits. This review delves into recent progress in applying multi-omics approaches to elucidate the genetic, epigenetic, and metabolic networks associated with key traits in plants. We emphasize the potential of these integrative strategies to enhance crop improvement, optimize agricultural practices, and promote sustainable environmental management. Furthermore, we explore future prospects in the field, underscoring the importance of cutting-edge technological advancements and the need for interdisciplinary collaboration to address ongoing challenges. By bridging various omics platforms, this review aims to provide a holistic framework for advancing research in plant biology and agriculture.

Genome-wide association study (GWAS) uncovers candidate genes linked to the germination performance of bread wheat (Triticum aestivum L.) under salt stress

BACKGROUND

Improving the germination performance of bread wheat is an important breeding target in many wheat-growing countries where seedlings are often established in soils with high salinity levels. This study sought to characterize the molecular mechanisms underlying germination performance in salt-stressed wheat. To achieve this goal, a genome-wide association study (GWAS) was performed on 292 Iranian bread wheat accessions, including 202 landraces and 90 cultivars.

RESULTS

A total of 10 and 15 functional marker-trait associations (MTAs) were detected under moderate (60 mM NaCl) and severe (120 mM NaCl) salinity, respectively. From genomic annotation, 17 candidate genes were identified that were functionally annotated to be involved in the germination performance of salt-stressed wheat, such as CHX2, PK2, PUBs, and NTP10. Most of these genes play key roles in DNA/RNA/ATP/protein binding, transferase activity, transportation, phosphorylation, or ubiquitination and some harbored unknown functions that collectively may respond to salinity as a complex network.

CONCLUSION

These findings, including the candidate genes, respective pathways, marker-trait associations (MTAs), and in-depth phenotyping of wheat accessions, improve knowledge of the mechanisms responsible for better germination performance of wheat seedlings under salinity conditions.

Genetic Variation in Wheat Root Transcriptome Responses to Salinity: A Comparative Study of Tolerant and Sensitive Genotypes

Salt tolerance is a critical trait for plant survival and productivity in saline environments. Development of salt tolerant crops is a practical strategy for addressing soil salinity issues. In this study, RNA-Seq analysis was performed using two wheat cultivars with contrasting salt tolerance (Neixiang188, tolerant and Barra, sensitive) at 6 h and 24 h after salinity treatment to determine the genetic variations reflected in the RNA expression patterns and identify key genes associated with salt tolerance. Our results revealed that there were 2983 upregulated and 1091 downregulated differentially expressed genes (DEGs), which were found in common in the two accessions. Meanwhile, 529 salt tolerant associated DEGs were subjected to GO function annotation, KEGG enrichment, and protein-protein interaction (PPI) network prediction. Finally, a theoretical framework outlining the salt tolerance mechanisms of Neixiang188 was proposed. It can be inferred that Neixiang188 possesses superior ion homeostasis, ROS detoxification, and osmotic adjustment abilities compared to Barra when subjected to saline stress. The present research sheds light on the genetic foundation of salt tolerance in wheat and offers candidate genes for genetic manipulation. Our research insights enhance the comprehension of the molecular mechanisms underlying salt stress responses and could guide future breeding efforts for improving salt tolerance in crops.

Expression interplay of genes coding for calcium-binding proteins and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca2+ signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3'-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding for calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding proteins was found to be enriched for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of genes coding for proteins with EF-hand domain, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding proteins, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3' -UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability.

Ploidy variation induces butterfly effect on chromatin topology in wheat

Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.

Assessment of the salt tolerance of diverse bread wheat (Triticum aestivum L.) genotypes during the early growth stage under hydroponic culture conditions

Objectives

Soil salinity affects the growth of crop plants, leading to reduced productivity, and is a major challenge for wheat production worldwide. Various adaptations and mitigation approaches in combination with tolerant wheat genotypes can be useful for the sustainability of crop production in saline environments. However, the development of salt-tolerant wheat genotypes is one of the best and most efficient solutions for obtaining desirable yields. Considering these issues, an investigation was carried out under hydroponic nutrient culture conditions to assess the genetic variability and selection of salt-tolerant wheat genotypes by categorizing inequitable morphophysiological and genetic variability as well as multivariate analysis.

Methods

To meet the objectives of this study, 100 wheat genotypes were tested hydroponically in 0 (control) and 15 dS m-1 salt solutions.

Conclusion

For all the wheat genotypes grown under saline conditions, the shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), total fresh weight (TFW), shoot dry weight (SDW), root dry weight (RDW), and total dry weight (TDW) decreased significantly. Furthermore, significant variation was observed among the genotypes in terms of their characteristics only under saline conditions. In the case of genetic diversity analysis, a high genotypic coefficient of variation (GCV), phenotypic coefficient of variation (PCV), genetic advance in the percentage of the mean (GAM) and high heritability (h2b) were recorded for all tested wheat genotypes based on the SDW, RDW and TDW. Correlation analysis for both genotypic and phenotypic relationships revealed strong positive correlations for TDW, SDW, TFW and SFW. Principal component analysis (PCA) revealed that TDW, TFW, SDW, and SFW were the most discriminative variables for the wheat genotypes, which was confirmed by discriminant function analysis (DFA). PCA-biplot analysis also revealed significant positive correlations between SDW and SFW and between TDW and TFW. Hierarchical cluster analysis was performed for ten clusters based on the relative performance of the genotypes, where the genotypes were characterized into salt-tolerant, medium-salt-tolerant, medium-salt-susceptible and salt-susceptible groups. Among the genotypes, G11, G25 and G29 under cluster VII were categorized as salt tolerant based on their outstanding performance in terms of characteristics only under saline conditions. D2 analysis proved that the wheat genotypes of this cluster were highly divergent from the other cluster genotypes; as a result, these genotypes might be utilized as parents in the development of salt-tolerant wheat genotypes. The current study concluded that SDW and TDW could be employed as criteria for selecting and defining salt-tolerant genotypes during the early growth stage of wheat.

KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance

Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.

Exploring Salinity Tolerance Mechanisms in Diverse Wheat Genotypes Using Physiological, Anatomical, Agronomic and Gene Expression Analyses

Salinity is a widespread abiotic stress that devastatingly impacts wheat growth and restricts its productivity worldwide. The present study is aimed at elucidating biochemical, physiological, anatomical, gene expression analysis, and agronomic responses of three diverse wheat genotypes to different salinity levels. A salinity treatment of 5000 and 7000 ppm gradually reduced photosynthetic pigments, anatomical root and leaf measurements and agronomic traits of all evaluated wheat genotypes (Ismailia line, Misr 1, and Misr 3). In addition, increasing salinity levels substantially decreased all anatomical root and leaf measurements except sclerenchyma tissue upper and lower vascular bundle thickness compared with unstressed plants. However, proline content in stressed plants was stimulated by increasing salinity levels in all evaluated wheat genotypes. Moreover, Na+ ions content and antioxidant enzyme activities in stressed leaves increased the high level of salinity in all genotypes. The evaluated wheat genotypes demonstrated substantial variations in all studied characters. The Ismailia line exhibited the uppermost performance in photosynthetic pigments under both salinity levels. Additionally, the Ismailia line was superior in the activity of superoxide dismutase (SOD), catalase activity (CAT), peroxidase (POX), and polyphenol oxidase (PPO) enzymes followed by Misr 1. Moreover, the Ismailia line recorded the maximum anatomical root and leaf measurements under salinity stress, which enhanced its tolerance to salinity stress. The Ismailia line and Misr 3 presented high up-regulation of H+ATPase, NHX2 HAK, and HKT genes in the root and leaf under both salinity levels. The positive physiological, anatomical, and molecular responses of the Ismailia line under salinity stress were reflected on agronomic performance and exhibited superior values of all evaluated agronomic traits.

Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat

Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.

Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat

Genomic regions governing days to heading (DH), days to maturity (DM), plant height (PH), thousand-kernel weight (TKW), and test weight (TW) were investigated in a set of 190 RILs derived from a cross between a widely cultivated wheat-variety, Kachu (DPW-621-50), and a high-zinc variety, Zinc-Shakti. The RIL population was genotyped using 909 DArTseq markers and phenotyped in three environments. The constructed genetic map had a total genetic length of 4665 cM, with an average marker density of 5.13 cM. A total of thirty-seven novel quantitative trait loci (QTL), including twelve for PH, six for DH, five for DM, eight for TKW and six for TW were identified. A set of 20 stable QTLs associated with the expression of DH, DM, PH, TKW, and TW were identified in two or more environments. Three novel pleiotropic genomic-regions harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the DArTseq markers were located on important putative candidate genes such as MLO-like protein, Phytochrome, Zinc finger and RING-type, Cytochrome P450 and pentatricopeptide repeat, involved in the regulation of pollen maturity, the photoperiodic modulation of flowering-time, abiotic-stress tolerance, grain-filling duration, thousand-kernel weight, seed morphology, and plant growth and development. The identified novel QTLs, particularly stable and co-localized QTLs, will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).

Conditional QTL mapping for seed germination and seedling traits under salt stress and candidate gene prediction in wheat

Breeding new wheat varieties with salt resistance is one of the best ways to solve a constraint on the sustainability and expansion of wheat cultivation. Therefore, understanding the molecular components or genes related to salt tolerance must contribute to the cultivation of salt-tolerant varieties. The present study used a recombinant inbred line (RIL) population to genetically dissect the effects of different salt stress concentrations on wheat seed germination and seedling traits using two quantitative trait locus (QTL) mapping methods. A total of 31 unconditional and 11 conditional QTLs for salt tolerance were identified on 11 chromosomes explaining phenotypic variation (PVE) ranging from 2.01 to 65.76%. Of these, 15 major QTLs were found accounting for more than 10% PVE. QTL clusters were detected on chromosomes 2A and 3B in the marker intervals 'wPt-8328 and wPt-2087' and 'wPt-666008 and wPt-3620', respectively, involving more than one salt tolerance trait. QRdw3B and QSfw3B.2 were most consistent in two or more salt stress treatments. 16 candidate genes associated with salt tolerance were predicted in wheat. These results could be useful to improve salt tolerance by marker-assisted selection (MAS) and shed new light on understanding the genetic basis of salt tolerance in wheat.

Genetic Dissection of Drought Tolerance of Elite Bread Wheat (Triticum aestivum L.) Genotypes Using Genome Wide Association Study in Morocco

Drought is one of the most important yield-limiting factors in Morocco. Identification and deployment of drought-tolerant wheat varieties are important to cope with the challenge of terminal moisture stress and increase wheat productivity. A panel composed of 200 elite spring bread wheat genotypes was phenotyped for yield and agronomic traits for 2 years (2020 and 2021) in Morocco under rainfed and irrigated environments. The panel was genotyped using 20K SNPs and, after filtration, a total of 15,735 SNP markers were used for a genome-wide association study (GWAS) using a mixed linear model (MLM) to identify marker-trait associations (MTA) and putative genes associated with grain yield and yield-related traits under rainfed and irrigated conditions. Significant differences were observed among the elite genotypes for grain yield and yield-related traits. Grain yield performance ranged from 0.97 to 6.16 t/ha under rainfed conditions at Sidi Al-Aidi station and from 3.31 to 9.38 t/h under irrigated conditions at Sidi Al-Aidi station, while Grain yield at Merchouch station ranged from 2.32 to 6.16 t/h under rainfed condition. A total of 159 MTAs (p < 0.001) and 46 genes were discovered, with 67 MTAs recorded under rainfed conditions and 37 MTAs recorded under irrigated conditions at the Sidi Al-Aidi station, while 55 MTAs were recorded under rainfed conditions at Merchouch station. The marker ‘BobWhite_c2988_493’ on chromosome 2B was significantly correlated with grain yield under rainfed conditions. Under irrigated conditions, the marker ‘AX-94653560’ on chromosome 2D was significantly correlated with grain yield at Sidi Al-Aidi station. The maker ‘RAC875_c17918_321’ located on chromosome 4A, associated with grain yield was linked with the gene TraesCS4A02G322700, which encodes for F-box domain-containing protein. The markers and candidate genes discovered in this study should be further validated for their potential use in marker-assisted selection to generate high-yielding wheat genotypes with drought tolerance.

Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps

A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r²) ranged between 0.57 and 0.74. The r² values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.)

Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).

Capturing Wheat Phenotypes at the Genome Level

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Increase Crop Resilience to Heat Stress Using Omic Strategies

Varieties of various crops with high resilience are urgently needed to feed the increased population in climate change conditions. Human activities and climate change have led to frequent and strong weather fluctuation, which cause various abiotic stresses to crops. The understanding of crops' responses to abiotic stresses in different aspects including genes, RNAs, proteins, metabolites, and phenotypes can facilitate crop breeding. Using multi-omics methods, mainly genomics, transcriptomics, proteomics, metabolomics, and phenomics, to study crops' responses to abiotic stresses will generate a better, deeper, and more comprehensive understanding. More importantly, multi-omics can provide multiple layers of information on biological data to understand plant biology, which will open windows for new opportunities to improve crop resilience and tolerance. However, the opportunities and challenges coexist. Interpretation of the multidimensional data from multi-omics and translation of the data into biological meaningful context remained a challenge. More reasonable experimental designs starting from sowing seed, cultivating the plant, and collecting and extracting samples were necessary for a multi-omics study as the first step. The normalization, transformation, and scaling of single-omics data should consider the integration of multi-omics. This review reports the current study of crops at abiotic stresses in particular heat stress using omics, which will help to accelerate crop improvement to better tolerate and adapt to climate change.

High-LD SNP markers exhibiting pleiotropic effects on salt tolerance at germination and seedlings stages in spring wheat

Salt tolerance at germination and seedling growth stages was investigated. GWAS revealed nine genomic regions with pleiotropic effects on salt tolerance. Salt tolerant genotypes were identified for future breeding program. With 20% of the irrigated land worldwide affected by it, salinity is a serious threat to plant development and crop production. While wheat is the most stable food source worldwide, it has been classified as moderately tolerant to salinity. In several crop plants; such as barley, maize and rice, it has been shown that salinity tolerance at seed germination and seedling establishment is under polygenic control. As yield was the ultimate goal of breeders and geneticists, less attention has been paid to understanding the genetic architecture of salt tolerance at early stages. Thus, the genetic control of salt tolerance at these stages is poorly understood relative to the late stages. In the current study, 176 genotypes of spring wheat were tested for salinity tolerance at seed germination and seedling establishment. Genome-Wide Association Study (GWAS) has been used to identify the genomic regions/genes conferring salt tolerance at seed germination and seedling establishment. Salinity stress negatively impacted all germination and seedling development parameters. A set of 137 SNPs showed significant association with the traits of interest. Across the whole genome, 33 regions showed high linkage disequilibrium (LD). These high LD regions harbored 15 SNPs with pleiotropic effect (i.e. SNPs that control more than one trait). Nine genes belonging to different functional groups were found to be associated with the pleiotropic SNPs. Noteworthy, chromosome 2B harbored the gene TraesCS2B02G135900 that acts as a potassium transporter. Remarkably, one SNP marker, reported in an early study, associated with salt tolerance was validated in this study. Our findings represent potential targets of genetic manipulation to understand and improve salinity tolerance in wheat.

Genome-wide Association Study for Starch Pasting Properties in Chinese Spring Wheat

In order to understand the genetic basis of starch pasting viscosity characteristics of Chinese spring wheat, we assessed the genetic variation of RVA parameters determined by the Rapid Visco Analyser in a panel of 192 Chinese spring wheat accessions grown in Er'shi, Shihezi and Zhaosu during 2012 and 2013 cropping seasons. A genome-wide association study with 47,362 single nucleotide polymorphism (SNP) markers was conducted to detect marker-trait associations using mixed linear model. Phenotypic variations of RVA parameters ranged from 1.6 to 30.7% and broad-sense heritabilities ranged from 0.62 to 0.91. Forty-one SNP markers at 25 loci were significantly associated with seven RVA traits in at least two environments; among these, 20 SNPs were located in coding sequences (CDS) of 18 annotation genes, which can lead to discovering novel genes underpinning starch gelatinization in spring wheat. Haplotype analysis revealed one block for breakdown (BD) on chromosome 3B and two blocks for pasting temperature (T) on chromosome 7B. Cultivars with superior haplotypes at these loci showed better starch pasting viscosity than the average of all cultivars surveyed. The identified loci and associated markers provide valuable sources for future functional characterization and genetic improvement of starch quality in wheat.

Genome-Wide Association Study of Grain Number in Common Wheat From Shanxi Under Different Water Regimes

Water availability is a crucial environmental factor on grain number in wheat, which is one of the important yield-related traits. In this study, a diverse panel of 282 wheat accessions were phenotyped for grain number per spike (GNS), spikelet number (SN), basal sterile spikelet number (BSSN), and apical sterile spikelet number (ASSN) under different water regimes across two growing seasons. Correlation analysis showed that GNS is significantly correlated with both SN and BSSN under two water regimes. A total of 9,793 single nucleotide polymorphism (SNP) markers from the 15 K wheat array were employed for genome-wide association study (GWAS). A total of 77 significant marker-trait associations (MTAs) for investigated traits as well as 8 MTAs for drought tolerance coefficient (DTC) were identified using the mixed linear model. Favored alleles for breeding were inferred according to their estimated effects on GNS, based on the mean difference of varieties. Frequency changes in favored alleles associated with GNS in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of GNS in wheat breeding.

GWAS Case Studies in Wheat

With the advancements in next-generation sequencing technologies, leading to millions of single nucleotide polymorphisms in all crop species including wheat, genome-wide association study (GWAS) has become a leading approach for trait dissection. In wheat, GWAS has been conducted for a plethora of traits and more and more studies are being conducted and reported in journals. While application of GWAS has become a routine in wheat using the standardized approaches, there has been a great leap forward using newer models and combination of GWAS with other sets of data. This chapter has reviewed all these latest advancements in GWAS in wheat by citing the most important studies and their outputs. Specially, we have focused on studies that conducted meta-GWAS, multilocus GWAS, haplotype-based GWAS, Environmental- and Eigen-GWAS, and/or GWAS combined with gene regulatory network and pathway analyses or epistatic interactions analyses; all these have taken the association mapping approach to new heights in wheat.

Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat (Triticum aestivum L.)

A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01112-0.

Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat (Triticum aestivum L.)

Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.

Genome-wide association mapping reveals key genomic regions for physiological and yield-related traits under salinity stress in wheat (Triticum aestivum L.)

A genome-wide association study (GWAS) was conducted using six different multi-locus GWAS models and 35K SNP array to demarcate genomic regions underlying reproductive stage salinity tolerance. Marker-trait association analysis was performed for salt tolerance indices (STI) of 11 morpho-physiological traits, and the actual concentrations of Na⁺ and K⁺, and the Na⁺/K⁺ ratio in flag leaf. A total of 293 significantly associated quantitative trait nucleotides (QTNs) for 14 morpho-physiological traits were identified. Of these 293 QTNs, 12 major QTNs with R² ≥ 10.0% were detected in three or more GWAS models. Novel major QTNs were identified for plant height, number of effective tillers, biomass, grain yield, thousand grain weight, Na⁺ and K⁺ content, and the Na⁺/K⁺ ratio in flag leaf. Moreover, 48 candidate genes were identified from the associated genomic regions. The QTNs identified in this study could potentially be targeted for improving salinity tolerance in wheat.

Application of Genomics to Understand Salt Tolerance in Lentil

Soil salinity is a major abiotic stress, limiting lentil productivity worldwide. Understanding the genetic basis of salt tolerance is vital to develop tolerant varieties. A diversity panel consisting of 276 lentil accessions was screened in a previous study through traditional and image-based approaches to quantify growth under salt stress. Genotyping was performed using two contrasting methods, targeted (tGBS) and transcriptome (GBS-t) genotyping-by-sequencing, to evaluate the most appropriate methodology. tGBS revealed the highest number of single-base variants (SNPs) (c. 56,349), and markers were more evenly distributed across the genome compared to GBS-t. A genome-wide association study (GWAS) was conducted using a mixed linear model. Significant marker-trait associations were observed on Chromosome 2 as well as Chromosome 4, and a range of candidate genes was identified from the reference genome, the most plausible being potassium transporters, which are known to be involved in salt tolerance in related species. Detailed mineral composition performed on salt-treated and control plant tissues revealed the salt tolerance mechanism in lentil, in which tolerant accessions do not transport Na⁺ ions around the plant instead localize within the root tissues. The pedigree analysis identified two parental accessions that could have been the key sources of tolerance in this dataset.