Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat

Genome-wide association analysis of spike and kernel traits in the U.S. hard winter wheat

A better understanding of the genetic control of spike and kernel traits that have higher heritability can help in the development of high-yielding wheat varieties. Here, we identified the marker-trait associations (MTAs) for various spike- and kernel-related traits in winter wheat (Triticum aestivum L.) through genome-wide association studies (GWAS). An association mapping panel comprising 297 hard winter wheat accessions from the U.S. Great Plains was evaluated for eight spike- and kernel-related traits in three different environments. A GWAS using 15,590 single-nucleotide polymorphisms (SNPs) identified a total of 53 MTAs for seven spike- and kernel-related traits, where the highest number of MTAs were identified for spike length (16) followed by the number of spikelets per spike (15) and spikelet density (11). Out of 53 MTAs, 14 were considered to represent stable quantitative trait loci (QTL) as they were identified in multiple environments. Five multi-trait MTAs were identified for various traits including the number of spikelets per spike (NSPS), spikelet density (SD), kernel width (KW), and kernel area (KA) that could facilitate the pyramiding of yield-contributing traits. Further, a significant additive effect of accumulated favorable alleles on the phenotype of four spike-related traits suggested that breeding lines and cultivars with a higher number of favorable alleles could be a valuable resource for breeders to improve yield-related traits. This study improves the understanding of the genetic basis of yield-related traits in hard winter wheat and provides reliable molecular markers that will facilitate marker-assisted selection (MAS) in wheat breeding programs.

A 'wiring diagram' for source strength traits impacting wheat yield potential

Source traits are currently of great interest for the enhancement of yield potential; for example, much effort is being expended to find ways of modifying photosynthesis. However, photosynthesis is but one component of crop regulation, so sink activities and the coordination of diverse processes throughout the crop must be considered in an integrated, systems approach. A set of 'wiring diagrams' has been devised as a visual tool to integrate the interactions of component processes at different stages of wheat development. They enable the roles of chloroplast, leaf, and whole-canopy processes to be seen in the context of sink development and crop growth as a whole. In this review, we dissect source traits both anatomically (foliar and non-foliar) and temporally (pre- and post-anthesis), and consider the evidence for their regulation at local and whole-plant/crop levels. We consider how the formation of a canopy creates challenges (self-occlusion) and opportunities (dynamic photosynthesis) for components of photosynthesis. Lastly, we discuss the regulation of source activity by feedback regulation. The review is written in the framework of the wiring diagrams which, as integrated descriptors of traits underpinning grain yield, are designed to provide a potential workspace for breeders and other crop scientists that, along with high-throughput and precision phenotyping data, genetics, and bioinformatics, will help build future dynamic models of trait and gene interactions to achieve yield gains in wheat and other field crops.

Genome-wide association study reveals a NAC transcription factor TaNAC074 linked to pre-harvest sprouting tolerance in wheat

Twelve QTL associated with pre-harvest sprouting tolerance were identified using association analysis in wheat. Two markers were validated and a candidate gene TaNAC074 for Qgpf.cas-3B.2 was verified using Agrobacterium-mediated transformation. Pre-harvest sprouting (PHS) is a considerable global threat to wheat yield and quality. Due to this threat, breeders must identify quantitative trait loci (QTL) and genes conferring PHS-tolerance (PHST) to reduce the negative effects of PHS caused by low seed dormancy. In this study, we evaluated a panel of 302 diverse wheat genotypes for PHST in four environments and genotyped the panel with a high-density wheat 660 K SNP array. By using a genome-wide association study (GWAS), we identified 12 stable loci significantly associated with PHST (P < 0.0001), explaining 3.34 - 9.88% of the phenotypic variances. Seven of these loci co-located with QTL and genes reported previously. Five loci (Qgpf.cas-3B.2, Qgpf.cas-3B.3, Qgpf.cas-3B.4, Qgpf.cas-7B.2, and Qgpf.cas-7B.3), located in genomic regions with no known PHST QTL or genes, are likely to be new QTL conferring PHST. Additionally, two molecular markers were developed for Qgpf.cas-3A and Qgpf.cas-7B.3, and validated using a different set of 233 wheat accessions. Finally, the PHST-related function of candidate gene TaNAC074 for Qgpf.cas-3B.2 was confirmed by CAPS (cleaved amplified polymorphic sequences) marker association analysis in 233 wheat accessions and by expression and phenotypic analysis of transgenic wheat. Overexpression of TaNAC074 significantly reduced seed dormancy in wheat. This study contributes to broaden the genetic basis and molecular marker-assisted breeding of PHST.

Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities

Wheat production and productivity are challenged by recurrent droughts associated with climate change globally. Drought and heat stress resilient cultivars can alleviate yield loss in marginal production agro-ecologies. The ability of some crop genotypes to thrive and yield in drought conditions is attributable to the inherent genetic variation and environmental adaptation, presenting opportunities to develop drought-tolerant varieties. Understanding the underlying genetic, physiological, biochemical, and environmental mechanisms and their interactions is key critical opportunity for drought tolerance improvement. Therefore, the objective of this review is to document the progress, challenges, and opportunities in breeding for drought tolerance in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for adaptation to drought-prone environments, (2) opportunities such as genetic variation in wheat for drought tolerance, selection methods, the interplay between above-ground phenotypic traits and root attributes in drought adaptation and drought-responsive attributes and (3) approaches, technologies and innovations in drought tolerance breeding. In the end, the paper summarises genetic gains and perspectives in drought tolerance breeding in wheat. The review will serve as baseline information for wheat breeders and agronomists to guide the development and deployment of drought-adapted and high-performing new-generation wheat varieties.

GWAS to Identify Novel QTNs for WSCs Accumulation in Wheat Peduncle Under Different Water Regimes

Water-soluble carbohydrates (WSCs) play a vital role in water stress avoidance and buffering wheat grain yield. However, the genetic architecture of stem WSCs' accumulation is partially understood, and few candidate genes are known. This study utilizes the compressed mixed linear model-based genome wide association study (GWAS) and heuristic post GWAS analyses to identify causative quantitative trait nucleotides (QTNs) and candidate genes for stem WSCs' content at 15 days after anthesis under different water regimes (irrigated, rainfed, and drought). Glucose, fructose, sucrose, fructans, total non-structural carbohydrates (the sum of individual sugars), total WSCs (anthrone based) quantified in the peduncle of 301 bread wheat genotypes under multiple environments (E01-E08) pertaining different water regimes, and 14,571 SNPs from "35K Axiom Wheat Breeders" Array were used for analysis. As a result, 570 significant nucleotide trait associations were identified on all chromosomes except for 4D, of which 163 were considered stable. A total of 112 quantitative trait nucleotide regions (QNRs) were identified of which 47 were presumable novel. QNRs qWSC-3B.2 and qWSC-7A.2 were identified as the hotspots. Post GWAS integration of multiple data resources prioritized 208 putative candidate genes delimited into 64 QNRs, which can be critical in understanding the genetic architecture of stem WSCs accumulation in wheat under optimum and water-stressed environments. At least 19 stable QTNs were found associated with 24 prioritized candidate genes. Clusters of fructans metabolic genes reported in the QNRs qWSC-4A.2 and qWSC-7A.2. These genes can be utilized to bring an optimum combination of various fructans metabolic genes to improve the accumulation and remobilization of stem WSCs and water stress tolerance. These results will further strengthen wheat breeding programs targeting sustainable wheat production under limited water conditions.

Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies

Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.

Genome-Wide Association of Stem Carbohydrate Accumulation and Remobilization during Grain Growth in Bread Wheat (Triticum aestivum L.) in Mediterranean Environments

Water deficit represents an important challenge for wheat production in many regions of the world. Accumulation and remobilization of water-soluble carbohydrates (WSCs) in stems are part of the physiological responses regulated by plants to cope with water stress and, in turn, determine grain yield (GY). The genetic mechanisms underlying the variation in WSC are only partially understood. In this study, we aimed to identify Single Nucleotide Polymorphism (SNP) markers that account for variation in a suite of WSC and GY, evaluated in 225 cultivars and advanced lines of spring wheat. These genotypes were established in two sites in the Mediterranean region of Central Chile, under water-limited and full irrigation conditions, and assessed in two growing seasons, namely anthesis and maturity growth periods. A genome-wide association study (GWAS) was performed by using 3243 SNP markers. Genetic variance accounted for 5 to 52% of phenotypic variation of the assessed traits. A rapid linkage disequilibrium decay was observed across chromosomes (r² ≤ 0.2 at 2.52 kbp). Marker-trait association tests identified 96 SNPs related to stem weight (SW), WSCs, and GY, among other traits, at the different sites, growing seasons, and growth periods. The percentage of SNPs that were part of the gene-coding regions was 34%. Most of these genes are involved in the defensive response to drought and biotic stress. A complimentary analysis detected significant effects of different haplotypes on WSC and SW, in anthesis and maturity. Our results evidence both genetic and environmental influence on WSC dynamics in spring wheat. At the same time, they provide a series of markers suitable for supporting assisted selection approaches and functional characterization of genes.

Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat

GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated. Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding.

Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

Genetic dissection of stem WSC accumulation and remobilization in wheat (Triticum aestivum L.) under terminal drought stress

BACKGROUND

The accumulation and remobilization of stem water soluble carbohydrates (WSC) are determinant physiological traits highly influencing yield potential in wheat against drought stress. However, knowledge gains of the genetic control are still limited. A hexaploid wheat population of 120 recombinant inbred lines were developed to identify quantitative trait loci (QTLs) and to dissect the genetic basis underlying eight traits related to stem WSC under drought stress (DS) and well-watered (WW) conditions across three environments.

RESULTS

Analysis of variance (ANOVA) revealed larger environmental and genotypic effects on stem WSC-related traits, indicating moderate heritabilities of 0.51-0.72. A total of 95 additive and 88 pairs of epistatic QTLs were identified with significant additive and epistatic effects, as well as QTL× water environmental interaction (QEI) effects. Most of additive QTLs and additive QEIs associated with drought-stressed environments functioned genetic effects promoting pre-anthesis WSC levels and stem WSC remobilization to developing grains. Compared to other genetic components, both genetic effects were performed exclusive contributions to phenotypic variations in stem WSC-related traits. Nineteen QTL clusters were identified on chromosomes 1B, 2A, 2B, 2D, 3B, 4B, 5A, 6A, 6B and 7A, suggestive of the genetic linkage or pleiotropy. Thirteen additive QTLs were detectable repeatedly across two of the three water environments, indicating features of stable expressions. Some loci were consistent with those reported early and were further discussed.

CONCLUSION

Stem WSC-related traits were inherited predominantly by additive and QEI effects with a moderate heritability. QTL cluster regions were suggestive of tight linkage or pleiotropy in the inheritance of these traits. Some stable and common loci, as well as closely linked molecular markers, had great potential in marker-assisted selection to improve stem WSC-related traits in wheat, especially under drought-stressed environments.

QTL mapping for grain yield-related traits in bread wheat via SNP-based selective genotyping

We identified four chromosome regions harboring QTL for grain yield-related traits, and breeder-friendly KASP markers were developed and validated for marker-assisted selection. Identification of major stable quantitative trait loci (QTL) for grain yield-related traits is important for yield potential improvement in wheat breeding. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) were evaluated for thousand grain weight (TGW), grain length (GL), grain width (GW), and grain number per spike (GNS) in 10 environments and for grain filling rate in six environments. Sixty RILs, with 30 higher and 30 lower TGW, respectively, were genotyped using the wheat 660 K SNP array for preliminary QTL mapping. Four genetic regions on chromosomes 1AL, 2BS, 3AL, and 5B were identified to have a significant effect on TGW-related traits. A set of Kompetitive Allele Specific PCR markers were converted from the SNP markers on the above target chromosomes and used to genotype all 266 RILs. The mapping results confirmed the QTL named Qgw.caas-1AL, Qgl.caas-3AL, Qtgw.caas-5B, and Qgl.caas-5BS on the targeted chromosomes, explaining 5.0-20.6%, 5.7-15.7%, 5.5-17.3%, and 12.5-20.5% of the phenotypic variation for GW, GL, TGW, and GL, respectively. A novel major QTL for GNS on chromosome 5BS, explaining 5.2-15.2% of the phenotypic variation, was identified across eight environments. These QTL were further validated using BC₁F₄ populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines) and 186 advanced breeding lines. Collectively, selective genotyping is a simple, economic, and effective approach for rapid QTL mapping and can be generally applied to genetic mapping studies for important agronomic traits.

Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.)

Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding. Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Q_bifcgr.cas-3AS/Qfcgr.cas-3AS, Q_bifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Q_bifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Q_bigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Q_bigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.

Mapping QTLs of flag leaf morphological and physiological traits related to aluminum tolerance in wheat (Triticum aestivum L.)

Genetic improvement of aluminum (Al) tolerance is one of the cost-effective solutions to improve plant productivity in acidic soils around the world. This study was performed to progress our understanding of the genetic mechanisms of aluminum tolerance underlying wheat (Triticum aestivum L.) flag leaf morphological and physiological traits. A recombinant inbred line population derived from SeriM82 and Babax was used for mapping quantitative trait loci (QTL) in wheat for tolerance to Al toxicity through 477 DNA markers. Based on a single-locus analysis, 48 QTLs including 16 putative and 32 suggestive QTLs were identified for all studied traits. Individual QTL explained 4.57-11.29% of the phenotypic variance in different environments during both the crop seasons. These QTLs located unevenly throughout the wheat genome. Among them, 52.08%, 29.17%, and 18.75% were in the A, B, and D genomes, respectively. Based on two-locus analysis, 54 additive QTLs and 6 pairs of epistatic effects were detected, among which 29 additive and 5 pairs of epistatic QTLs showed significant QTL × environment interactions. The highest number of stable QTLs was identified on genome A. Determining a number of QTL clusters indicated tight linkage or pleiotropy in the inheritance of different traits. The stable and major QTLs controlling traits in this research can be applied for verification in different environments and genetic backgrounds and identifying superior allelic variations in wheat to increase the performance of selection of high yielding lines adapted to Al stress in breeding programs.

Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research

Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.

Drought Stress Tolerance in Wheat and Barley: Advances in Physiology, Breeding and Genetics Research

Climate change is a major threat to most of the agricultural crops grown in tropical and sub-tropical areas globally. Drought stress is one of the consequences of climate change that has a negative impact on crop growth and yield. In the past, many simulation models were proposed to predict climate change and drought occurrences, and it is extremely important to improve essential crops to meet the challenges of drought stress which limits crop productivity and production. Wheat and barley are among the most common and widely used crops due to their economic and social values. Many parts of the world depend on these two crops for food and feed, and both crops are vulnerable to drought stress. Improving drought stress tolerance is a very challenging task for wheat and barley researchers and more research is needed to better understand this stress. The progress made in understanding drought tolerance is due to advances in three main research areas: physiology, breeding, and genetic research. The physiology research focused on the physiological and biochemical metabolic pathways that plants use when exposed to drought stress. New wheat and barley genotypes having a high degree of drought tolerance are produced through breeding by making crosses from promising drought-tolerant genotypes and selecting among their progeny. Also, identifying genes contributing to drought tolerance is very important. Previous studies showed that drought tolerance is a polygenic trait and genetic constitution will help to dissect the gene network(s) controlling drought tolerance. This review explores the recent advances in these three research areas to improve drought tolerance in wheat and barley.

Molecular Characterization of 87 Functional Genes in Wheat Diversity Panel and Their Association With Phenotypes Under Well-Watered and Water-Limited Conditions

Modern breeding imposed selection for improved productivity that largely influenced the frequency of superior alleles underpinning traits of breeding interest. Therefore, molecular diagnosis for the allelic variations of such genes is important to manipulate beneficial alleles in wheat molecular breeding. We analyzed a diversity panel largely consisted of advanced lines derived from synthetic hexaploid wheats for allelic variation at 87 functional genes or loci of breeding importance using 124 high-throughput KASP markers. We also developed two KASP markers for water-soluble carbohydrate genes (TaSST-D1 and TaSST-A1) associated with plant height and thousand grain weight (TGW) in the diversity panel. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn-D3), thousand grain weight (TaCKX-D1, TaTGW6-A1, TaSus1-7B, and TaCwi-D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds-D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranged from 96.4 to 100%. The association analysis of functional genes with agronomic and biochemical traits under well-watered (WW) and water-limited (WL) conditions revealed that 21 marker-trait associations (MTAs) were consistently detected in both moisture conditions. The major developmental genes such as Vrn-A1, Rht-D1, and Ppd-B1 had the confounding effect on several agronomic traits including plant height, grain size and weight, and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced grain weight in the diversity panel. Graphical genotyping approach was used to identify accessions with maximum number of favorable alleles, thus likely to have high breeding value. These results improved our knowledge on the selection of favorable and unfavorable alleles through unconscious selection breeding and identified the opportunities to deploy alleles with effects in wheat breeding.

Depositing ability of stem of winter wheat varieties of different periods of selection

Adaptation of high-yielding winter wheat crops to changes in climatic conditions has great importance for food security of countries. The remobilization of stem assimilates for grain filling is one of the possible ways of increasing wheat yield in unfavourable environmental conditions. Field experiments in natural conditions with three old and three modern varieties of winter wheat were performed to compare depositing abilities of their stems. The objective of this study was a comparative analysis of the parameters of depositing capacity of stems of the main shoots for identification of the criteria for assessing grain productivity of winter wheat. The parameters of depositing capacity of the stem of the main shoots of three old winter wheat varieties (1997, 2003, and 2008) and three modern ones (2013, 2014 and 2016) were studied in field conditions with natural conditions of water supply (Kyiv Oblast, Ukraine). During the period of formation of reproductive organs (April and May), the amount of precipitation, respectively, was only 17% and 68% of long-term values and average monthly air temperature was 3–4 ºС higher than the climatic norm. We analyzed the variability of the parameters of depositing capacity of the stem of the main shoot and grain productivity of the ear of six wheat winter varieties which differed by time of selection. In unfavourable conditions during the period of formation of reproductive organs the modern winter wheat varieties had an 11% higher yield on average compared to the older ones. It was determined that the highest mass of grain from the ear of the main shoots (1.9–2.1 g) belonged to Odeska 267 variety, a drought-tolerant variety from earlier selection, and three modern varieties – Raihorodka, Prydniprovska and Darunok Podillia. It is demonstrated that these varieties also exceeded two old varieties (Podolianka and Yednist) by stem dry matter weight of main shoot at anthesis by 0.3–0.6 g. The highest content of non-structural carbohydrates at this phase was observed in Odeska 267, Raihorodka and Darunok Podillia varieties (273–307 mg/stem). Correlation analysis revealed the significant correlation between mass of grain from ear and dry matter of stem at anthesis and full ripeness, as well mass of grain from ear and the amount of non-structural carbohydrates at anthesis. Therefore, modern varieties of winter wheat and the drought-tolerant variety have higher yield, weight of dry matter of stem of the main shoot at anthesis and grain productivity of the ear, compared to old varieties. The results of this study indicate that the mass of dry matter of the stem of the main shoot at anthesis can be used as a marker of the grain productivity of winter wheat.

Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS

Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders' 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10 P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7-47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement.

Genetic analysis of drought response of wheat following either chemical desiccation or the use of a rain-out shelter

Simulating drought stress during the breeding process has been proposed as a way to select varieties under naturally non-stressful conditions. The aim of the study was to characterise the genetic basis of the response of 111 spring wheat (Triticum aestivum L.) varieties and landraces to chemical desiccation and to rain-out shelter drought. The effect of the rain-out shelter was a 15% reduction in plant height, spike length and thousand seed weight (TSW); in contrast, the desiccant treatment induced a 15% reduction in seed number, a 35-72% loss in TSW and a reduction in subsequent germination of 12%. A genome-wide association analysis revealed 263 significant marker-trait associations (MTAs), of which 246 involved days to anthesis, plant height, spike length, number of spikelets, seed number, TSW and germination from the non-treated plants. Only four and five MTAs involved TSW from plants grown under the rain-out shelter and the chemical desiccation, respectively, and harboured the Sugar-Dependent6 gene. Seven MTAs involved seed number for chemical desiccated plants. Both, chemical desiccation and rain-out shelter drought identified same tolerant genotypes. Concluding, both approaches are suitable to simulate different drought scenarios. However, there was a strong environmental impact for chemical desiccation which may increase the complexity of this tolerance mechanism.

Overexpression of TaCML20, a calmodulin-like gene, enhances water soluble carbohydrate accumulation and yield in wheat

Calcium (Ca²⁺ ) is a universal messenger that mediates intracellular responses to extracellular stimuli in living organisms. Calmodulin (CaM) and calmodulin-like (CML) proteins are the important Ca²⁺ sensors in plants that decode Ca²⁺ -signatures to execute downstream intracellular level responses. Several studies indicate the interlinking of Ca²⁺ and sugar signaling in plants; however, no genes have been functionally characterized to provide molecular evidence. Our study found that expression of TaCML20 was significantly correlated with water soluble carbohydrate (WSC) concentrations in recombinant inbred lines in wheat. TaCML20 has four EF-hand motifs that may facilitate the binding of Ca²⁺ . To explore the role of CML20, we generated TaCML20 overexpressing transgenic lines in wheat. These lines accumulated higher WSC concentrations in the shoots, and we also found a significantly increased transcript level of sucrose:sucrose-1-fructosyltransferase (1-SST) in the internodes compared with the control plants. In addition, TaCML20 overexpressing plants showed significantly increased tillers per plant and also increased about 19% of grain weight per plant compared with control plants. The results also suggested a role for TaCML20 in drought stress, as its transcripts significantly increased in the shoots of wild-type plants under water deficit. These results uncovered the role of CML20 in determining multiple traits in wheat.

Evaluating the Utility of Carbon Isotope Discrimination for Wheat Breeding in the Pacific Northwest

Many wheat (Triticum aestivum L.) production regions are threatened annually by drought stress. Carbon isotope discrimination (Δ) has been identified as a potentially useful trait in breeding for improved drought tolerance in certain environments. Broad use of Δ as a selection criterion is limited, however, mainly due to an inconsistent relationship observed between grain yield and Δ and, to a lesser extent, because of the high resource demand associated with phenotyping. The efficiency of selection may be improved by the identification and verification of molecular markers for use in marker-assisted selection (MAS), and a reliable relationship to grain yield may be established based on a location's total amount and distribution of precipitation over the growing season. Given the environmental variability in precipitation dynamics, it is necessary to evaluate this relationship in target breeding environments. In this study, grain Δ was collected on a panel of 480 advanced soft white winter wheat varieties grown in five Pacific Northwest environments. A genome-wide association study approach was used to evaluate the amenability of grain Δ to MAS. The genetic architecture of grain Δ was determined to be characterized by multiple, small effect marker-trait associations with limited repeatability across environments, suggesting that MAS will be ineffective at improving Δ selection efficiency. Further, the relationship between grain yield and Δ ranged from neutral (r = -0.01) to moderately positive (r = 0.44) in the target environments. Such moderate correlations, coupled with variability in this relationship, indicate that direct selection for Δ may not be beneficial.

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

Drought and heat waves commonly co-occur in many wheat-growing regions causing significant crop losses. The identification of stress associated quantitative trait loci, particularly those for yield, is problematic due to their association with plant phenology and the high genetic × environment interaction. Here we studied a panel of 315 diverse, spring type accessions of bread wheat (Triticum aestivum) in pots in a semi-controlled environment under combined drought and heat stress over 2 years. Importantly, we treated individual plants according to their flowering time. We found 134 out of the 145 identified loci for grain weight that were not associated with either plant phenology or plant height. The majority of loci uncovered here were novel, with favorable alleles widespread in Asian and African landraces providing opportunities for their incorporation into modern varieties through breeding. Using residual heterozygosity in lines from a nested association mapping population, we were able to rapidly develop near-isogenic lines for important target loci. One target locus on chromosome 6A contributed to higher grain weight, harvest index, thousand kernel weight, and grain number under drought and heat stress in field conditions consistent with allelic effects demonstrated in the genome-wide association study.

Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments

Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.

Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat

Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticumaestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annotated as tryptophan decarboxylase) was functionally identified to influence the content of tryptamine in vitro. Our study demonstrated the power and efficiency of multi-locus GWAS models in crop metabolome research and provided new insights into understanding FAA biosynthesis in wheat.

Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum)

Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown. Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi. In order to identify genomic regions involved in mycorrhization, these genotypes were analyzed using the wheat 90k iSelect chip, resulting in 17 823 polymorphic mapped markers, which were used in a genome-wide association study. Significant genotypic differences (P < 0.0001) were detected in the ability to form symbiosis and 30 significant markers associated with root colonization, representing six QTL regions, were detected on chromosomes 3A, 4A and 7A, and candidate genes located in these QTL regions were proposed. The results reported here provide key insights into the genetics of root colonization by mycorrhizal fungi in wheat.

The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa

Harnessing stem carbohydrate dynamics in grasses offers an opportunity to help meet future demands for plant-based food, fiber and fuel production, but requires a greater understanding of the genetic controls that govern the synthesis, interconversion and transport of such energy reserves. We map out a blueprint of the genetic architecture of rice (Oryza sativa) stem nonstructural carbohydrates (NSC) at two critical developmental time-points using a subpopulation-specific genome-wide association approach on two diverse germplasm panels followed by quantitative trait loci (QTL) mapping in a biparental population. Overall, 26 QTL are identified; three are detected in multiple panels and are associated with starch-at-maturity, sucrose-at-maturity and NSC-at-heading. They tag OsHXK6 (rice hexokinase), ISA2 (rice isoamylase) and a tandem array of sugar transporters. This study provides the foundation for more in-depth molecular investigation to validate candidate genes underlying rice stem NSC and informs future comparative studies in other agronomically vital grass species.