Genomic dissection of drought resistance in durum wheat x wild emmer wheat recombinant inbreed line population

Plasticity of Root System Architecture and Whole Transcriptome Responses Underlying Nitrogen Deficiency Tolerance Conferred by a Wild Emmer Wheat QTL

Our aim was to elucidate mechanisms underlying nitrogen (N)-deficiency tolerance in bread wheat (cultivar Ruta), conferred by a wild emmer wheat QTL (WEW; IL99). We hypothesised that the tolerance in IL99 is driven by enhanced N-uptake through modification of root system architecture (RSA) underscored by transcriptome modifications. Severe N-deficiency (0.1 N for 26 days) triggered significantly higher plasticity in IL99 compared to Ruta by modifying 16 RSA traits; nine of which were IL99-specific. The change in root growth in IL99 was collectively characterised by a transition in root orientation from shallow to steep, increased root number and length, and denser networks, enabling nutrient acquisition from a larger volume and deeper soil layers. Gene ontology and KEGG-enrichment analyses highlighted IL99-specific pathways and candidate genes elevated under N-deficiency. This included Jasmonic acid metabolism, a key hormone mediating RSA plasticity (AOS1, TIFY, MTB2, MYC2), and lignification-mediated root strengthening (CYP73A, 4CL). 'N-metabolism' was identified as a main shared pathway to IL99 and Ruta, with enhanced nitrate uptake predominant in IL99 (NRT2.4), while remobilisation was the main strategy in Ruta (NRT2.3). These findings provide novel insights into wheat plasticity response underlying tolerance to N-deficiency and demonstrate the potential of WEW for improving N-uptake under suboptimal conditions.

Wheat Drought Tolerance: Unveiling a Synergistic Future with Conventional and Molecular Breeding Strategies

The development of wheat cultivars capable of withstanding drought conditions is necessary for global food security. Conventional breeding, emphasizing the exploitation of inherent genetic diversity by selecting wheat genotypes exhibiting superior drought-related traits, including root architecture, water use efficiency, and stress-responsive genes, has been used by breeders. Simultaneously, molecular techniques such as marker-assisted selection and gene editing are deployed to accelerate the identification and integration of specific drought-responsive genes into elite wheat lines. Cutting-edge genomic tools play a pivotal role in decoding the genetic basis of wheat drought tolerance, enabling the precise identification of key genomic regions and facilitating breeding decisions. Gene-editing technologies, deployed judiciously, ensure the targeted enhancement of desirable traits without compromising the overall genomic integrity of wheat varieties. This review introduces a strategic amalgamation of conventional and molecular breeding approaches for developing drought-tolerant wheat. The review aims to accelerate progress by seamlessly merging traditional breeding methods with advanced molecular tools, and it also underscores the potential of a synergistic future for enhancing wheat drought resilience, providing a roadmap for the development of resilient wheat varieties essential for sustainable agriculture in the 21st century.

Intraspecific variation for heat stress tolerance in wild emmer-derived durum wheat populations

High temperatures pose a major threat to wheat productivity and necessitate the development of new cultivars that are resilient to future heat stress. Wild emmer (Triticum turgidum L. ssp. dicoccoides), which is a direct progenitor of domesticated durum wheat (Triticum turgidum L. ssp. durum) and contributor to the A and B genome of bread wheat (Triticum aestivum), offers a valuable genetic reservoir for developing climate-resilient wheat. However, the morphology of wild emmer is different from that of durum and bread wheat, in particular, the spikelets are fragile and naturally fall off, making it difficult to study its agronomic traits. In this study, we created nine backcrossed families between the popular durum wheat cultivar 'Miki 3' and nine wild emmer accessions collected from northern and southern lineages of this species. The objective was to investigate the intraspecific genetic variation in wild emmer and identify traits associated with heat stress tolerance. We evaluated these nine families under multi-environments ranging from optimum to severe heat stress conditions in Japan and Sudan and measured important agronomic traits. The result showed that two families, developed from accessions of both northern and southern lineages exhibited high harvest index, elevated chlorophyll content, and reduced canopy temperature under heat stress. Additionally, one family developed from an accession of the southern lineage displayed high biomass, harvest index, and seed number under heat-stress conditions. These three families produced high heat tolerant lines with unique introgressed segments from their wild emmer parents on chromosomes 1A, 2B, 5B, 6B, and 7B, which may be linked to heat resilience. From these results, we were able to identify significant intraspecific diversity between the wild emmer accessions in terms of heat stress tolerance. However, no significant tendency between the northern and southern lineages of wild emmer has been identified. These findings emphasize the need to harness not only the interspecific but also the intraspecific genetic variation of wild emmer diversity to uncover valuable genes for heat stress tolerance in wheat breeding programs.

Genome-wide association mapping for stay-green and stem reserve mobilization traits in wheat (Triticum aestivum L.) under combined heat and drought stress

Stay-green (SG) and stem reserve mobilization (SRM) are two significant mutually exclusive traits, which contributes to grain-filling during drought and heat stress in wheat. The current research was conducted in a genome-wide association study (GWAS) panel consisting of 278 wheat genotypes of advanced breeding lines to find the markers linked with SG and SRM traits and also to screen the superior genotypes. SG and SRM traits, viz. soil plant analysis development (SPAD) value, canopy temperature (CT), normalized difference vegetation index (NDVI), leaf senescence rate (LSR) and stem reserve mobilization efficiency (SRE) were recorded. The trial was conducted in α-lattice design, under control and combined heat and drought stress (HD). Analysis of variance and descriptive statistics showed a significant difference across the evaluated traits. The highest mean of SRE (31.7%) and SRM (0.42 g/stem) was reported in HD, while highest SRE in HD and lowest in control was 52.56% and 15.7%, respectively. Genotyping was carried out using the 35 K Axiom R Wheat Breeder's Array, 14,625 SNPs were kept after filtering. Through GWAS, 36 significant marker trait associations (MTAs) were identified on 16 distinct chromosomes; out of this, 22 MTAs were found under control and 14 MTAs under HD. Candidate genes that code for UDP-glycosyltransferase 73C4-like and protein detoxification 40-like was linked to SPAD and CT respectively. One MTAs was detected for SRM on chromosome 6B that code for wall associated receptor kinase 4 like. These SNPs can be utilized to generate cultivars that adapt to climate change by a marker-assisted gene transfer.

Integrating high-throughput phenotyping and genome-wide association studies for enhanced drought resistance and yield prediction in wheat

Drought, especially terminal drought, severely limits wheat growth and yield. Understanding the complex mechanisms behind the drought response in wheat is essential for developing drought-resistant varieties. This study aimed to dissect the genetic architecture and high-yielding wheat ideotypes under terminal drought. An automated high-throughput phenotyping platform was used to examine 28 392 image-based digital traits (i-traits) under different drought conditions during the flowering stage of a natural wheat population. Of the i-traits examined, 17 073 were identified as drought-related. A genome-wide association study (GWAS) identified 5320 drought-related significant single-nucleotide polymorphisms (SNPs) and 27 SNP clusters. A notable hotspot region controlling wheat drought tolerance was discovered, in which TaPP2C6 was shown to be an important negative regulator of the drought response. The tapp2c6 knockout lines exhibited enhanced drought resistance without a yield penalty. A haplotype analysis revealed a favored allele of TaPP2C6 that was significantly correlated with drought resistance, affirming its potential value in wheat breeding programs. We developed an advanced prediction model for wheat yield and drought resistance using 24 i-traits analyzed by machine learning. In summary, this study provides comprehensive insights into the high-yielding ideotype and an approach for the rapid breeding of drought-resistant wheat.

Independent genetic factors control floret number and spikelet number in Triticum turgidum ssp

Wheat grain yield is a complex trait resulting from a trade-off among many distinct components. During wheat evolution, domestication events and then modern breeding have strongly increased the yield potential of wheat plants, by enhancing spike fertility. To address the genetic bases of spike fertility in terms of spikelet number per spike and floret number per spikelet, a population of 110 recombinant inbred lines (RILS) obtained crossing a Triticum turgidum ssp. durum cultivar (Latino) and a T. dicoccum accession (MG5323) was exploited. Being a modern durum and a semi-domesticated genotype, respectively, the two parents differ for spike architecture and fertility, and thus the corresponding RIL population is the ideal genetic material to dissect genetic bases of yield components. The RIL population was phenotyped in four environments. Using a high-density SNP genetic map and taking advantage of several genome sequencing available for Triticeae, a total of 94 QTLs were identified for the eight traits considered; these QTLs were further reduced to 17 groups, based on their genetic and physical co-location. QTLs controlling floret number per spikelet and spikelet number per spike mapped in non-overlapping chromosomal regions, suggesting that independent genetic factors determine these fertility-related traits. The physical intervals of QTL groups were considered for possible co-location with known genes functionally involved in spike fertility traits and with yield-related QTLs previously mapped in tetraploid wheat. The most interesting result concerns a QTL group on chromosome 5B, associated with spikelet number per spike, since it could host genes still uncharacterized for their association to spike fertility. Finally, we identified two different regions where the trade-off between fertility related traits and kernel weight is overcome. Further analyses of these regions could pave the way for a future identification of new genetic loci contributing to fertility traits essential for yield improvement in durum wheat.

QTL Mapping of Yield-Related Traits in Tetraploid Wheat Based on Wheat55K SNP Array

To enhance the understanding of yield-related traits in tetraploid wheat, it is crucial to investigate and identify genes that govern superior yield characteristics. This study utilized the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line (RIL) population consisting of 120 lines developed through the crossbreeding of two tetraploid wheat varieties, Qin Hei-1 (QH-1) and Durum Wheat (DW). An investigation and analysis were conducted on 11 yield-related traits, including peduncle length (PL), neck length (NL), spike length (SL), flowering date (FD), heading date (HD), thousand-kernel weight (TKW), kernel area ratio (KAR), kernel circumference (KC), kernel length (KL), kernel width (KW), and kernel length-width ratio (KL-WR), over a period of three years in two locations, Yang Ling, Shaanxi, and Lin He, Inner Mongolia. The analysis identified nine stable loci among eight agronomic traits, named QSL.QD-1A.1, QNL.QD-4B.2, QPL.QD-4B.1, QFD.QD-2B, QHD.QD-2B.1, QHD.QD-4B, QKC.QD-4B.2, QKL-WR.QD-4B.6, and QKL.QD-4B.2. Among them, the additive effects of three QTLs, QSL.QD-1A.1, QNL.QD-4B.2, and QFD.QD-2B, were positive, indicating that the enhancing alleles at these loci were derived from the parent line QH-1. These three QTLs showed significant positive effects on the phenotypes of the population materials. Furthermore, potential functional genes were identified within the mapping intervals of QSL.QD-1A.1 and QNL.QD-4B.2, which regulate the development of spike length and neck length, respectively. These results provide potential QTLs and candidate genes, which broaden the genetic basis of agronomic traits related to yield, such as SL, NL, PL, and FD, and benefits for wheat breeding and improvement.

Characterization and Mapping of a Rolling Leaf Mutant Allele rlT73 on Chromosome 1BL of Wheat

Leaf rolling is regarded as an important morphological trait in wheat breeding. Moderate leaf rolling is helpful to keep leaves upright and improve the photosynthesis of plants, leading to increased yield. However, studies on the identification of genomic regions/genes associated with rolling leaf have been reported less frequently in wheat. In this study, a rolling leaf mutant, T73, which has paired spikelets, dwarfism, and delayed heading traits, was obtained from a common wheat landrace through ethyl methanesulfonate mutagenesis. The rlT73 mutation caused an increase in the number of epidermal cells on the abaxial side and the shrinkage of bulliform cells on the adaxial side, leading to an adaxially rolling leaf phenotype. Genetic analysis showed that the rolling leaf phenotype was controlled by a single recessive gene. Further Wheat55K single nucleotide polymorphism array-based bulked segregant analysis and molecular marker mapping delimited rlT73 to a physical interval of 300.29-318.33 Mb on the chromosome arm 1BL in the Chinese Spring genome. We show that a point mutation at the miRNA165/166 binding site of the HD zipper class III transcription factor on 1BL altered its transcriptional level, which may be responsible for the rolling leaf phenotype. Our results suggest the important role of rlT73 in regulating wheat leaf development and the potential of miRNA-based gene regulation for crop trait improvement.

Genomic regions involved in the control of 1,000-kernel weight in wild relative-derived populations of durum wheat

Terminal drought is one of the most common and devastating climatic stress factors affecting durum wheat (Triticum durum Desf.) production worldwide. The wild relatives of this crop are deemed a vast potential source of useful alleles to adapt to this stress. A nested association mapping (NAM) panel was generated using as a recurrent parent the Moroccan variety 'Nachit' derived from Triticum dicoccoides and known for its large grain size. This was recombined to three top-performing lines derived from T. dicoccoides, T. araraticum, and Aegilops speltoides, for a total of 426 inbred progenies. This NAM was evaluated across eight environments (Syria, Lebanon, and Morocco) experiencing different degrees of terminal moisture stress over two crop seasons. Our results showed that drought stress caused on average 41% loss in yield and that 1,000-kernel weight (TKW) was the most important trait for adaptation to it. Genotyping with the 25K TraitGenetics array resulted in a consensus map of 1,678 polymorphic SNPs, spanning 1,723 cM aligned to the reference 'Svevo' genome assembly. Kinship distinguished the progenies in three clades matching the parent of origin. A total of 18 stable quantitative trait loci (QTLs) were identified as controlling various traits but independent from flowering time. The most significant genomic regions were named Q.ICD.NAM-04, Q.ICD.NAM-14, and Q.ICD.NAM-16. Allelic investigation in a second germplasm panel confirmed that carrying the positive allele at all three loci produced an average TKW advantage of 25.6% when field-tested under drought conditions. The underlying SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and successfully validated in a third germplasm set, where they explained up to 19% of phenotypic variation for TKW under moisture stress. These findings confirm the identification of critical loci for drought adaptation derived from wild relatives that can now be readily exploited via molecular breeding.

Meta-QTL analysis in wheat: progress, challenges and opportunities

Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.

Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP

KEY MESSAGE

Simultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a genome-wide association study was performed. Two statistical models revealed dozens of marker-trait associations (MTAs), each explaining up to 30%. phenotypic variance. Two markers on chromosomes 2A and 6B were consistently identified by both models and were found to be significantly associated with GY and GPC. MTAs identified for phenological traits co-mapped to well-known genes (i.e., Ppd-1, Vrn-1). The significance values (p-values) that measure the strength of the association of each single nucleotide polymorphism marker with the target traits were used to perform genomic prediction by using a weighted genomic best linear unbiased prediction model. The trained models were ultimately used to predict the agronomic performances of an independent durum wheat panel, confirming the utility of genomic prediction, although environmental conditions and genetic backgrounds may still be a challenge to overcome. The results generated through our study confirmed the utility of GPD and GYD to mitigate the inverse GY and GPC relationship in wheat, provided novel markers for marker-assisted selection and opened new ways to develop cultivars through genomic prediction approaches.

Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize

KEY MESSAGE

Multi-trial genome wide association study of plasticity indices allow to detect QTLs specifically involved in the genotype x water availability interaction. Concerns regarding high maize yield losses due to increasing occurrences of drought events are growing, and breeders are still looking for molecular markers for drought tolerance. However, the genetic determinism of traits in response to drought is highly complex and identification of causal regions is a tremendous task. Here, we exploit the phenotypic data obtained from four trials carried out on a phenotyping platform, where a diversity panel of 254 maize hybrids was grown under well-watered and water deficit conditions, to investigate the genetic bases of the drought response in maize. To dissociate drought effect from other environmental factors, we performed multi-trial genome-wide association study on well-watered and water deficit phenotypic means, and on phenotypic plasticity indices computed from measurements made for six ecophysiological traits. We identify 102 QTLs and 40 plasticity QTLs. Most of them were new compared to those obtained from a previous study on the same dataset. Our results show that plasticity QTLs cover genetic regions not identified by QTLs. Furthermore, for all ecophysiological traits, except one, plasticity QTLs are specifically involved in the genotype by water availability interaction, for which they explain between 60 and 100% of the variance. Altogether, QTLs and plasticity QTLs captured more than 75% of the genotype by water availability interaction variance, and allowed to find new genetic regions. Overall, our results demonstrate the importance of considering phenotypic plasticity to decipher the genetic architecture of trait response to stress.

Multivariate analysis and genetic dissection of staygreen and stem reserve mobilisation under combined drought and heat stress in wheat (Triticum aestivum L.)

Introduction: Abiotic stresses significantly reduce crop yield by adversely affecting many physio-biochemical processes. Several physiological traits have been targeted and improved for yield enhancement in limiting environmental conditions. Amongst them, staygreen and stem reserve mobilisation are two important mutually exclusive traits contributing to grain filling under drought and heat stress in wheat. Henceforth, the present study was carried out to identify the QTLs governing these traits and to identify the superiors' lines through multi-trait genotype-ideotype distance index (MGIDI) Methods: A mapping population consisting of 166 recombinant inbred lines (RILs) developed from a cross between HD3086 and HI1500 was utilized in this study. The experiment was laid down in alpha lattice design in four environmental conditions viz. Control, drought, heat and combined stress (heat and drought). Genotyping of parents and RILs was carried out with 35 K Axiom® array (Wheat breeder array). Results and Discussion: Medium to high heritability with a moderate to high correlation between traits was observed. Principal component analysis (PCA) was performed to derive latent variables in the original set of traits and the relationship of these traits with latent variables.From this study, 14 QTLs were identified, out of which 11, 2, and 1 for soil plant analysis development (SPAD) value, leaf senescence rate (LSR), and stem reserve mobilisation efficiency (SRE) respectively. Quantitative trait loci (QTLs) for SPAD value harbored various genes like Dirigent protein 6-like, Protein FATTY ACID EXPORT 3, glucan synthase-3 and Ubiquitin carboxyl-terminal hydrolase, whereas QTLs for LSR were found to contain various genes like aspartyl protease family protein, potassium transporter, inositol-tetrakisphosphate 1-kinase, and DNA polymerase epsilon subunit D-like. Furthermore, the chromosomal region for SRE was found to be associated with serine-threonine protein kinase. Serine-threonine protein kinases are involved in many signaling networks such as ABA mediated ROS signaling and acclimation to environmental stimuli. After the validation of QTLs in multilocation trials, these QTLs can be used for marker-assisted selection (MAS) in breeding programs.

Molecular Mechanism Underlying the Sorghum sudanense (Piper) Stapf. Response to Osmotic Stress Determined via Single-Molecule Real-Time Sequencing and Next-Generation Sequencing

Drought, as a widespread environmental factor in nature, has become one of the most critical factors restricting the yield of forage grass. Sudangrass (Sorghum sudanense (Piper) Stapf.), as a tall and large grass, has a large biomass and is widely used as forage and biofuel. However, its growth and development are limited by drought stress. To obtain novel insight into the molecular mechanisms underlying the drought response and excavate drought tolerance genes in sudangrass, the first full-length transcriptome database of sudangrass under drought stress at different time points was constructed by combining single-molecule real-time sequencing (SMRT) and next-generation transcriptome sequencing (NGS). A total of 32.3 Gb of raw data was obtained, including 20,199 full-length transcripts with an average length of 1628 bp after assembly and correction. In total, 11,921 and 8559 up- and down-regulated differentially expressed genes were identified between the control group and plants subjected to drought stress. Additionally, 951 transcription factors belonging to 50 families and 358 alternative splicing events were found. A KEGG analysis of 158 core genes exhibiting continuous changes over time revealed that 'galactose metabolism' is a hub pathway and raffinose synthase 2 and β-fructofuranosidase are key genes in the response to drought stress. This study revealed the molecular mechanism underlying drought tolerance in sudangrass. Furthermore, the genes identified in this study provide valuable resources for further research into the response to drought stress.

Quantitative trait loci for rolled leaf in a wheat EMS mutant from Jagger

Two QTLs with major effects on rolled leaf trait were consistently detected on chromosomes 1A (QRl.hwwg-1AS) and 5A (QRl.hwwg-5AL) in the field experiments. Rolled leaf (RL) is a morphological strategy to protect plants from dehydration under stressed field conditions. Identification of quantitative trait loci (QTLs) underlining RL is essential to breed drought-tolerant wheat cultivars. A mapping population of 154 recombinant inbred lines was developed from the cross between JagMut1095, a mutant of Jagger, and Jagger to identify quantitative trait loci (QTLs) for the RL trait. A linkage map of 3106 cM was constructed with 1003 unique SNPs from 21 wheat chromosomes. Two consistent QTLs were identified for RL on chromosomes 1A (QRl.hwwg-1AS) and 5A (QRl.hwwg-5AL) in all field experiments. QRl.hwwg-1AS explained 24-56% of the phenotypic variation and QRl.hwwg-5AL explained up to 20% of the phenotypic variation. The combined percent phenotypic variation associated with the two QTLs was up to 61%. Analyses of phenotypic and genotypic data of recombinants generated from heterogeneous inbred families of JagMut1095 × Jagger delimited QRl.hwwg-1AS to a 6.04 Mb physical interval. This work lays solid foundation for further fine mapping and map-based cloning of QRl.hwwg-1AS.

QTL mapping of maize (Zea mays L.) kernel traits under low-phosphorus stress

Low-phosphorus stress significantly impacts the development of maize kernels. In this study, the phosphor efficient maize genotype 082 and phosphor deficient maize genotype Ye107, were used to construct an F2:3 population. QTL mapping was then employed to determine the genetic basis of differences in the maize kernel traits of the two parents in a low-phosphorus environment. This analysis revealed several major QTL that control environmental impacts on kernel length, width, thickness, and weight. These QTL were detected in all three environments and were distributed on five genome segments of chromosomes 3, 5, 6, and 9, and some new kernel-trait QTL were also detected (eg: Qkwid6, Qkthi3, Qkwei9, and Qklen3-1). These environmentally insensitive QTL can be stably expressed in low phosphorus environments, indicating that they can lay a foundation for the breeding of high phosphorus utilization efficiency germplasm.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01300-0.

Environment-oriented selection criteria to overcome controversies in breeding for drought resistance in wheat

Wheat is one of the most important cereal crops, representing a fundamental source of calories and protein for the global human population. Drought stress (DS) is a widespread phenomenon, already affecting large wheat-growing areas worldwide, and a major threat for cereal productivity, resulting in consistent losses in average grain yield (GY). Climate change is projected to exacerbate DS incidence and severity by increasing temperatures and changing rainfall patterns. Estimating that wheat production has to substantially increase to guarantee food security to a demographically expanding human population, the need for breeding programs focused on improving wheat drought resistance is manifest. Drought occurrence, in terms of time of appearance, duration, frequency, and severity, along the plant's life cycle varies significantly among different environments and different agricultural years, making it difficult to identify reliable phenological, morphological, and functional traits to be used as effective breeding tools. The situation is further complicated by the presence of confounding factors, e.g., other concomitant abiotic stresses, in an open-field context. Consequently, the relationship between morpho-functional traits and GY under water deficit is often contradictory; moreover, controversies have emerged not only on which traits are to be preferred, but also on how one specific trait should be desired. In this review, we attempt to identify the possible causes of these disputes and propose the most suitable selection criteria in different target environments and, thus, the best trait combinations for breeders in different drought contexts. In fact, an environment-oriented approach could be a valuable solution to overcome controversies in identifying the proper selection criteria for improving wheat drought resistance.

Leaf rolling in bread wheat (Triticum aestivum L.) is controlled by the upregulation of a pair of closely linked/duplicate zinc finger homeodomain class transcription factors during moisture stress conditions

Zinc finger-homeodomain (ZF-HDs) class IV transcriptional factors (TFs) is a plant-specific transcription factor and play a key role in stress responses, plant growth, development, and hormonal signaling. In this study, two new leaf rolling TFs genes, namely TaZHD1 and TaZHD10, were identified in wheat using comparative genomic analysis of the target region that carried a major QTL for leaf rolling identified through multi-environment phenotyping and high throughput genotyping of a RIL population. Structural and functional annotation of the candidate ZHD genes with its closest rice orthologs reflects the species-specific evolution and, undoubtedly, validates the notions of remote-distance homology concept. Meanwhile, the morphological analysis resulted in contrasting difference for leaf rolling in extreme RILs between parental lines HD2012 and NI5439 at booting and heading stages. Transcriptome-wide expression profiling revealed that TaZHD10 transcripts showed significantly higher expression levels than TaZHD1 in all leaf tissues upon drought stress. The relative expression of these genes was further validated by qRT-PCR analysis, which also showed consistent results across the studied genotypes at the booting and anthesis stage. The contrasting modulation of these genes under drought conditions and the available evidenced for its epigenetic behavior that might involve the regulation of metabolic and gene regulatory networks. Prediction of miRNAs resulted in five Tae-miRs that could be associated with RNAi mediated control of TaZHD1 and TaZHD10 putatively involved in the metabolic pathway controlling rolled leaf phenotype. Gene interaction network analysis indicated that TaZHD1 and TaZHD10 showed pleiotropic effects and might also involve other functions in wheat in addition to leaf rolling. Overall, the results increase our understanding of TaZHD genes and provide valuable information as robust candidate genes for future functional genomics research aiming for the breeding of wheat varieties tolerant to leaf rolling.

Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS

BACKGROUND

Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition.

RESULTS

Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H²-dependent PCR; rhAMP).

CONCLUSIONS

The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.

Dissection of a grain yield QTL from wild emmer wheat reveals sub-intervals associated with culm length and kernel number

Genetic diversity in wheat has been depleted due to domestication and modern breeding. Wild relatives are a valuable source for improving drought tolerance in domesticated wheat. A QTL region on chromosome 2BS of wild emmer wheat (Triticum turgidum ssp. dicoccoides), conferring high grain yield under well-watered and water-limited conditions, was transferred to the elite durum wheat cultivar Uzan (T. turgidum ssp. durum) by a marker-assisted backcross breeding approach. The 2B introgression line turned out to be higher yielding but also exhibited negative traits that likely result from trans-, cis-, or linkage drag effects from the wild emmer parent. In this study, the respective 2BS QTL was subjected to fine-mapping, and a set of 17 homozygote recombinants were phenotyped at BC4F5 generation under water-limited and well-watered conditions at an experimental farm in Israel and at a high-throughput phenotyping platform (LemnaTec-129) in Germany. In general, both experimental setups allowed the identification of sub-QTL intervals related to culm length, kernel number, thousand kernel weight, and harvest index. Sub-QTLs for kernel number and harvest index were detected specifically under either drought stress or well-watered conditions, while QTLs for culm length and thousand-kernel weight were detected in both conditions. Although no direct QTL for grain yield was identified, plants with the sub-QTL for kernel number showed a higher grain yield than the recurrent durum cultivar Uzan under well-watered and mild drought stress conditions. We, therefore, suggest that this sub-QTL might be of interest for future breeding purposes.

Precision phenotyping across the life cycle to validate and decipher drought-adaptive QTLs of wild emmer wheat (Triticum turgidum ssp. dicoccoides) introduced into elite wheat varieties

Drought events or the combination of drought and heat conditions are expected to become more frequent due to global warming, and wheat yields may fall below their long-term average. One way to increase climate-resilience of modern high-yielding varieties is by their genetic improvement with beneficial alleles from crop wild relatives. In the present study, the effect of two beneficial QTLs introgressed from wild emmer wheat and incorporated in the three wheat varieties BarNir, Zahir and Uzan was studied under well-watered conditions and under drought stress using non-destructive High-throughput Phenotyping (HTP) throughout the life cycle in a single pot-experiment. Plants were daily imaged with RGB top and side view cameras and watered automatically. Further, at two time points, the quantum yield of photosystem II was measured with a top view FluorCam. The QTL carrying near isogenic lines (NILs) were compared with their corresponding parents by t-test for all non-invasively obtained traits and for the manually determined agronomic and yield parameters. Data quality of phenotypic traits (repeatability) in the controlled HTP experiment was above 85% throughout the life cycle and at maturity. Drought stress had a strong effect on growth in all wheat genotypes causing biomass reduction from 2% up to 70% at early and late points in the drought period, respectively. At maturity, the drought caused 47-55% decreases in yield-related traits grain weight, straw weight and total biomass and reduced TKW by 10%, while water use efficiency (WUE) increased under drought by 29%. The yield-enhancing effect of the introgressed QTLs under drought conditions that were previously demonstrated under field/screenhouse conditions in Israel, could be mostly confirmed in a greenhouse pot experiment using HTP. Daily precision phenotyping enabled to decipher the mode of action of the QTLs in the different genetic backgrounds throughout the entire wheat life cycle. Daily phenotyping allowed a precise determination of the timing and size of the QTLs effect (s) and further yielded information about which image-derived traits are informative at which developmental stage of wheat during the entire life cycle. Maximum height and estimated biovolume were reached about a week after heading, so experiments that only aim at exploring these traits would not need a longer observation period. To obtain information on different onset and progress of senescence, the CVa curves represented best the ongoing senescence of plants. The QTL on 7A in the BarNir background was found to improve yield under drought by increased biomass growth, a higher photosynthetic performance, a higher WUE and a "stay green effect."

A comprehensive meta-QTL analysis for yield-related traits of durum wheat (Triticum turgidum L. var. durum) grown under different water regimes

Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.

Chromosome 3A harbors several pleiotropic and stable drought-responsive alleles for photosynthetic efficiency selected through wheat breeding

Water deficit is the most severe stress factor in crop production threatening global food security. In this study, we evaluated the genetic variation in photosynthetic traits among 200 wheat cultivars evaluated under drought and rainfed conditions. Significant genotypic, treatments, and their interaction effects were detected for chlorophyll content and chlorophyll fluorescence parameters. Drought stress reduced the effective quantum yield of photosystem II (YII) from the anthesis growth stage on. Leaf chlorophyll content measured at anthesis growth stages was significantly correlated with YII and non-photochemical quenching under drought conditions, suggesting that high throughput chlorophyll content screening can serve as a good indicator of plant drought tolerance status in wheat. Breeding significantly increased the photosynthetic efficiency as newer released genotypes had higher YII and chlorophyll content than the older ones. GWAS identified a stable drought-responsive QTL on chromosome 3A for YII, while under rainfed conditions, it detected another QTL on chromosome 7A for chlorophyll content across both growing seasons. Molecular analysis revealed that the associated alleles of AX-158576783 (515.889 Mbp) on 3A co-segregates with the NADH-ubiquinone oxidoreductase (TraesCS3A02G287600) gene involved in ATP synthesis coupled electron transport and is proximal to WKRY transcription factor locus. This allele on 3A has been positively selected through breeding and has contributed to increasing the grain yield.

Harnessing the diversity of wild emmer wheat for genetic improvement of durum wheat

The multiple derivative lines (MDLs) characterized in this study offer a promising strategy for harnessing the diversity of wild emmer wheat for durum and bread wheat improvement. Crop domestication has diminished genetic diversity and reduced phenotypic plasticity and adaptation. Exploring the adaptive capacity of wild progenitors offer promising opportunities to improve crops. We developed a population of 178 BC₁F₆ durum wheat (Triticum turgidum ssp. durum) lines by crossing and backcrossing nine wild emmer wheat (T. turgidum ssp. dicoccoides) accessions with the common durum wheat cultivar 'Miki 3'. Here, we describe the development of this population, which we named as multiple derivative lines (MDLs), and demonstrated its suitability for durum wheat breeding. We genotyped the MDL population, the parents, and 43 Sudanese durum wheat cultivars on a Diversity Array Technology sequencing platform. We evaluated days to heading and plant height in Dongola (Sudan) and in Tottori (Japan). The physical map length of the MDL population was 9 939 Mb with an average of 1.4 SNP/Mb. The MDL population had greater diversity than the Sudanese cultivars. We found high gene exchange between the nine wild emmer accessions and the MDL population, indicating that the MDL captured most of the diversity in the wild emmer accessions. Genome-wide association analysis identified three loci for days to heading on chromosomes 1A and 5A in Dongola and one on chromosome 3B in Tottori. For plant height, common genomic loci were found on chromosomes 4A and 4B in both locations, and one genomic locus on chromosome 7B was found only in Dongola. The results revealed that the MDLs are an effective strategy towards harnessing wild emmer wheat diversity for wheat genetic improvement.

Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement

Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.

Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars

Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.

One Hundred Candidate Genes and Their Roles in Drought and Salt Tolerance in Wheat

Drought and salinity are major constraints to agriculture. In this review, we present an overview of the global situation and the consequences of drought and salt stress connected to climatic changes. We provide a list of possible genetic resources as sources of resistance or tolerant traits, together with the previous studies that focused on transferring genes from the germplasm to cultivated varieties. We explained the morphological and physiological aspects connected to hydric stresses, described the mechanisms that induce tolerance, and discussed the results of the main studies. Finally, we described more than 100 genes associated with tolerance to hydric stresses in the Triticeae. These were divided in agreement with their main function into osmotic adjustment and ionic and redox homeostasis. The understanding of a given gene function and expression pattern according to hydric stress is particularly important for the efficient selection of new tolerant genotypes in classical breeding. For this reason, the current review provides a crucial reference for future studies on the mechanism involved in hydric stress tolerance and the use of these genes in mark assistance selection (MAS) to select the wheat germplasm to face the climatic changes.

Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

Background

Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. O. nivara inhabits swampy areas with a seasonally dry climate, which is an ideal material to discover drought tolerance alleles. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown.

Results

Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1246 lncRNAs were identified, including 1091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes enriched in stress responsive GO terms; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare.

Conclusion

We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07754-4.

Deciphering the genetic basis of wheat seminal root anatomy uncovers ancestral axial conductance alleles

Root axial conductance, which describes the ability of water to move through the xylem, contributes to the rate of water uptake from the soil throughout the whole plant lifecycle. Under the rainfed wheat agro-system, grain-filling is typically occurring during declining water availability (i.e., terminal drought). Therefore, preserving soil water moisture during grain filling could serve as a key adaptive trait. We hypothesized that lower wheat root axial conductance can promote higher yields under terminal drought. A segregating population derived from a cross between durum wheat and its direct progenitor wild emmer wheat was used to underpin the genetic basis of seminal root architectural and functional traits. We detected 75 QTL associated with seminal roots morphological, anatomical and physiological traits, with several hotspots harbouring co-localized QTL. We further validated the axial conductance and central metaxylem QTL using wild introgression lines. Field-based characterization of genotypes with contrasting axial conductance suggested the contribution of low axial conductance as a mechanism for water conservation during grain filling and consequent increase in grain size and yield. Our findings underscore the potential of harnessing wild alleles to reshape the wheat root system architecture and associated hydraulic properties for greater adaptability under changing climate.

Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat

Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.

Wild and Domestic Differences in Plant Development and Responses to Water Deficit in Cicer

There is growing interest in widening the genetic diversity of domestic crops using wild relatives to break linkage drag and/or introduce new adaptive traits, particularly in narrow crops such as chickpea. To this end, it is important to understand wild and domestic adaptive differences to develop greater insight into how wild traits can be exploited for crop improvement. Here, we study wild and domestic Cicer development and water-use over the lifecycle, measuring responses to reproductive water deficit, a key Mediterranean selection pressure, using mini-lysimeters (33 L round pots) in common gardens under contrasting water regimes. Wild and domestic Cicer were consistently separated by later phenology, greater water extraction and lower water use efficiency (WUE) and harvest index in the former, and much greater yield-responsiveness in the latter. Throughout the lifecycle, there was greater vegetative investment in wild, and greater reproductive investment in domestic Cicer, reflected in root and harvest indices, rates of leaf area, and pod growth. Domestic WUE was consistently greater than wild, suggesting differences in water-use regulation and partitioning. Large wild-domestic differences revealed in this study are indicative of evolution under contrasting selection pressures. Cicer domestication has selected for early phenology, greater early vigor, and reproductive efficiency, attributes well-suited to a time-delimited production system, where the crop is protected from grazing, disease, and competition, circumstances that do not pertain in the wild. Wild Cicer attributes are more competitive: higher peak rates of leaf area growth, greater ad libitum water-use, and extraction under terminal drought associated with greater vegetative dry matter allocation, leading to a lower reproductive capacity and efficiency than in domestic chickpea. These traits strengthen competitive capacity throughout the growing season and are likely to facilitate recovery from grazing, two significant selection pressures faced by wild, rather than domesticated Cicer. While increased water extraction may be useful for improving chickpea drought tolerance, this trait must be evaluated independently of the other associated wild traits. To this end, the wild-domestic populations have been developed.

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder’s SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575–AX-95124447 (5D:338665301–5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.

Genome-Wide Association Mapping of Seedling Drought Tolerance in Winter Wheat

In the southern Great Plains of the United States, winter wheat grown for dual-purpose is often planted early, which puts it at risk for drought stress at the seedling stage in the autumn. To map quantitative trait loci (QTL) associated with seedling drought tolerance, a genome-wide association study (GWAS) was performed on a hard winter wheat association mapping panel. Two sets of plants were planted in the greenhouse initially under well-watered conditions. At the five-leaf stage, one set continued to receive the optimum amount of water, whereas watering was withdrawn from the other set (drought stress treatment) for 14 days to mimic drought stress. Large phenotypic variation was observed in leaf chlorophyll content, leaf chlorophyll fluorescence, shoot length, number of leaves per seedling, and seedling recovery. A mixed linear model analysis detected multiple significant QTL associated with seedling drought tolerance-related traits on chromosomes 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6B, and 7B. Among those, 12 stable QTL responding to drought stress for various traits were identified. Shoot length and leaf chlorophyll fluorescence were good indicators in responding to drought stress because most of the drought responding QTL detected using means of these two traits were also detected in at least two experimental repeats. These stable QTL are more valuable for use in marker-assisted selection during wheat breeding. Moreover, different traits were mapped on several common chromosomes, such as 1B, 2B, 3B, and 6B, and two QTL clusters associated with three or more traits were located at 107-130 and 80-83 cM on chromosomes 2B and 6B, respectively. Furthermore, some QTL detected in this study co-localized with previously reported QTL for root and shoot traits at the seedling stage and canopy temperature at the grain-filling stage of wheat. In addition, several of the mapped chromosomes were also associated with drought tolerance during the flowering or grain-filling stage in wheat. Some significant single-nucleotide polymorphisms (SNPs) were aligned to candidate genes playing roles in plant abiotic stress responses. The SNP markers identified in this study will be further validated and used for marker-assisted breeding of seedling drought tolerance during dual-purpose wheat breeding.

GenoTypeMapper: graphical genotyping on genetic and sequence-based maps

BACKGROUND

The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable.

RESULTS

We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time.

CONCLUSIONS

In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.

Current Progress in Understanding and Recovering the Wheat Genes Lost in Evolution and Domestication

The modern cultivated wheat has passed a long evolution involving origin of wild emmer (WEM), development of cultivated emmer, formation of spelt wheat and finally establishment of modern bread wheat and durum wheat. During this evolutionary process, rapid alterations and sporadic changes in wheat genome took place, due to hybridization, polyploidization, domestication, and mutation. This has resulted in some modifications and a high level of gene loss. As a result, the modern cultivated wheat does not contain all genes of their progenitors. These lost genes are novel for modern wheat improvement. Exploring wild progenitor for genetic variation of important traits is directly beneficial for wheat breeding. WEM wheat (Triticum dicoccoides) is a great genetic resource with huge diversity for traits. Few genes and quantitative trait loci (QTL) for agronomic, quantitative, biotic and abiotic stress-related traits have already been mapped from WEM. This resource can be utilized for modern wheat improvement by integrating identified genes or QTLs through breeding.

Selection criteria for high-yielding and early-flowering bread wheat hybrids under heat stress

Hybrid performance during wheat breeding can be improved by analyzing genetic distance (GD) among wheat genotypes and determining its correlation with heterosis. This study evaluated the GD between 16 wheat genotypes by using 60 simple sequence repeat (SSR) markers to classify them according to their relationships and select those with greater genetic diversity, evaluate the correlation of the SSR marker distance with heterotic performance and specific combining ability (SCA) for heat stress tolerance, and identify traits that most influence grain yield (GY). Eight parental genotypes with greater genetic diversity and their 28 F1 hybrids generated using diallel crossing were evaluated for 12 measured traits in two seasons. The GD varied from 0.235 to 0.911 across the 16 genotypes. Cluster analysis based on the GD estimated using SSRs classified the genotypes into three major groups and six sub-groups, almost consistent with the results of principal coordinate analysis. The combined data indicated that five hybrids showed 20% greater yield than mid-parent or better-parent. Two hybrids (P2 × P4) and (P2 × P5), which showed the highest performance of days to heading (DH), grain filling duration (GFD), and GY, and had large genetic diversity among themselves (0.883 and 0.911, respectively), were deemed as promising heat-tolerant hybrids. They showed the best mid-parent heterosis and better-parent heterosis (BPH) for DH (-11.57 and -7.65%; -13.39 and -8.36%, respectively), GFD (12.74 and 12.17%; 12.09 and 10.59%, respectively), and GY (36.04 and 20.04%; 44.06 and 37.73%, respectively). Correlation between GD and each of BPH and SCA effects based on SSR markers was significantly positive for GFD, hundred kernel weight, number of kernels per spike, harvest index, GY, and grain filling rate and was significantly negative for DH. These correlations indicate that the performance of wheat hybrids with high GY and earliness could be predicted by determining the GD of the parents by using SSR markers. Multivariate analysis (stepwise regression and path coefficient) suggested that GFD, hundred kernel weight, days to maturity, and number of kernels per spike had the highest influence on GY.

ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)

Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F₁ population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1⁷²³G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F₁ plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.

Selenium mitigates salt-induced oxidative stress in durum wheat (Triticum durum Desf.) seedlings by modulating chlorophyll fluorescence, osmolyte accumulation, and antioxidant system

Hydroponic experiments were conducted to investigate the effects of different concentrations of sodium selenate (Na₂SeO₄) and sodium selenite (Na₂SeO₃) on durum wheat seed germination and seedling growth under salt stress. The treatments used were 0 and 50 mM NaCl solutions, each supplemented with Na₂SeO₄ or Na₂SeO₃ at 0, 0.1, 1, 2, 4, 8, or 10 μM. Salt alone significantly inhibited seed germination and reduced seedling growth. Addition of low concentrations (0.1-4 μM) of Na₂SeO₄ or Na₂SeO₃ mitigated the adverse effects of salt stress on seed germination, biomass accumulation, and other physiological attributes. Among them, 1 μM Na₂SeO₄ was most effective at restoring seed germination rate, germination energy, and germination index, significantly increasing these parameters by about 12.35, 24.17, and 11.42%, respectively, compared to salt-stress conditions. Adding low concentrations of Na₂SeO₄ or Na₂SeO₃ to the salt solution also had positive effects on chlorophyll fluorescence indices, decreased the concentrations of free proline and malondialdehyde, as well as electrolyte leakage, and increased catalase, superoxide dismutase, and peroxidase activities in roots and shoots. However, high concentrations (8-10 μM) of Na₂SeO₄ or Na₂SeO₃ disrupted seed germination and seedling growth, with damage caused by Na₂SeO₃ being more severe than that by Na₂SeO₄. It is thus clear that exogenous selenium can improve the adaptability of processing wheat to salt stress and maintain higher photosynthetic rate by decreasing the accumulation of reactive oxygen species and alleviating the degree of membrane lipid peroxidation. Na₂SeO₄ was more effective than Na₂SeO₃ at all given concentrations.

Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat (Triticum aestivum L.)

Meta-QTL (MQTL) analysis for drought tolerance was undertaken in bread wheat to identify consensus and robust MQTLs using 340 known QTLs from 11 earlier studies; 13 MQTLs located on 6 chromosomes (1D, 3B, 5A, 6D, 7A and 7D) were identified, with maximum of 4 MQTLs on chromosome 5A. Mean confidence intervals for MQTLs were much narrower (mean, 6.01 cM; range 2.07-19.46 cM), relative to those in original QTLs (mean, 13.6 cM; range, 1.0-119.1 cM). Two MQTLs, namely MQTL4 and MQTL12, were major MQTLs with potential for use in marker-assisting breeding. As many as 228 candidate genes (CGs) were also identified using 6 of the 13 MQTLs. In-silico expression analysis of these 228 CGs allowed identification of 14 important CGs, with + 3 to - 8 fold change in expression under drought (relative to normal conditions) in a tolerant cv. named TAM107. These CGs encoded proteins belonging to the following families: NAD-dependent epimerase/dehydratase, protein kinase, NAD(P)-binding domain protein, heat shock protein 70 (Hsp70), glycosyltransferase 2-like, etc. Important MQTLs and CGs identified in the present study should prove useful for future molecular breeding and for the study of molecular basis of drought tolerance in cereals in general and wheat in particular.

Identification of quantitative trait loci for carbon isotope ratio (δ13C) in a recombinant inbred population of soybean

KEY MESSAGE

QTL analysis identified 16 QTLs, grouped in eight loci on seven soybean chromosomes that were associated with carbon isotope ratio (δ13C) in a biparental recombinant inbred population. Drought is a major limitation to soybean yield, and the frequency of drought stress is likely to increase under future climatic scenarios. Water use efficiency (WUE) is associated with drought tolerance, and carbon isotope ratio (δ13C) is positively correlated with WUE. In this study, 196 F6-derived recombinant inbred lines from a cross of PI 416997 (high WUE) × PI 567201D (low WUE) were evaluated in four environments to identify genomic regions associated with δ13C. There were positive correlations of δ13C values between different environments (0.67 ≤ r ≤ 0.78). Genotype, environment, and genotype × environment interactions had significant effects on δ13C. Narrow sense heritability of δ13C was 90% when estimated across environments. There was a total of 16 QTLs on seven chromosomes with individual QTLs explaining between 2.5 and 29.9% of the phenotypic variation and with additive effects ranging from 0.07 to 0.22‰. These 16 QTLs likely identified eight loci based on their overlapping confidence intervals. Of these eight loci, two loci on chromosome 20 (Gm20) were detected in at least three environments and were considered as stable QTLs. Additive QTLs on Gm20 showed epistatic interactions with 10 QTLs present across nine chromosomes. Five QTLs were identified across environments and showed significant QTL × environment interactions. These findings demonstrate that additive QTLs and QTL × QTL interactions play significant roles in genetic control of the δ13C trait. Markers flanking identified QTLs may facilitate marker-assisted selection to accumulate desirable QTLs to improve WUE and drought tolerance in soybean.

Emmer wheat (Triticum dicoccon Schrank) improves water use efficiency and yield of hexaploid bread wheat

Emmer wheat (Triticum dicoccon Schrank) is a potential source of new genetic diversity for the improvement of hexaploid bread wheat. Emmer wheat was crossed and backcrossed to bread wheat and 480 doubled haploids (DHs) were produced from BC₁F₁ plants with hexaploid appearance derived from 19 crossses. These DHs were screened under well-watered conditions (E1) in 2013 to identify high-yielding materials with similar phenology. One-hundred and eighty seven DH lines selected on this basis, 4 commercial bread wheat cultivars and 9 bread wheat parents were then evaluated in extensive field experiments under two contrasting moisture regimes in north-western NSW in 2014 and 2015. A significant range in the water-use-efficiency of grain production (WUE_Grain) was observed among the emmer derivatives. Of these, 8 hexaploid lines developed from 8 different emmer wheat parents had significantly improved intrinsic water-use-efficiency (WUE_intr) and instantaneous water-use-efficiency (WUE_i) compared to their bread wheat recurrent parents. Accurate and large scale field-based phenotyping was effective in identifying emmer wheat derived lines with superior performance to their hexaploid bread wheat recurrent parents under moisture stress.

Mapping of QTLs Associated with Yield and Yield Related Traits in Durum Wheat (Triticum durum Desf.) Under Irrigated and Drought Conditions

Global durum wheat consumption (Triticum durum Desf.) is ahead of its production. One reason for this is abiotic stress, e.g., drought. Breeding for resistance to drought is complicated by the lack of fast, reproducible screening techniques and the inability to routinely create defined and repeatable water stress conditions. Here, we report the first analysis of dissection of yield and yield-related traits in durum wheat in Pakistan, seeking to elucidate the genetic components of yield and agronomic traits. Analysis of several traits revealed a total of 221 (160 with logarithm of odds (LOD) > 2 ≤ 3 and 61 with LOD > 3) quantitative trait loci (QTLs) distributed on all fourteen durum wheat chromosomes, of which 109 (78 with LOD > 2 ≤ 3 and 31 with LOD > 3) were observed in 2016-17 (S1) and 112 (82 with LOD > 2 ≤ 3 and 30 with LOD > 3) were observed in 2017-18 (S2). Allelic profiles of yield QTLs on chromosome 2A and 7B indicate that allele A of Xgwm895 and allele B of Xbarc276 can enhance the Yd up to 6.16% in control and 5.27% under drought. Moreover, if combined, a yield gain of up to 11% would be possible.

Variation in phosphorus and sulfur content shapes the genetic architecture and phenotypic associations within the wheat grain ionome

Dissection of the genetic basis of wheat ionome is crucial for understanding the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur-containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic correlations within ionome. Adjustment of element concentrations for the effect of variation in phosphorus and sulfur seed content resulted in drastic change of phenotypic correlations between the elements. The genetic architecture of wheat grain ionome was characterized by quantitative trait loci (QTL) analysis using a cross between durum and wild emmer wheat. QTL analysis of the adjusted traits and two-trait analysis of the initial traits paired with either P or S considerably improved QTL detection power and accuracy, resulting in the identification of 105 QTLs and 617 QTL effects for 11 elements. Candidate gene search revealed some potential functional associations between QTLs and corresponding genes within their intervals. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.

Genetic control of some plant growth characteristics of bread wheat (Triticum aestivum L.) under aluminum stress

BACKGROUND

Biomass yield is an important trait for wheat breeding programs. Enhancing the yield of the aerial components of wheat cultivars will be an integral part of future wheat improvement. Aluminum (Al) toxicity is one of the main factors limiting wheat growth and production in acid soils, which occur on up to 50% of the arable lands of the world especially in tropical and subtropical regions.

OBJECTIVE

Our objective was to identify quantitative trait loci (QTL) of plant growth characteristics and yield in wheat.

METHODS

A recombinant inbred line (RIL) population consisting of 167 lines, derived from a cross between SeriM82 and Babax were evaluated under two Al treatments (+ Al, 800 µM of Al; -Al, 0 µM of Al) in the field based on an alpha lattice design with two replications for two consecutive crop seasons.

RESULTS

A total of 40 QTLs including nine putative and 31 suggestive QTLs were found for all traits using the composite interval mapping (CIM) method. By mixed model-based composite interval mapping (MCIM) method, 42 additive QTLs and nine pairs of epistatic effects were detected for studied traits, of which 20 additive and six pairs of epistatic QTLs showed significant QTL × environment interactions. Most of the detected QTLs across environments were stable, and the highest number of stable QTLs was related to A genome. Co-localization of QTL was found on linkage groups (LGs) 2B, 4B, 6A-a, and 7A (CIM method) and 2A-d, and 6A-a (MCIM method).

CONCLUSION

These results have implications for selection strategies in biomass yield and for increasing the yield of the aerial part of wheat following further evaluations in various genetic backgrounds and environments.

A Genome-Wide Association Study of Highly Heritable Agronomic Traits in Durum Wheat

Uncovering the genetic basis of key agronomic traits, and particularly of drought tolerance, addresses an important priority for durum wheat improvement. Here, a genome-wide association study (GWAS) in 493 durum wheat accessions representing a worldwide collection was employed to address the genetic basis of 17 agronomically important traits and a drought wilting score. Using a linear mixed model with 4 inferred subpopulations and a kinship matrix, we identified 90 marker-trait-associations (MTAs) defined by 78 markers. These markers could be merged into 44 genomic loci by linkage disequilibrium (r 2 > 0.2). Based on sequence alignment of the markers to the reference genome of bread wheat, we identified 14 putative candidate genes involved in enzymes, hormone-response, and transcription factors. The GWAS in durum wheat and a previous quantitative trait locus (QTL) analysis in bread wheat identified a consensus QTL locus.4B.1 conferring drought tolerance, which was further scanned for the presence of potential candidate genes. A haplotype analysis of this region revealed that two minor haplotypes were associated with both drought tolerance and reduced plant stature, thought to be the effect of linkage with the semi-dwarfing gene Rht-B1. Haplotype variants in the key chromosome 4B region were informative regarding evolutionary divergence among durum, emmer and bread wheat. Over all, the data are relevant in the context of durum wheat improvement and the isolation of genes underlying variation in some important quantitative traits.

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

The Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi-parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre-breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.

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.

QTLian breeding for climate resilience in cereals: progress and prospects

The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consumed globally. Drought, waterlogging, heat, salinity, and mineral toxicity are the key abiotic stresses drastically affecting crop yield. Conventional plant breeding approaches towards abiotic stress tolerance have gained success to limited extent, due to the complex (multigenic) nature of these stresses. Progress in breeding climate-resilient crop plants has gained momentum in the last decade, due to improved understanding of the physiochemical and molecular basis of various stresses. A good number of genes have been characterized for adaptation to various stresses. In the era of novel molecular markers, mapping of QTLs has emerged as viable solution for breeding crops tolerant to abiotic stresses. Therefore, molecular breeding-based development and deployment of high-yielding climate-resilient crop cultivars together with climate-smart agricultural practices can pave the path to enhanced crop yields for smallholder farmers in areas vulnerable to the climate change. Advances in fine mapping and expression studies integrated with cheaper prices offer new avenues for the plant breeders engaged in climate-resilient plant breeding, and thereby, hope persists to ensure food security in the era of climate change.