Improvement Of Agronomic Traits Research Articles

OsNF-YA8 promotes starch accumulation and influences seed traits by positively regulating starch biosynthesis in rice

The storage substances of rice are critical factors that simultaneously affect grain yield and quality. Starch is the major component in the endosperm, directly affecting the seed yield as well as the cooking and eating quality of grains. Growing evidence suggests that some transcription factors are involved in regulating seed traits and starch biosynthesis. Here, we reveal the role of an NF-Y transcription factor gene, OsNF-YA8, in regulation of seed traits and starch accumulation. OsNF-YA8 encodes a rice NF-YA protein containing the 166-amino acid. The RT-qPCR showed that OsNF-YA8 is expressed in roots, stems, leaves, flag leaves, and panicles, and dramatically increased in panicle during rice filling. Intracellular localization analysis showed that OsNF-YA8 is a nucleus-localized protein. In the OsNF-YA8 overexpression lines, rice grain length increased by 13.80–14.21 %, rice grain thickness decreased by 3.22–6.65 %, and the total starch content increased by 14.70–33.14 %. The overexpression of the OsNF-YA8 also decreased average starch granule size, and changed starch properties. Moreover, OsNF-YA8-overexpression up-regulated the expressions of genes involved in sucrose synthesis/transport and starch synthesis. By contrast, RNAi of OsNF-YA8 decreased the grain length, grain width, 1000 grain weight and starch content of rice seeds, and down-regulated the expressions of genes involved in sucrose synthesis/transport and starch synthesis. These results suggest that OsNF-YA8 enhances starch accumulation and confers seed traits by positively regulating starch biosynthesis in rice. The findings provide a new perspective on genetic improvement of crop agronomic traits and seed quality.

MicroRNA166: Old Players and New Insights into Crop Agronomic Traits Improvement.

MicroRNA (miRNA), a type of non-coding RNA, is crucial for controlling gene expression. Among the various miRNA families, miR166 stands out as a highly conserved group found in both model and crop plants. It plays a key role in regulating a wide range of developmental and environmental responses. In this review, we explore the diverse sequences of MIR166s in major crops and discuss the important regulatory functions of miR166 in plant growth and stress responses. Additionally, we summarize how miR166 interacts with other miRNAs and highlight the potential for enhancing agronomic traits by manipulating the expression of miR166 and its targeted HD-ZIP III genes.

A plasma membrane-localized transporter remobilizes aleurone layer magnesium for seed germination in rice.

The aleurone layer in cereal grains acts as a major reservoir of essential mineral nutrients, significantly influencing seed germination. However, the molecular mechanism underlying the redistribution of nutrients from the aleurone layer in the germinating seed is still not well understood. Here, in rice, we identified a plasma membrane (PM) localized magnesium transporter, MAGNESIUM RELEASE TRANSPORTER 3 (MGR3), is critical for seed germination. OsMGR3 is predominantly expressed in the aleurone layer cells of endosperm, facilitating magnesium remobilization during germination. Non-invasive Micro-test Technology assay data demonstrated that the loss-of-function of OsMGR3 restrained magnesium efflux from the aleurone layer. In the embryo/endosperm grafting experiment, we observed that the mutation of OsMGR3 in the aleurone layer suppressed the growth and differentiation of the embryo during germination. Furthermore, magnesium fluorescence imaging revealed the osmgr3 mutant seeds showed impaired exportation of aleurone layer-stored magnesium to the embryo, consequently delaying germination. Importantly, we discovered that disrupting OsMGR3 could inhibit pre-harvest sprouting without affecting rice yield and quality. Therefore, the magnesium efflux transporter OsMGR3 in the aleurone layer represents a promising genetic target for future agronomic trait improvement.

Multiplex-genome-editing based rapid directional improvement of complex traits in rice.

Although thousands of genes have been identified or cloned in rice (Oryza sativa) in the last two decades, the majority of them have only been separately characterized in specific varieties or single-gene modified backgrounds, thus limiting their practical application. We developed an optimized multiplex genome editing (MGE) toolbox that can efficiently assemble and stably express up to twelve sgRNA targets in a single plant expression vector. In this study, we established the MGE-based Rapid Directional Improvement (MRDI) strategy for directional improvement of complex agronomic traits in one small-scale rice transformation. This approach provides a rapid and practical procedure, encompassing sgRNA assembly, transgene-free screening and the creation of promising germplasm, by combining the precision of gene editing with phenotype-based field breeding. The MRDI strategy was used to generate the full diversity of twelve main agronomic genes in rice cultivar FXZ for the directional improvement of its growth duration and plant architecture. After applying the MRDI to FXZ, ideal plants with the desired traits of early heading date reduced plant height, and more effective panicles were generated without compromising yield, blast resistance and grain quality. Furthermore, the results of whole-genome sequencing (WGS), including the analysis of structural variations (SVs) and single nucleotide variations (SNVs) in the MGE plants, confirmed the high specificity and low frequency of unwanted mutations associated with this strategy. The MRDI breeding strategy would be a robust approach for exploring and applying crucial agronomic genes, as well as for generating novel elite germplasm in the future.

Advancements in Genetic Enhancement: CRISPR/Cas-Mediated Genome Editing in Leguminous Crops

Legumes play a crucial role in human nutrition and sustainable agriculture due to their high protein content and health-promoting phytochemicals. To accelerate genetic gain in yield, stress resilience, and nutritional quality, extensive efforts are underway. Recent advancements in genomic resources have paved the way for the application of cutting-edge breeding technologies like genomic selection and genome editing in legume crops. This review focuses on the latest advancements in CRISPR/Cas9-based gene editing technology, specifically tailored for improving traits in legume crops. While successful gene-editing methods have been established for crops like soybean, cowpea, and chickpea, challenges remain, particularly in overcoming the recalcitrance of certain legumes to gene transfer and regeneration in vitro. Strategies to enhance transformation and regeneration rates through modifications in culture methods and DNA delivery are discussed. Despite the potential benefits of gene editing in legume breeding, regulatory barriers pose significant challenges. A comparison of regulatory environments in different regions sheds light on the importance of favourable regulations and public acceptance for realizing CRISPR's potential in enhancing global food security. Additionally, leguminous crops are vital for their nutritional properties, nitrogen-fixing abilities, and contribution to sustainable agriculture. Traditional breeding methods focused on increasing yield, while recent advancements in genome editing techniques, notably CRISPR-Cas technology, have revolutionized the improvement of agronomic traits in legumes. This chapter provides insights into the application of genome editing tools for enhancing traits such as stress tolerance, yield, and seed content in grain legumes. Furthermore, it discusses the challenges and prospects associated with enhancing grain legumes using molecular breeding techniques. Genome editing has been successfully employed in diverse legumes, including model species like Medicago and widely cultivated crops such as soybean and chickpea, offering exciting opportunities for enhancing agronomic characteristics.

Enhancing genome-wide populus trait prediction through deep convolutional neural networks.

As a promising model, genome-based plant breeding has greatly promoted the improvement of agronomic traits. Traditional methods typically adopt linear regression models with clear assumptions, neither obtaining the linkage between phenotype and genotype nor providing good ideas for modification. Nonlinear models are well characterized in capturing complex nonadditive effects, filling this gap under traditional methods. Taking populus as the research object, this paper constructs a deep learning method, DCNGP, which can effectively predict the traits including 65 phenotypes. The method was trained on three datasets, and compared with other four classic models-Bayesian ridge regression (BRR), Elastic Net, support vector regression, and dualCNN. The results show that DCNGP has five typical advantages in performance: strong prediction ability on multiple experimental datasets; the incorporation of batch normalization layers and Early-Stopping technology enhancing the generalization capabilities and prediction stability on test data; learning potent features from the data and thus circumventing the tedious steps of manual production; the introduction of a Gaussian Noise layer enhancing predictive capabilities in the case of inherent uncertainties or perturbations; fewer hyperparameters aiding to reduce tuning time across datasets and improve auto-search efficiency. In this way, DCNGP shows powerful predictive ability from genotype to phenotype, which provide an important theoretical reference for building more robust populus breeding programs.

Insights into Wheat Genotype‒Sphaerodes mycoparasitica Interaction to Improve Crop Yield and Defence against Fusarium graminearum: An Integration of FHB Biocontrol in Canadian Wheat Breeding Programmes.

Fusarium head blight (FHB) is a major threat to wheat crop production and food security worldwide. The creation of resistant wheat cultivars is an essential component of an integrated strategy against Fusarium graminearum, the primary aetiological agent that causes FHB. The results of this study show that the deployment of proto-cooperative interactions between wheat genotypes and mycoparasitic biocontrol agents (BCAs) can improve crop yield and plant resistance in controlling the devastating effects of FHB on wheat agronomic traits. A Fusarium-specific mycoparasite, Sphaerodes mycoparasitica, was found to be compatible with common and durum wheat hosts, thus allowing the efficient control of F. graminearum infection in plants. Four genotypes of wheat, two common wheat, and two durum wheat cultivars with varying FHB resistance levels were used in this greenhouse study. The BCA treatments decreased FHB symptoms in all four cultivars and improved the agronomic traits such as spike number, spike weight, seed weight, plant biomass, and plant height which are vital to grain yield. Conversely, the F. graminearum 3ADON chemotype treatment decreased the agronomic trait values by up to 44% across cultivars. Spike number, spike weight, and seed weight were the most improved traits by the BCA. A more measurable improvement in agronomic traits was observed in durum wheat cultivars compared to common wheat.

S-ABA Enhances Rice Salt Tolerance by Regulating Na+/K+ Balance and Hormone Homeostasis.

In order to explore the regulating role and the physiological and biochemical mechanisms of trans-abscisic acid (hereinafter referred as S-ABA) in the process of rice growth and development under salt stress, we took Chaoyou 1000 and Yuxiangyouzhan as materials and set up three salt concentration treatments, CK0 (Control treatment), N1 (50 mmol L-1 NaCl), and N2 (100 mmol L-1 NaCl), in potted trials; we aimed to study the mechanism of rice's response to salt stress from the perspective of agricultural traits and physiological biochemicals and to improve rice's resistance to salt stress through exogenously applying the regulating technology of S-ABA. The following results were obtained: Under salt stress, the growth of rice was significantly suppressed compared to CK0, exhibiting notable increases in agricultural indicators, photosynthesis efficiency, and the NA+ content of leaves. However, we noted a significant decrease in the K+ content in the leaves, alongside a prominent increase in NA+/K+ and a big increase in MDA (malondialdehyde), H2O2 (hydrogen peroxide), and O2- (superoxide anion). This caused the cytomembrane permeability to deteriorate. By applying S-ABA under salt stress (in comparison with salt treatment), we promoted improvements in agronomic traits, enhanced photosynthesis, reduced the accumulation of NA+ in leaves, increased the K+ content and the activity of antioxidant enzymes, and reduced the active oxygen content, resulting in a sharp decrease in the impact of salt stress on rice's development. The application of S-ABA decreased the endogenous ABA (abscisic acid) content under salt stress treatment but increased the endogenous GA (gibberellin) and IAA (indole acetic acid) contents and maintained the hormonal homeostasis in rice plants. To summarize, salt stress causes damage to rice growth, and the exogenous application of S-ABA can activate the pouring system mechanism of rice, suppress the outbreak of active oxygen, and regulate NA+/K+ balance and hormone homeostasis in the blades, thus relieving the salt stress.

Genetic gains in early maturing maize hybrids developed by the International Maize and Wheat Improvement Center in Southern Africa during 2000-2018.

Genetic gain estimation in a breeding program provides an opportunity to monitor breeding efficiency and genetic progress over a specific period. The present study was conducted to (i) assess the genetic gains in grain yield of the early maturing maize hybrids developed by the International Maize and Wheat Improvement Center (CIMMYT) Southern African breeding program during the period 2000-2018 and (ii) identify key agronomic traits contributing to the yield gains under various management conditions. Seventy-two early maturing hybrids developed by CIMMYT and three commercial checks were assessed under stress and non-stress conditions across 68 environments in seven eastern and southern African countries through the regional on-station trials. Genetic gain was estimated as the slope of the regression of grain yield and other traits against the year of first testing of the hybrid in the regional trial. The results showed highly significant (p< 0.01) annual grain yield gains of 118, 63, 46, and 61 kg ha-1 year-1 under optimum, low N, managed drought, and random stress conditions, respectively. The gains in grain yield realized in this study under both stress and non-stress conditions were associated with improvements in certain agronomic traits and resistance to major maize diseases. The findings of this study clearly demonstrate the significant progress made in developing productive and multiple stress-tolerant maize hybrids together with other desirable agronomic attributes in CIMMYT's hybrid breeding program.

Epigenetics and the improvement of crop plants

Epigenetics is a term that refers to the changes in gene expression that are heritable and induced by DNA methylation, histones post-translational modifications, or sncRNA, not resulting from the DNA sequence rearrangements. Epigenetic modifications influence gene expression, and thus, the plasticity of plants' development and phenotype in response to external and internal factors. Until recently, the only known epigenetic modification of the DNA in eukaryotic organisms was 5-methylcytosine. The growing interest in epigenetics and the development of sensitive detection methods enabled the discovery of other modifications of the DNA nitrogenous bases, i.e., 4-methylcytosine and 6-methyladenine. However, whilst research on the 5mC distribution and role in eukaryotic organisms is widespread, analyses regarding 6mA are scarced. Nevertheless, there are indications of a potential epigenetic role of 6-methyladenine in eukaryotic genomes. Understanding epigenetic mechanisms, which are triggered in response to environmental changes, is crucial for agriculture. This review shows epigenetic mechanisms, with particular emphasis on adenine methylation in plants, as well as the role of epigenetic variation in epibreeding, affecting the improvement of agronomic traits.

Genome-Wide Identification and Expression Analyses of the FAR1/FHY3 Gene Family Provide Insight into Inflorescence Development in Maize.

As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding.

Diversity of transgene integration and gene-editing events in wheat (Triticum aestivum L.) transgenic plants generated using Agrobacterium-mediated transformation.

Improvement in agronomic traits in crops through gene editing (GE) relies on efficient transformation protocols for delivering the CRISPR/Cas9-coded transgenes. Recently, a few embryogenesis-related genes have been described, the co-delivery of which significantly increases the transformation efficiency with reduced genotype-dependency. Here, we characterized the transgenic and GE events in wheat (cv. Fielder) when transformed with GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) chimeric gene. Transformation efficiency in our experiments ranged from 22% to 68%, and the editing events were faithfully propagated into the following generation. Both low- and high-copy-number integration events were recovered in the T0 population with various levels of integrity of the left and right T-DNA borders. We also generated a population of wheat plants with 10 different gRNAs targeting 30 loci in the genome. A comparison of the epigenetic profiles at the target sites and editing efficiency revealed a significant positive correlation between chromatin accessibility and mutagenesis rate. Overall, the preliminary screening of transgene quality and GE events in the T0 population of plants regenerated through the co-delivery of GRF-GIF can allow for the propagation of the best candidates for further phenotypic analysis.

Toward breeding pigmented rice balancing nutrition and yield

A recent study by Sedeek et al. provides multiomic resources that illustrate the genetic diversity, metabolites, elemental composition, and the possibility of agronomic trait improvement, through genome-editing technology, for nutrient-rich pigmented rice. This will guide future rice breeding programs for balancing optimal agronomic traits and excellent nutritional quality.

Establishment of targeted mutagenesis in soybean protoplasts using CRISPR/Cas9 RNP delivery via electro-transfection.

The soybean (Glycine max L.) is an important crop with high agronomic value. The improvement of agronomic traits through gene editing techniques has broad application prospects in soybean. The polyethylene glycol (PEG)-mediated cell transfection has been successfully used to deliver the CRISPR/Cas9-based ribonucleoprotein (RNP) into soybean protoplasts. However, several downstream analyses or further cell regeneration protocols might be hampered by PEG contamination within the samples. Here in this study, we attempted to transfect CRISPR/Cas9 RNPs into trifoliate leaf-derived soybean protoplasts using Neon electroporation to overcome the need for PEG transfection for the first time. We investigated different electroporation parameters including pulsing voltage (V), strength and duration of pulses regarding protoplast morphology, viability, and delivery of CRISPR/Cas9. Electroporation at various pulsing voltages with 3 pulses and 10 ms per pulse was found optimal for protoplast electro-transfection. Following electro-transfection at various pulsing voltages (500V, 700V, 1,000 V, and 1,300 V), intact protoplasts were observed at all treatments. However, the relative frequency of cell viability and initial cell divisions decreased with increasing voltages. Confocal laser scanning microscopy (CLSM) confirmed that the green fluorescent protein (GFP)-tagged Cas9 was successfully internalized into the protoplasts. Targeted deep sequencing results revealed that on-target insertion/deletion (InDel) frequencies were increased with increasing voltages in protoplasts electro-transfected with CRISPR/Cas9 RNPs targeting constitutive pathogen response 5 (CPR5). InDel patterns ranged from +1 bp to -6 bp at three different target sites in CPR5 locus with frequencies ranging from 3.8% to 8.1% following electro-transfection at 1,300 V and 2.1% to 3.8% for 700V and 1,000 V, respectively. Taken together, our results demonstrate that the CRISPR/Cas9 RNP system can be delivered into soybean protoplasts by the Neon electroporation system for efficient and effective gene editing. The electro-transfection system developed in this study would also further facilitate and serve as an alternative delivery method for DNA-free genome editing of soybean and other related species for genetic screens and potential trait improvement.

Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines

Due to the relatively brief domestication history of sugar beet (Beta vulgaris ssp. vulgaris), our understanding of the genomic diversity and functional genes in its cultivars is limited, resulting in slow breeding progress. To address this issue, a total of 306 germplasm materials of major cultivars and breeding lines from China, the USA, and Europe were selected for genome resequencing. We investigated population structure and genetic diversity and performed selective scanning of genomic regions, identifying six novel genes associated with important agronomic traits: the candidate genes DFAX2 and P5CS for skin roughness; the candidate genes FRO5, GL24, and PPR91 for root yield and sugar yield, and the pleiotropic candidate gene POLX for flourishing growth vigour, plant height, crown size, flesh coarseness, and sugar yield. In addition, we constructed a protein–protein interaction network map and a phenotype-gene network map, which provide valuable information for identifying and characterizing functional genes affecting agronomic traits in sugar beet. Overall, our study sheds light on the future improvement of sugar beet agronomic traits at the molecular level.

Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years

Key messageSelection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp of chomosome 5H in European two-rowed spring barleys, possibly originating from North Africa.Plant breeding and selection have shaped the genetic composition of modern crops over the past decades and centuries and have led to great improvements in agronomic and quality traits. Knowledge of the genetic composition of breeding germplasm is essential to make informed decisions in breeding programs. In this study, we characterized the structure and composition of 209 barley cultivars representative of the European two-rowed spring barley germplasm of the past 190 years. Utilizing high-density SNP marker data, we identified a distinct centromeric haplotype spanning a ~ 250 Mbp large region on chromosome 5H which likely was first introduced into the European breeding germplasm in the early to mid-twentieth century and has been non-recombining and under strong positive selection over the past 70 years. Almost all cultivars in our panel that were released after 2000 carry this new haplotype, suggesting that this region carries one or several genes conferring highly beneficial traits. Using the global barley collection of the German Federal ex situ gene bank at IPK Gatersleben, we found the new haplotype at high frequencies in six-rowed spring-type landraces from Northern Africa, from which it may have been introduced into modern European barley germplasm via southern European landraces. The presence of a 250 Mbp genomic region characterized by lack of recombination and high levels of fixation in modern barley germplasm has substantial implications for the genetic diversity of the modern barley germplasm and for barley breeding.

Gene expression and expression quantitative trait locianalyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding.

Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.

Utilizing Genetic Resources for Agronomic Trait Improvement

Genetic resources hold the key to adapting crops to a changing climate; they are a source of many new alleles that can be used in plant breeding to improve already-existing cultivars [...]

An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges.

Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.

Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.).

Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.