AB-QTL analysis reveals new alleles associated to proline accumulation and leaf wilting under drought stress conditions in barley (Hordeum vulgare L.)

Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population

Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.

Common Bean (Phaseolus vulgaris L.) NAC Transcriptional Factor PvNAC52 Enhances Transgenic Arabidopsis Resistance to Salt, Alkali, Osmotic, and ABA Stress by Upregulating Stress-Responsive Genes

The NAC family of transcription factors includes no apical meristem (NAM), Arabidopsis thaliana transcription activator 1/2 (ATAF1/2), and cup-shaped cotyledon (CUC2) proteins, which are unique to plants, contributing significantly to their adaptation to environmental challenges. In the present study, we observed that the PvNAC52 protein is predominantly expressed in the cell membrane, cytoplasm, and nucleus. Overexpression of PvNAC52 in Arabidopsis strengthened plant resilience to salt, alkali, osmotic, and ABA stresses. PvNAC52 significantly (p < 0.05) reduced the degree of oxidative damage to cell membranes, proline content, and plant water loss by increasing the expression of MSD1, FSD1, CSD1, POD, PRX69, CAT, and P5CS2. Moreover, the expression of genes associated with abiotic stress responses, such as SOS1, P5S1, RD29A, NCED3, ABIs, LEAs, and DREBs, was enhanced by PvNAC52 overexpression. A yeast one-hybrid assay showed that PvNAC52 specifically binds to the cis-acting elements ABRE (abscisic acid-responsive elements, ACGTG) within the promoter. This further suggests that PvNAC52 is responsible for the transcriptional modulation of abiotic stress response genes by identifying the core sequence, ACGTG. These findings provide a theoretical foundation for the further analysis of the targeted cis-acting elements and genes downstream of PvNAC52 in the common bean.

Analyzing the Diversity of MYB Family Response Strategies to Drought Stress in Different Flax Varieties Based on Transcriptome Data

The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.

New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health

As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.

Identifying developmental QTL alleles with favorable effect on grain yield components under late-terminal drought in spring barley MAGIC population

Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield-related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above-ground yield-related traits under well-watered (WW) and late-terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene Ppd-H1 with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late-terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene HvSUT2. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.

Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley

INTRODUCTION

Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance.

OBJECTIVES

To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley.

METHODS

Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes.

RESULTS

Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley.

CONCLUSION

Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.

Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement

Developing a new rice variety requires tremendous efforts and years of input. To improve the defect traits of the excellent varieties becomes more cost and time efficient than breeding a completely new variety. Kongyu 131 is a high-performing japonica variety with early maturity, high yield, wide adaptability and cold resistance, but the poor-lodging resistance hinders the industrial production of Kongyu 131 in the Northeastern China. In this study, we attempted to improve the lodging resistance of Kongyu 131 from perspectives of both gene and trait. On the one hand, by QTL analysis and fine mapping we discovered the candidate gene loci. The following CRISPR/Cas9 and transgenic complementation study confirmed that Sd1 dominated the lodging resistance and favourable allele was mined for precise introduction and improvement. On the other hand, the Sd1 allelic variant was identified in Kongyu 131 by sequence alignment, then introduced another excellent allelic variation by backcrossing. Then, the two new resulting Kongyu 131 went through the field evaluation under different environments, planting densities and nitrogen fertilizer conditions. The results showed that the plant height of upgraded Kongyu 131 was 17%-26% lower than Kongyu 131 without penalty in yield. This study demonstrated a precise and targeted way to update the rice genome and upgrade the elite rice varieties by improving only a few gene defects from the perspective of breeding.

Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses

Abiotic stresses cause a significant decrease in productivity and growth in agricultural products, especially barley. Breeding has been considered to create resistance against abiotic stresses. Pyramiding genes for tolerance to abiotic stresses through selection based on molecular markers connected to Mega MQTLs of abiotic tolerance can be one of the ways to reach Golden Barley. In this study, 1162 original QTLs controlling 116 traits tolerant to abiotic stresses were gathered from previous research and mapped from various populations. A consensus genetic map was made, including AFLP, SSR, RFLP, RAPD, SAP, DArT, EST, CAPS, STS, RGA, IFLP, and SNP markers based on two genetic linkage maps and 26 individual linkage maps. Individual genetic maps were created by integrating individual QTL studies into the pre-consensus map. The consensus map covered a total length of 2124.43 cM with an average distance of 0.25 cM between markers. In this study, 585 QTLs and 191 effective genes related to tolerance to abiotic stresses were identified in MQTLs. The most overlapping QTLs related to tolerance to abiotic stresses were observed in MQTL6.3. Furthermore, three MegaMQTL were identified, which explained more than 30% of the phenotypic variation. MQTLs, candidate genes, and linked molecular markers identified are essential in barley breeding and breeding programs to develop produce cultivars resistant to abiotic stresses.

Genetic and morpho-physiological analyses of the tolerance and recovery mechanisms in seedling stage spring wheat under drought stress

Drought is one of the complex abiotic stresses that affect the growth and production of wheat in arid and semiarid countries. In this study, a set of 172 diverse spring wheat genotypes from 20 different countries were assessed under drought stress at the seedling stage. Besides seedling length, two types of traits were recorded, namely: tolerance traits (days to wilting, leaf wilting, and the sum of leaf wilting), and recovery traits (days to regrowth, regrowth biomass, and drought survival rate). In addition, tolerance index, recovery index, and drought tolerance index (DTI) were estimated to select the most drought tolerant genotypes. Moreover, leaf protein content (P), amino acid (AM), proline content (PRO), glucose (G), fructose (F), and total soluble carbohydrates (TSC) were measured under control and drought conditions to study the changes in each physiological trait due to drought stress. All genotypes showed a high significant genetic variation in all the physio-morphological traits scored under drought stress. High phenotypic and genotypic correlations were found among all seedling morphological traits. Among the studied indices, the drought tolerance index (DTI) had the highest phenotypic and genotypic correlations with all tolerance and recovery traits. The broad-sense heritability (H²) estimates were high for morphological traits (83.85–92.27), while the physiological traits ranged from 96.41 to 98.68 under the control conditions and from 97.13 to 99.99 under drought stress. The averages of the physiological traits (proteins, amino acids, proline, glucose, fructose, and total soluble carbohydrates) denoted under drought stress were higher than those recorded under well-watered conditions except for proteins. In this regard, amino acids, glucose, and total soluble carbohydrates had a significant correlation with all morphological traits. The selection for drought tolerance revealed 10 tolerant genotypes from different countries (8 genotypes from Egypt, one from Morocco, and one from the United States). These selected genotypes were screened for the presence of nine specific TaDREB1 alleles. Six primers were polymorphic among the selected genotypes. Genetic diversity among the selected genotypes was investigated using 21,450 SNP markers. The results of the study shed light on the different mechanisms for drought tolerance that wheat plants use to tolerate and survive under drought stress. The genetic analysis performed in this study suggested the most suitable genotypes for selective breeding at the seedling stage under water deficit.

QTLs Controlling Physiological and Morphological Traits of Barley (Hordeum vulgare L.) Seedlings under Salinity, Drought, and Normal Conditions

To identify the genomic regions for the physiological and morphological traits of barley genotypes under normal salinity and drought, a set of 103 recombinant inbred line (RIL) populations, developed between Badia and Kavir crosses, was evaluated under phytotron conditions in a completely randomized design in 2019. Linkage maps were prepared using 152 SSR markers, 72 ISSR, 7 IRAP, 29 CAAT, 27 SCoT, and 15 iPBS alleles. The markers were assigned to seven barley chromosomes and covered 999.29 centimorgans (cM) of the barley genome. In addition, composite interval mapping showed 8, 9, and 26 quantitative trait loci (QTLs) under normal, drought, and salinity stress conditions, respectively. Our results indicate the importance of chromosomes 1, 4, 5, and 7 in salinity stress. These regions were involved in genes controlling stomata length (LR), leaf number (LN), leaf weight (LW), and genetic score (SCR). Three major stable pleiotropic QTLs (i.e., qSCS-1, qRLS-1, and qLNN-1) were associated with SCR, root length (RL), and root number (RN) in both treatments (i.e., normal and salinity), and two major stable pleiotropic QTLs (i.e., qSNN-3 and qLWS-3) associated with the stomata number (SN) and LW appeared to be promising for marker-assisted selection (MAS). Two major-effect QTLs (i.e., SCot8-B-CAAT5-D and HVM54-Bmag0571) on chromosomes 1 and 2 were characterized for their positive allele effect, which can be used to develop barley varieties concerning drought conditions. The new alleles (i.e., qLWS-4a, qSLS-4, qLNS-7b, qSCS-7, and qLNS-7a) identified in this study are useful in pyramiding elite alleles for molecular breeding and marker assisted selection for improving salinity tolerance in barley.

Contrasting Water Withholding Responses of Young Maize Plants Reveal Link Between Lipid Peroxidation and Osmotic Regulation Corroborated by Genetic Analysis

Linking biochemistry and genetics of tolerance to osmotic stress is of interest for understanding plant adaptations to unfavorable conditions. The aims of this study were to investigate the variability in responses of panel of elite maize inbred lines to water withholding for stress-related traits through association study and to identify pathways linked to detected associations for better understanding of maize stress responses. Densely genotyped public and expired Plant Variety Protection Certificate (ex-PVP) inbred lines were planted in controlled conditions (16-h/8-h day/night, 25°C, 50% RH) in control (CO) and exposed to 10-day water withholding (WW). Traits analyzed were guaiacol peroxidase activity (GPOD), total protein content (PROT), lipid peroxidation (TBARS), hydrogen peroxide accumulation (H₂O₂), proline accumulation (proline), and current water content (CWC). Proline accumulation was found to be influenced by H₂O₂ and TBARS signaling pathways acting as an accumulation-switching mechanism. Most of the associations detected were for proline (29.4%) and TBARS (44.1%). Gene ontology (GO) enrichment analysis showed significant enrichment in regulation of integral membrane parts and peroxisomes along with regulation of transcription and polysaccharide catabolism. Dynamic studies involving inbreds with extreme phenotypes are needed to elucidate the role of this signaling mechanism in regulation of response to water deficit.

Detection and Verification of QTL for Salinity Tolerance at Germination and Seedling Stages Using Wild Barley Introgression Lines

Salinity is one of the major environmental factors that negatively affect crop development, particularly at the early growth stage of a plant and consequently the final yield. Therefore, a set of 50 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) was used to detect QTL alleles improving germination and seedling growth under control, 75 mM, and 150 mM NaCl conditions. Large variation was observed for germination and seedling growth related traits that were highly heritable under salinity stress. In addition, highly significant differences were obtained for five salinity tolerance indices and between treatments as well. A total of 90 and 35 significant QTL were identified for ten investigated traits and for tolerance indices, respectively. The Hsp introgression alleles are involved in improving salinity tolerance at forty (43.9%) out of 90 QTL including introgression lines S42IL-109 (2H), S42IL-116 (4H), S42IL-132 (6H), S42IL-133 (7H), S42IL-148 (6H), and S42IL-176 (5H). Interestingly, seven exotic QTL alleles were successfully validated in the wild barley ILs including S42IL-127 (5H), 139 (7H), 125 (5H), 117 (4H), 118 (4H), 121 (4H), and 137 (7H). We conclude that the barley introgression lines contain numerous germination and seedling growth-improving novel QTL alleles, which are effective under salinity conditions.

Association analysis, genetic diversity and population structure of barley (Hordeum vulgare L.) under heat stress conditions using SSR and ISSR markers linked to primary and secondary metabolites

BACKGROUND

Barley is one of the major cereal crops, which can provide a significant source of genes for stress tolerance due to its high diversity and adaptability. Metabolite traits are considered to be significant for adaptation of barley to heat stress.

METHODS AND RESULTS

In the present study, genetic relationships between 120 barley genotypes were determined with 50 simple sequence repeat (SSR) and 26 inter simple sequence repeat (ISSR) markers under heat stress and non-stress conditions. Moreover, genetic diversity of barley accessions was investigated using the studied markers covering 7 chromosomes of barley.

RESULTS

In general, 153 and 85 polymorphic alleles were detected for SSR and ISSR and number of the observed polymorphic allele varied between 2-9 and 2-6, with an average of 3.26 and 3.26 alleles per locus, respectively. Markers of Bmag0223, GBMS180/180, HVM7, ISSR22, ISSR25, and ISSR48 were the most informative due to their high polymorphism information content value demonstrating that putative techniques utilized in this research can be powerful and valuable tools in breeding program of barley. Association analysis was performed between 9 important traits and SSR and ISSR markers using four statistical models. The results revealed that the model containing both population structure (Q) and general similarity in genetic background arising from shared kinship (K) factors reduced false positive associations between markers and phenotypes.

CONCLUSIONS

According to the results, some of markers related to more than one trait under normal conditions (ISSR31-2, HVM62, and GBMS180/180) and heat stress conditions (ISSR20-5, EBmac635, HVM14, and ISSR37-3) were determined, which can be considered to be the most interesting candidates for further studies and simultaneously will provide a useful target for the future breeding programs, such as marker-assisted selection (MAS).

Association analysis of physiological traits in spring barley (Hordeum vulgare L.) under water-deficit conditions

In the present study, 148 commercial barley cultivars were assessed by 14 AFLP primer combinations and 32 SSRs primer pairs. Population structure, linkage disequilibrium, and genomic regions associated with physiological traits under drought stress were investigated. The phenotypic results showed a high level of diversity between studied cultivars. The studied barley cultivars were divided into two subgroups. Linkage disequilibrium analysis revealed that r 2 values among all possible marker pairs have an average value of 0.0178. The mixed linear model procedure showed that totally, 207 loci had a significant association with investigated traits. 120 QTLs out of 207 were detected for traits under normal conditions, and 90 QTLs were detected for traits under drought stress conditions. Identified QTLs after validation and transferring to SCAR markers in the case of AFLPs can be used to develop MAS strategies for barley breeding programs. Some common markers were identified for a particular trait or some traits across normal and drought stress conditions. These markers show low interaction with environmental conditions (stable markers); therefore, selection by them for a trait under normal conditions will improve the trait value under stress conditions, too.

A Wild Allele of Pyrroline-5-Carboxylate Synthase1 Leads to Proline Accumulation in Spikes and Leaves of Barley Contributing to Improved Performance Under Reduced Water Availability

Water stress (WS) during spike development strongly affects final grain yield and grain quality in cereals. Proline, an osmoprotectant amino-acid, may contribute to alleviating the effects of cell and tissue dehydration. We studied five spring barley genotypes contrasting in their drought response, including two introgression lines, S42IL-143 and S42IL-141, harboring a Pyrroline-5-carboxylate synthase1- P5cs1 allele originating from the wild barley accession ISR42-8. We tested the hypothesis that barley genotypes harboring a wild allele at P5cs1 locus are comparatively more drought-tolerant at the reproductive stage by inducing proline accumulation in their immature spikes. At the booting stage, we subjected plants to well-watered and WS treatments until physiological maturity. Several morpho-physiological traits had significant genotype by treatment interaction and reduction under WS. Varying levels of genotypic proline accumulation and differences in WS tolerance were observed. Spike proline accumulation was higher than leaf proline accumulation for all genotypes under WS. Also, introgression lines carrying a wild allele at P5cs1 locus had a markedly higher spike and leaf proline content compared with the other genotypes. These introgression lines showed milder drought symptoms compared with elite genotypes, remained photosynthetically active under WS, and maintained their intrinsic water use efficiency. These combined responses contributed to the achievement of higher final seed productivity. Magnetic resonance imaging (MRI) of whole spikes at the soft dough stage showed an increase in seed abortion among the elite genotypes compared with the introgression lines 15 days after WS treatment. Our results suggest that proline accumulation at the reproductive stage contributes to the maintenance of grain formation under water shortage.

Detailed Genetic Analysis for Identifying QTLs Associated with Drought Tolerance at Seed Germination and Seedling Stages in Barley

Drought induces several challenges for plant development, growth, and production. These challenges become more severe, in particular, in arid and semiarid countries like Egypt. In terms of production, barley ranks fourth after wheat, maize, and rice. Seed germination and seedling stages are critical stages for plant establishment and growth. In the current study, 60 diverse barley genotypes were tested for drought tolerance using two different treatments: control (0-PEG) and drought (20%-PEG). Twenty-two traits were estimated for seed germination and seedling parameters. All traits were reduced under drought stress, and a significant variation was found among genotypes under control and stress conditions. The broad-sense heritability estimates were very high under both control and drought for all traits. It ranged from 0.63 to 0.97 under the control condition and from 0.89 to 0.97 under drought, respectively. These high heritabilities suggested that genetic improvement of drought tolerance in barley at both stages is feasible. The principal component analysis revealed that root-related parameters account for the largest portion of phenotypic variation in this collection. The single-marker analysis (SMA) resulted in 71 quantitative trait loci (QTLs) distributed across the seven chromosomes of barley. Thirty-three QTLs were detected for root-length-related traits. Many hotspots of QTLs were detected for various traits. Interestingly, some markers controlled many traits in a pleiotropic manner; thus, they can be used to control multiple traits at a time. Some QTLs were constitutive, i.e., they are mapped under control and drought, and targeting these QTLs makes the selection for drought tolerance a single-step process. The results of gene annotation analysis revealed very potential candidate genes that can be targeted to select for drought tolerance.

Closing the Phenotyping Gap: High Resolution UAV Time Series for Soybean Growth Analysis Provides Objective Data from Field Trials

Close remote sensing approaches can be used for high throughput on-field phenotyping in the context of plant breeding and biological research. Data on canopy cover (CC) and canopy height (CH) and their temporal changes throughout the growing season can yield information about crop growth and performance. In the present study, sigmoid models were fitted to multi-temporal CC and CH data obtained using RGB imagery captured with a drone for a broad set of soybean genotypes. The Gompertz and Beta functions were used to fit CC and CH data, respectively. Overall, 90.4% fits for CC and 99.4% fits for CH reached an adjusted R2 > 0.70, demonstrating good performance of the models chosen. Using these growth curves, parameters including maximum absolute growth rate, early vigor, maximum height, and senescence were calculated for a collection of soybean genotypes. This information was also used to estimate seed yield and maturity (R8 stage) (adjusted R2 = 0.51 and 0.82). Combinations of parameter values were tested to identify genotypes with interesting traits. An integrative approach of fitting a curve to a multi-temporal dataset resulted in biologically interpretable parameters that were informative for relevant traits.

Regulation of L-proline biosynthesis, signal transduction, transport, accumulation and its vital role in plants during variable environmental conditions

Background

In response to various environmental stresses, many plant species synthesize L-proline in the cytosol and accumulates in the chloroplasts. L-Proline accumulation in plants is a well-recognized physiological reaction to osmotic stress prompted by salinity, drought and other abiotic stresses. L-Proline plays several protective functions such as osmoprotectant, stabilizing cellular structures, enzymes, and scavenging reactive oxygen species (ROS), and keeps up redox balance in adverse situations. In addition, ample-studied osmoprotective capacity, L-proline has been also ensnared in the regulation of plant improvement, including flowering, pollen, embryo, and leaf enlargement.

Scope and conclusions

Albeit, ample is now well-known about L-proline metabolism, but certain characteristics of its biological roles are still indistinct. In the present review, we discuss the L-proline accumulation, metabolism, signaling, transport and regulation in the plants. We also discuss the effects of exogenous L-proline during different environmental conditions. L-Proline biosynthesis and catabolism are controlled by several cellular mechanisms, of which we identify only very fewer mechanisms. So, in the future, there is a requirement to identify such types of cellular mechanisms.

Novel Maize NAC Transcriptional Repressor ZmNAC071 Confers Enhanced Sensitivity to ABA and Osmotic Stress by Downregulating Stress-Responsive Genes in Transgenic Arabidopsis

NAC TFs play crucial roles in response to abiotic stresses in plants. Here, ZmNAC071 was identified as a nuclear located transcriptional repressor. Overexpression of ZmNAC071 in Arabidopsis enhanced sensitivity of transgenic plants to ABA and osmotic stress. The expression levels of SODs, PODs, P5CSs, and AtMYB61 were inhibited by ZmNAC071, which results in reduced ROS scavenging and proline content, increased ROS level, and water loss. Besides, the expression levels of some ABA or abiotic stress-related genes, like ABIs, RD29A, DREBs, and LEAs were also significantly inhibited by ZmNAC071. Yeast one-hybrid assay demonstrated that ZmNAC071 specifically bound to the cis-acting elements containing CGT[G/A] core sequences in the promoter of stress-related genes, suggesting that ZmNAC071 may participate in the regulation of transcription of these genes through recognizing the core sequences CGT[G/A]. These results will facilitate further studies concerning the cis-elements and downstream genes targeted by ZmNAC071 in maize.

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.

Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.)

Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits.

The LmSAP gene isolated from the halotolerant Lobularia maritima improves salt and ionic tolerance in transgenic tobacco lines

The A20/AN1 zinc-finger domain-containing proteins of the stress-associated proteins (SAPs) family are fast emerging as potential candidates for biotechnological approaches to improve abiotic stress tolerance in plants. We identified LmSAP, one of the SAPs genes in Lobularia maritima (L.) Desv., a halophyte brassicaceae, through its transcript accumulation in response to salinity and ionic stresses. Sequence homology analysis revealed that LmSAP contains two conserved zinc-finger domains A20 and AN1. Phylogeny analyses showed that LmSAP exhibited high amino acid sequence identity to other plant SAPs. Heterologous expression of LmSAP in yeast increased cell tolerance to salt and osmotic stress. In addition, the overexpression of LmSAP conferred high salt and ionic tolerance to transgenic tobacco plants. Transgenic tobacco seedlings showed higher survival rates and antioxidant activities under salt and ionic stresses. Enhanced antioxidant activities paralleled lower malondialdehyde and superoxide anion O2- levels in the LmSAP transgenic seedlings. Overall, our results suggest that overexpression of LmSAP enhanced salt tolerance by maintaining ionic balance and limiting oxidative and osmotic stresses.

Updating the elite rice variety Kongyu 131 by improving the Gn1a locus

BACKGROUND

Kongyu 131 is an elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability. However, there is potential to improve the yield of Kongyu 131 because of the relatively few grains per panicle compared with other varieties. Hence, we rebuilt the genome of Kongyu 131 by replacing the GRAIN NUMBER1a (Gn1a) locus with a high-yielding allele from a big panicle indica rice variety, GKBR. High-resolution melting (HRM) analysis was used for single nucleotide polymorphism (SNP) genotyping.

RESULTS

Quantitative trait locus (QTL) analysis of the BC₃F₂ population showed that the introgressed segment carrying the Gn1a allele of GKBR significantly increased the branch number and grain number per panicle. Using 5 SNP markers designed against the sequence within and around Gn1a, the introgressed chromosome segment was shortened to approximately 430 Kb to minimize the linkage drag by screening recombinants in the target region. Genomic components of the new Kongyu 131 were detected using 220 SNP markers evenly distributed across 12 chromosomes, suggesting that the recovery ratio of the recurrent parent genome (RRPG) was 99.89%. Compared with Kongyu 131, the yield per plant of the new Kongyu 131 increased by 8.3% and 11.9% at Changchun and Jiamusi, respectively.

CONCLUSIONS

To achieve the high yield potential of Kongyu 131, a minute chromosome fragment carrying the favorable Gn1a allele from the donor parent was introgressed into the genome of Kongyu 131, which resulted in a larger panicle and subsequent yield increase in the new Kongyu 131. These results indicate the feasibility of improving an undesirable trait of an elite variety by replacing only a small chromosome segment carrying a favorable allele.

QTL controlling grain filling under terminal drought stress in a set of wild barley introgression lines

Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.

Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.

Unmanned Aerial Vehicle Remote Sensing for Field-Based Crop Phenotyping: Current Status and Perspectives

Phenotyping plays an important role in crop science research; the accurate and rapid acquisition of phenotypic information of plants or cells in different environments is helpful for exploring the inheritance and expression patterns of the genome to determine the association of genomic and phenotypic information to increase the crop yield. Traditional methods for acquiring crop traits, such as plant height, leaf color, leaf area index (LAI), chlorophyll content, biomass and yield, rely on manual sampling, which is time-consuming and laborious. Unmanned aerial vehicle remote sensing platforms (UAV-RSPs) equipped with different sensors have recently become an important approach for fast and non-destructive high throughput phenotyping and have the advantage of flexible and convenient operation, on-demand access to data and high spatial resolution. UAV-RSPs are a powerful tool for studying phenomics and genomics. As the methods and applications for field phenotyping using UAVs to users who willing to derive phenotypic parameters from large fields and tests with the minimum effort on field work and getting highly reliable results are necessary, the current status and perspectives on the topic of UAV-RSPs for field-based phenotyping were reviewed based on the literature survey of crop phenotyping using UAV-RSPs in the Web of Science™ Core Collection database and cases study by NERCITA. The reference for the selection of UAV platforms and remote sensing sensors, the commonly adopted methods and typical applications for analyzing phenotypic traits by UAV-RSPs, and the challenge for crop phenotyping by UAV-RSPs were considered. The review can provide theoretical and technical support to promote the applications of UAV-RSPs for crop phenotyping.

Metabolite profiling of barley flag leaves under drought and combined heat and drought stress reveals metabolic QTLs for metabolites associated with antioxidant defense

Barley (Hordeum vulgare L.) is among the most stress-tolerant crops; however, not much is known about the genetic and environmental control of metabolic adaptation of barley to abiotic stresses. We have subjected a genetically diverse set of 81 barley accessions, consisting of Mediterranean landrace genotypes and German elite breeding lines, to drought and combined heat and drought stress at anthesis. Our aim was to (i) investigate potential differences in morphological, physiological, and metabolic adaptation to the two stress scenarios between the Mediterranean and German barley genotypes and (ii) identify metabolic quantitative trait loci (mQTLs). To this end, we have genotyped the investigated barley lines with an Illumina iSelect 9K array and analyzed a set of 57 metabolites from the primary C and N as well as antioxidant metabolism in flag leaves under control and stress conditions. We found that drought-adapted genotypes attenuate leaf carbon metabolism much more strongly than elite lines during drought stress adaptation. Furthermore, we identified mQTLs for flag leaf γ-tocopherol, glutathione, and succinate content by association genetics that co-localize with genes encoding enzymes of the pathways producing these antioxidant metabolites. Our results provide the molecular basis for breeding barley cultivars with improved abiotic stress tolerance.

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

Drought has become more frequent in Central Europe causing large losses in cereal yields, especially of spring crops. The development of new varieties with increased tolerance to drought is a key tool for improvement of agricultural productivity. Material for the study consisted of 100 barley recombinant inbred lines (RILs) (LCam) derived from the cross between Syrian and European parents. The RILs and parental genotypes were examined in greenhouse experiments under well-watered and water-deficit conditions. During vegetation the date of heading, yield and yield-related traits were measured. RIL population was genotyped with microsatellite and single nucleotide polymorphism markers. This population, together with two other populations, was the basis for the consensus map construction, which was used for identification of quantitative trait loci (QTLs) affecting the traits. The studied lines showed a large variability in heading date. It was noted that drought-treatment negatively affected the yield and its components, especially when applied at the flag leaf stage. In total, 60 QTLs were detected on all the barley chromosomes. The largest number of QTLs was found on chromosome 2H. The main QTL associated with heading, located on chromosome 2H (Q.HD.LC-2H), was identified at SNP marker 5880-2547, in the vicinity of Ppd-H1 gene. SNP 5880-2547 was also the closest marker to QTLs associated with plant architecture, spike morphology and grain yield. The present study showed that the earliness allele from the Syrian parent, as introduced into the genome of an European variety could result in an improvement of barley yield performance under drought conditions.

Meta-analysis of major QTL for abiotic stress tolerance in barley and implications for barley breeding

We projected meta-QTL (MQTL) for drought, salinity, and waterlogging tolerance to the physical map of barley through meta-analysis. The positions of these MQTL were refined and candidate genes were identified. Drought, salinity and waterlogging are three major abiotic stresses limiting barley yield worldwide. Breeding for abiotic stress-tolerant crops has drawn increased attention, and a large number of quantitative trait loci (QTL) for drought, salinity, and waterlogging tolerance in barley have been detected. However, very few QTL have been successfully used in marker-assisted selection (MAS) in breeding. In this study, we summarized 632 QTL for drought, salinity and waterlogging tolerance in barley. Among all these QTL, only 195 major QTL were used to conduct meta-analysis to refine QTL positions for MAS. Meta-analysis was used to map the summarized major QTL for drought, salinity, and waterlogging tolerance from different mapping populations on the barley physical map. The positions of identified meta-QTL (MQTL) were used to search for candidate genes for drought, salinity, and waterlogging tolerance in barley. Both MQTL3H.4 and MQTL6H.2 control drought tolerance in barley. Fine-mapped QTL for salinity tolerance, HvNax4 and HvNax3, were validated on MQTL1H.4 and MQTL7H.2, respectively. MQTL2H.1 and MQTL5H.3 were also the target regions for improving salinity tolerance in barley. MQTL4H.4 is the main region controlling waterlogging tolerance in barley with fine-mapped QTL for aerenchyma formation under waterlogging conditions. Detected and refined MQTL and candidate genes are crucial for future successful MAS in barley breeding.

Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace

Drought causes important losses in crop production every season. Improvement for drought tolerance could take advantage of the diversity held in germplasm collections, much of which has not been incorporated yet into modern breeding. Spanish landraces constitute a promising resource for barley breeding, as they were widely grown until last century and still show good yielding ability under stress. Here, we study the transcriptome expression landscape in two genotypes, an outstanding Spanish landrace-derived inbred line (SBCC073) and a modern cultivar (Scarlett). Gene expression of adult plants after prolonged stresses, either drought or drought combined with heat, was monitored. Transcriptome of mature leaves presented little changes under severe drought, whereas abundant gene expression changes were observed under combined mild drought and heat. Developing inflorescences of SBCC073 exhibited mostly unaltered gene expression, whereas numerous changes were found in the same tissues for Scarlett. Genotypic differences in physiological traits and gene expression patterns confirmed the different behavior of landrace SBCC073 and cultivar Scarlett under abiotic stress, suggesting that they responded to stress following different strategies. A comparison with related studies in barley, addressing gene expression responses to drought, revealed common biological processes, but moderate agreement regarding individual differentially expressed transcripts. Special emphasis was put in the search of co-expressed genes and underlying common regulatory motifs. Overall, 11 transcription factors were identified, and one of them matched cis-regulatory motifs discovered upstream of co-expressed genes involved in those responses.

Genetic analysis of proline concentration under osmotic stress in sunflower (Helianthus annuus L.)

Proline concentration has been often suggested as an indicator of osmotic stress. A better understanding of the genetics of this trait is however needed. In the present study, proline concentration has been assessed, together with root and stem growth, potassium, calcium and total soluble sugars concentration and stress injury symptoms, in seedlings of sunflower hybrids and their parents grown under control and osmotic conditions. Proline strongly accumulated with osmotic stress. Its concentration exhibited a large variation among genotypes and was higher in hybrids than in parental lines. A positive association was noted between proline concentration and osmotic adjustment that was reflected in a reduction of osmotic stress induced injury, as showed by the reduced number of calli in the hybrids with higher proline concentration. Broad and narrow sense heritability was higher under osmotic stress suggesting applying the selection in osmotic stress condition. In the control treatment, dominance effects explained most of the genetic variation for proline concentration while under osmotic stress both dominance and additive variance were high. The importance of dominance and additive effects suggested that several genomic regions are controlling this trait. Good general combiners, presumably carrying positive additive alleles affecting proline concentration, were identified.

Comparison of ground cover estimates from experiment plots in cotton, sorghum and sugarcane based on images and ortho-mosaics captured by UAV

Ground cover is an important physiological trait affecting crop radiation capture, water-use efficiency and grain yield. It is challenging to efficiently measure ground cover with reasonable precision for large numbers of plots, especially in tall crop species. Here we combined two image-based methods to estimate plot-level ground cover for three species, from either an ortho-mosaic or undistorted (i.e. corrected for lens and camera effects) images captured by cameras using a low-altitude unmanned aerial vehicle (UAV). Reconstructed point clouds and ortho-mosaics for the whole field were created and a customised image processing workflow was developed to (1) segment the 'whole-field' datasets into individual plots, and (2) 'reverse-calculate' each plot from each undistorted image. Ground cover for individual plots was calculated by an efficient vegetation segmentation algorithm. For 79% of plots, estimated ground cover was greater from the ortho-mosaic than from images, particularly when plants were small, or when older/taller in large plots. While there was a good agreement between the ground cover estimates from ortho-mosaic and images when the target plot was positioned at a near-nadir view near the centre of image (cotton: R2=0.97, sorghum: R2=0.98, sugarcane: R2=0.84), ortho-mosaic estimates were 5% greater than estimates from these near-nadir images. Because each plot appeared in multiple images, there were multiple estimates of the ground cover, some of which should be excluded, e.g. when the plot is near edge within an image. Considering only the images with near-nadir view, the reverse calculation provides a more precise estimate of ground cover compared with the ortho-mosaic. The methodology is suitable for high throughput phenotyping for applications in agronomy, physiology and breeding for different crop species and can be extended to provide pixel-level data from other types of cameras including thermal and multi-spectral models.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5-22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5-35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

Identification of genomic regions involved in tolerance to drought stress and drought stress induced leaf senescence in juvenile barley

BACKGROUND

Premature leaf senescence induced by external stress conditions, e.g. drought stress, is a main factor for yield losses in barley. Research in drought stress tolerance has become more important as due to climate change the number of drought periods will increase and tolerance to drought stress has become a goal of high interest in barley breeding. Therefore, the aim is to identify quantitative trait loci (QTL) involved in drought stress induced leaf senescence and drought stress tolerance in early developmental stages of barley (Hordeum vulgare L.) by applying genome wide association studies (GWAS) on a set of 156 winter barley genotypes.

RESULTS

After a four weeks stress period (BBCH 33) leaf colour as an indicator of leaf senescence, electron transport rate at photosystem II, content of free proline, content of soluble sugars, osmolality and the aboveground biomass indicative for drought stress response were determined in the control and stress variant in greenhouse pot experiments. Significant phenotypic variation was observed for all traits analysed. Heritabilities ranged between 0.27 for osmolality and 0.61 for leaf colour in stress treatment and significant effects of genotype, treatment and genotype x treatment were estimated for most traits analysed. Based on these phenotypic data and 3,212 polymorphic single nucleotide polymorphisms (SNP) with a minor allele frequency >5% derived from the Illumina 9 k iSelect SNP Chip, 181 QTL were detected for all traits analysed. Major QTLs for drought stress and leaf senescence were located on chromosome 5H and 2H. BlastX search for associated marker sequences revealed that respective SNPs are in some cases located in proteins related to drought stress or leaf senescence, e.g. nucleotide pyrophosphatase (AVP1) or serine/ threonin protein kinase (SAPK9).

CONCLUSIONS

GWAS resulted in the identification of many QTLs involved in drought stress and leaf senescence of which two major QTLs for drought stress and leaf senescence were located on chromosome 5H and 2H. Results may be the basis to incorporate breeding for tolerance to drought stress or leaf senescence in barley breeding via marker based selection procedures.

Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits

Background

Drought and salinity are two major abiotic stresses that severely limit barley production worldwide. Physiological and genetic complexity of these tolerance traits has significantly slowed the progress of developing stress-tolerant cultivars. Marker-assisted selection (MAS) may potentially overcome this problem. In the current research, seventy two double haploid (DH) lines from a cross between TX9425 (a Chinese landrace variety with superior drought and salinity tolerance) and a sensitive variety, Franklin were used to identify quantitative trait loci (QTL) for drought and salinity tolerance, based on a range of developmental and physiological traits.

Results

Two QTL for drought tolerance (leaf wilting under drought stress) and one QTL for salinity tolerance (plant survival under salt stress) were identified from this population. The QTL on 2H for drought tolerance determined 42% of phenotypic variation, based on three independent experiments. This QTL was closely linked with a gene controlling ear emergency. The QTL on 5H for drought tolerance was less affected by agronomic traits and can be effectively used in breeding programs. A candidate gene for this QTL on 5H was identified based on the draft barley genome sequence. The QTL for proline accumulation, under both drought and salinity stresses, were located on different positions to those for drought and salinity tolerance, indicating no relationship with plant tolerance to either of these stresses.

Conclusions

Using QTL mapping, the relationships between QTL for agronomic and physiological traits and plant drought and salinity tolerance were studied. A new QTL for drought tolerance which was not linked to any of the studied traits was identified. This QTL can be effectively used in breeding programs. It was also shown that proline accumulation under stresses was not necessarily linked with drought or salinity tolerance based on methods of phenotyping used in this experiment. The use of proline content in breeding programs can also be limited by the accuracy of phenotyping.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1243-8) contains supplementary material, which is available to authorized users.

Plant vigour at establishment and following defoliation are both associated with responses to drought in perennial ryegrass (Lolium perenne L.)

Periodic drought events present a significant and, with climate change, increasing constraint on temperate forage plants' production. Consequently, improving plants' adaptive response to abiotic stress is a key goal to ensure agricultural productivity in these regions. In this study we developed a new methodology, using both area-based comparison and soil water content measurements of individual non-irrigated and irrigated clones, to assess performance of perennial ryegrass (Lolium perenne L.) genotypes subjected to moisture stress in a simulated competitive environment. We applied this method to the evaluation of a full-sibling population from a pair cross between genotypes from a New Zealand cultivar and a Moroccan ecotype. Our hypothesis was that: (i) both leaf lamina regrowth after defoliation (LR) and plant vigour affect plant performance during drought and rehydration; and (ii) quantitative trait loci (QTLs) associated with plant performance under moisture stress could be identified. Differences amongst genotypes in dry matter (DM) production, early vigour at establishment, leaf elongation rate and LR were measured. LR explained most of the variation in DM production during exposure to moisture deficit and rehydration followed by plant vigour, indicated by initial DM production in both treatments and subsequent measures of DM production of irrigated clones. We identified two main QTL regions associated with DM production and LR, both during drought exposure and rehydration. Further research focused on these regions should improve our understanding of the genetic control of drought response in this forage crop and potentially other grass species with significant synteny, and support improvement in performance through molecular breeding approaches.

Detection of nitrogen deficiency QTL in juvenile wild barley introgression lines growing in a hydroponic system

BACKGROUND

In this report we studied the genetic regulation of juvenile development of wild barley introgression lines (S42ILs) under two contrasting hydroponic nitrogen (N) supplies. Ten shoot and root related traits were examined among 42 S42ILs and the recurrent parent 'Scarlett'. The traits included tiller number, leaf number, plant height, leaf and root length, leaf to root length ratio, shoots and root dry weight, shoot to root weight ratio, and chlorophyll content. Our aims were (1) to test the suitability of a hydroponic system for early detection of favourable S42ILs, (2) to locate quantitative trait loci (QTL) that control the examined traits, (3) to identify favourable wild barley alleles that improve trait performances in regard to N treatment and, finally, (4) to validate the identified QTL through comparison with previously reported QTL originating from the same parental cross.

RESULTS

The phenotypic data were analysed in a mixed model association study to detect QTL. The post-hoc Dunnett test identified 28 S42ILs that revealed significant (P < 0.01) effects for at least one trait. Forty-three, 41 and 42 S42ILs revealed effects across both N treatments, under low N and under high N treatment, respectively. Due to overlapping or flanking wild barley introgressions of the S42ILs, these associations were summarised to 58 QTL. In total, 12 QTL of the hydroponic N study corresponded to QTL that were also detected in field trials with adult plants of a similar S42IL set or of the original S42 population. For instance, S42IL-135, -136 and -137, revealed increasing Hsp effects for tiller number, leaf number, leaf length, plant height and leaf to root ratio on the long arm of chromosome 7H. These QTL correspond to QTL for ears per plant and plant height that were previously detected in field trials conducted with the same S42ILs or with the S42 population.

CONCLUSION

Our results suggest that the QTL we identified under hydroponic N cultivation partly correspond to QTL detected in field experiments. Due to this finding, screening of plants in early developmental stages grown in a hydroponic system may be a fast and cost effective method for early QTL detection and marker-assisted allelic selection, potentially speeding up elite barley breeding programs.