Candidate Genes For Tolerance Research Articles

Transcriptional profiling of wheat and wheat-rye addition lines to identify candidate genes for aluminum tolerance

A large-scale expression profiling study was performed to investigate candidate genes associated with the two quantitative trait loci for aluminum (Al) tolerance (Alt1 and Alt2). They have been identified in rye and localized on chromosomes 6R and 3R, respectively. Materials employed were hexaploid wheat (cv. Chinese Spring), and two wheatrye addition lines (3R-AL and 6R-AL). Seedlings were treated with and without Al for 24 h to examine genes upregulated or down-regulated by Al. Measurements of root growth at different Al concentrations showed the Al tolerance was higher in 3R-AL than in 6R-AL and wheat. Initial transcriptomic results revealed that more genes changed expression (>10 fold) in the wheat and in the 6R-AL line (moderately tolerant) than in the 3R-AL line (highly tolerant). A method was developed to determine whether candidate genes are involved in Al tolerance or in responses to Al toxicity. Real-time quantitative PCRs were carried out in a subset of six genes with known function in near isogenic rye lines 389 (Al-sensitive) and 390 (Al tolerant). All six genes were up-regulated by Al in line 389 but not in line 390, indicating that they were involved in Al stress response but not in Al tolerance mechanisms. Subsequent analysis of Arabidopsis lines with knockout mutations in homologues of these six genes showed an Al sensitivity similar to the wild-type, providing more evidence towards their participation in the response to stress rather than to Al tolerance. Once the stress response genes were ruled out, the focus was turned to the identification of tolerance genes by studying transcripts up-regulated and down-regulated in the tolerant 3R line with respect to wheat and 6R line. Finally, a list of candidate genes that could be conferring increased tolerance was obtained.

Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species.

BackgroundCrop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.MethodsIn this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology (TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were used to semantically integrate drought related information.ResultsTarget genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs associated with different traits that are responsive to multiple stresses. Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic tree was instrumental to infer the evolutionary relationship of the sorghum orthologs. The results also show specific genes responsible for various interrelated components of drought response mechanism such as drought tolerance, drought avoidance and drought escape.ConclusionsWe submit that this approach is novel and to our knowledge, has not been used previously in any other research; it enables us to perform cross-species queries for genes that are likely to be associated with multiple stress tolerance, as a means to identify novel targets for engineering stress resistance in sorghum and possibly, in other crop species.

Screening of rice landraces (Oryza sativa L.) for seedling stage salinity tolerance using morpho-physiological and molecular markers

Traditional rice landraces of coastal area in Bangladesh are distinct regarding their phenotype, response to salt stress and yield attributes. With characterization of these landraces, suitable candidate genes for salinity tolerance could be identified to introgress into modern rice varieties. Therefore, the aim of this experiment was to uncover prospective rice landraces tolerant to salinity. Relying on morphological, biochemical and molecular parameters 25 rice genotypes were tested for salt tolerance at germination and seedling stage. At germination stage 0 and 12 dSm−1 salinity were imposed on rice genotypes. Ward’s cluster analysis divided rice genotypes into three clusters (susceptible, moderately tolerant and tolerant) based on the physiological indices. The tolerant rice landraces to salinity were Sona Toly, Nakraji and Komol Bhog. At seedling stage screening was performed following IRRI standard protocol at 12 dSm−1 salinity level. Based on all morphological and biochemical parameters Komol Bhog was identified as the highly salinity tolerant landrace while Bolonga, Sona Toly, Dud Sail, Tal Mugur and Nakraji were found as tolerant to salinity. Molecular characterization using two simple sequence repeats (SSR) markers, viz. RM121 and RM337 displayed Bolonga, Til Kapor, Panbra, Sona Toly, Bina Sail, Komol Bhog, Nakraji, Tilkapur, Gajor Goria and Gota were tolerant landraces through genetic similarity in dendrogram. These identified salt-resistant landraces can be used as promising germplasm resources for breeding salt-tolerant high-yielding rice varieties in future.

Transcriptome changes induced by abiotic stresses in Artemisia annua

Artemisia annua is known to be the source of artemisinin worldwide which is an antimalarial compound but is synthesised in very limited amount in the plant. Most research laid emphasis on the methods of enhancing artemisinin but our study has been planned in a way that it may simultaneously address two problems encountered by the plant. Firstly, to know the effect on the artemisinin content in the era of climate change because the secondary metabolites tend to increase under stress. Secondly, to identify some of the stress responsive genes that could help in stress tolerance of the plant under abiotic stress. Hence, the A. annua plants were subjected to four abiotic stresses (salt, cold, drought and water-logging) and it was observed that the artemisinin content increased in all the stress conditions except drought. Next, in order to identify the stress responsive genes, the transcriptome sequencing of the plants under stress was carried out resulting in 89,362 transcripts for control and 81,328, 76,337, 90,470 and 96,493 transcripts for salt, cold, drought, and water logging stresses. This investigation provides new insights for functional studies of genes involved in multiple abiotic stresses and potential candidate genes for multiple stress tolerance in A. annua.

Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice.

Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.

Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings

Cold stress is a major problem in rice production. To rapidly identify genes for cold tolerance in Dongxiang wild rice (DWR, Oryza rufipogon Griff.), sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant (R) and susceptible (S) bulks of a backcross inbred lines (BILs) population (derived from Oryza sativa×O. rufipogon) and their parents. Single nucleotide polymorphisms (SNP)-index graphs and corresponding ρ(SNP-index) graphs (at 99 and 95% confidence levels) for R- and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes. Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon. Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion (InDel) markers (12-7 and 12-16) that were linked with candidate genes on chromosome 12 in DWR. These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

Key messageA region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines.Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China. We improved the method to assess cold tolerance at the bud burst stage in indica rice, and used severity of damage (SD) and seed survival rate (SR) as the cold-tolerant indices. Population structure analysis demonstrated that the Chinese indica panel was divided into three subgroups. In total, 47 significant single-nucleotide polymorphism (SNP) loci associated with SD and SR, were detected by association mapping based on mixed linear model. Because some loci overlapped between SD and SR, the loci contained 13 genome intervals and most of them have been reported previously. A major QTL for cold tolerance on chromosome 1 at the position of 31.6 Mb, explaining 13.2% of phenotypic variation, was selected for further analysis. Through LD decay, GO enrichment, RNA-seq data, and gene expression pattern analyses, we identified three genes (LOC_Os01g55510, LOC_Os01g55350 and LOC_Os01g55560) that were differentially expressed between cold-tolerant and cold-sensitive varieties, suggesting they may be candidate genes for cold tolerance. Together, our results provide a new method to assess cold tolerance in indica rice, and establish the foundation for isolating genes related to cold tolerance that could be used in rice breeding.

Candidate Genes and Molecular Markers Correlated to Physiological Traits for Heat Tolerance in Fine Fescue Cultivars.

Heat stress is one of the major abiotic factors limiting the growth of cool-season grass species during summer season. The objectives of this study were to assess genetic variations in the transcript levels of selected genes in fine fescue cultivars differing in heat tolerance, and to identify single nucleotide polymorphism (SNP) markers associated with candidate genes related to heat tolerance. Plants of 26 cultivars of five fine fescue species (Festuca spp.) were subjected to heat stress (38/33 °C, day/night temperature) in controlled environmental growth chambers. Physiological analysis including leaf chlorophyll content, photochemical efficiency, and electrolyte leakage demonstrated significant genetic variations in heat tolerance among fine fescue cultivars. The transcript levels of selected genes involved in photosynthesis (RuBisCO activase, Photosystem II CP47 reaction center protein), carbohydrate metabolism (Sucrose synthase), energy production (ATP synthase), growth regulation (Actin), oxidative response (Catalase), and stress protection (Heat shock protein 90) were positively correlated with the physiological traits for heat tolerance. SNP markers for those candidate genes exhibited heterozygosity, which could also separate heat-sensitive and heat-tolerant cultivars into clusters. The development of SNP markers for candidate genes in heat tolerance may allow marker-assisted breeding for the development of new heat-tolerant cultivars in fine fescue and other cool-season grass species.

QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified from the Mapping Populations Specifically Segregating for Fv/Fm in Wheat.

Despite the fact that Fv/Fm (maximum quantum efficiency of photosystem II) is the most widely used parameter for a rapid non-destructive measure of stress detection in plants, there are barely any studies on the genetic understanding of this trait under heat stress. Our aim was to identify quantitative trait locus (QTL) and the potential candidate genes linked to Fv/Fm for improved photosynthesis under heat stress in wheat (Triticum aestivum L.). Three bi-parental F2 mapping populations were generated by crossing three heat tolerant male parents (origin: Afghanistan and Pakistan) selected for high Fv/Fm with a common heat susceptible female parent (origin: Germany) selected for lowest Fv/Fm out of a pool of 1274 wheat cultivars of diverse geographic origin. Parents together with 140 F2 individuals in each population were phenotyped by Fv/Fm under heat stress (40°C for 3 days) around anthesis. The Fv/Fm decreased by 6.3% in the susceptible parent, 1–2.5% in the tolerant parents and intermediately 4–6% in the mapping populations indicating a clear segregation for the trait. The three populations were genotyped with 34,955 DArTseq and 27 simple sequence repeat markers, out of which ca. 1800 polymorphic markers mapped to 27 linkage groups covering all the 21 chromosomes with a total genome length of about 5000 cM. Inclusive composite interval mapping resulted in the identification of one significant and heat-stress driven QTL in each population on day 3 of the heat treatment, two of which were located on chromosome 3B and one on chromosome 1D. These QTLs explained about 13–35% of the phenotypic variation for Fv/Fm with an additive effect of 0.002–0.003 with the positive allele for Fv/Fm originating from the heat tolerant parents. Approximate physical localization of these three QTLs revealed the presence of 12 potential candidate genes having a direct role in photosynthesis and/or heat tolerance. Besides providing an insight into the genetic control of Fv/Fm in the present study, the identified QTLs would be useful in breeding for heat tolerance in wheat.

Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis.

Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.

OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies.

Water deficiencies are one of the most serious challenges to crop productivity. To improve our understanding of soil moisture stress, we performed RNA-Seq analysis using roots from 4-week-old rice seedlings grown in soil that had been subjected to drought conditions for 2–3 d. In all, 1,098 genes were up-regulated in response to soil moisture stress for 3 d, which causes severe damage in root development after recovery, unlikely that of 2 d. Comparison with previous transcriptome data produced in drought condition indicated that more than 68% of our candidate genes were not previously identified, emphasizing the novelty of our transcriptome analysis for drought response in soil condition. We then validated the expression patterns of two candidate genes using a promoter-GUS reporter system in planta and monitored the stress response with novel molecular markers. An integrating omics tool, MapMan analysis, indicated that RING box E3 ligases in the ubiquitin-proteasome pathways are significantly stimulated by induced drought. We also analyzed the functions of 66 candidate genes that have been functionally investigated previously, suggesting the primary roles of our candidate genes in resistance or tolerance relating traits including drought tolerance (29 genes) through literature searches besides diverse regulatory roles of our candidate genes for morphological traits (15 genes) or physiological traits (22 genes). Of these, we used a T-DNA insertional mutant of rice phytochrome B (OsPhyB) that negatively regulates a plant's degree of tolerance to water deficiencies through the control of total leaf area and stomatal density based on previous finding. Unlike previous result, we found that OsPhyB represses the activity of ascorbate peroxidase and catalase mediating reactive oxygen species (ROS) processing machinery required for drought tolerance of roots in soil condition, suggesting the potential significance of remaining uncharacterized candidate genes for manipulating drought tolerance in rice.

Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat

BackgroundPhenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is important for breeding cold-resistant wheat cultivars. In this study, we combined three computational techniques for the analysis of gene expression data from spring and winter wheat cultivars subjected to low temperature treatments. Our main objective was to construct a comprehensive network of cold response transcriptional events in wheat, and to identify novel cold tolerance candidate genes in wheat.ResultsWe assigned novel cold stress-related roles to 35 wheat genes, uncovered novel transcription (TF)-gene interactions, and identified 127 genes representing known and novel candidate targets associated with cold tolerance in wheat. Our results also show that delays in terms of activation or repression of the same genes across wheat cultivars play key roles in phenotypic differences among winter and spring wheat cultivars, and adaptation to low temperature stress, cold shock and cold acclimation.ConclusionsUsing three computational approaches, we identified novel putative cold-response genes and TF-gene interactions. These results provide new insights into the complex mechanisms regulating the expression of cold-responsive genes in wheat.

Cotton (Gossypium hirsutum L.) genotypes with contrasting K+/Na+ ion homeostasis: implications for salinity tolerance

Cotton (Gossypium hirsutum L.) possesses notable inter- and intraspecific salt tolerance variation, but the mechanisms underlying this variation are, more or less, unclear. To explore salt stress responses, Na+/K+ transport and the transcriptional profiles of salinity tolerance candidate genes (e.g., GhSOS1, GhNHX1, and GhAKT1) were evaluated in four cotton cultivars (differing in salt sensitivities) using electrophysiological and qRT-PCR assays. Physiology and lipid peroxidation assays revealed the following pattern of salt tolerance, in decreasing order: CZ91 > CCRI44 > CCRI49 > Z571. Salinity caused ion imbalances in plants, but ion homeostasis was more pronounced in Z571, which accumulated more Na+ and less K+ in leaves. In contrast, salt-tolerant cultivars, especially CZ91, retained less Na+, but more K+ under salt stress. The non-invasive micro-test technique revealed that Z571 exhibited a higher capacity to transport Na+ from roots to shoots, but a lower capacity to extrude Na+ and retain K+ in leaves under salinity. Meanwhile, NaCl-induced changes in Na+ and K+ ion homeostasis were less pronounced in salt-tolerant cultivars, increasing leaf K+/Na+ ratios under salinity. Additionally, NaCl increased the GhSOS1 transcript abundance in hypocotyls, but this increase was more pronounced in salt-sensitive Z571. On the other hand, NaCl significantly enhanced the transcript abundances of GhSOS1 in leaves and/or GhAKT1 in hypocotyls of salt-tolerant cultivars. NaCl also increased the GhNHX1 transcript abundance, but there was no strong correlation between GhNHX1 expression level and salt resistance. The present findings provided an explanation for salt tolerance variation in cotton, illuminating the transcriptional regulation of K+/Na+ transport and the maintenance of the K+/Na+ ratio as underlying attributes.

QTLs for stomatal and photosynthetic traits related to salinity tolerance in barley

BackgroundStomata regulate photosynthesis and transpiration, and these processes are critical for plant responses to abiotic stresses such as salinity. A barley double haploid population with 108 lines derived from a cross between CM72 (salt-tolerant) and Gairdner (salt-sensitive) was used to detect quantitative trait loci (QTLs) associated with stomatal and photosynthetic traits related to salinity tolerance.ResultsA total of 11 significant QTLs (LOD > 3.0) and 11 tentative QTLs (2.5 < LOD < 3.0) were identified. These QTLs are distributed on all the seven chromosomes, except 5H and explain 9.5–17.3% of the phenotypic variation. QTLs for biomass, intercellular CO2 concentration, transpiration rate and stomatal conductance under control conditions co-localised together. A QTL for biomass also co-located with one for transpiration rate under salinity stress. A linkage was found between stomatal pore area and gas exchange. A QTL for salinity tolerance also co-localised with QTLs for grain yield and biomass on chromosome 3H. Based on the draft barley genome, the candidate genes for salinity tolerance at this locus are proposed.ConclusionsThe lack of major QTLs for gas exchange and stomatal traits under control and saline conditions indicates a complex relationship between salinity and leaf gas exchange due to the fact that these complex quantitative traits are under the control of multiple genes.

Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance.

In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.

Designing future barley ideotypes using a crop model ensemble

Abstract Climate change and its associated higher frequency and severity of adverse weather events require genotypic adaptation. Process-based ecophysiological modelling offers a powerful means to better target and accelerate development of new crop cultivars. Barley ( Hordeum vulgare L.) is an important crop throughout the world, and a good model for study of the genetics of stress adaptation because many quantitative trait loci and candidate genes for biotic and abiotic stress tolerance have been identified in it. Here, we developed a new approach to design future crop ideotypes using an ensemble of eight barley simulation models (i.e. APSIM, CropSyst, HERMES, MCWLA, MONICA, SIMPLACE, SiriusQuality , and WOFOST), and applied it to design climate-resilient barley ideotypes for Boreal and Mediterranean climatic zones in Europe. The results showed that specific barley genotypes, represented by sets of cultivar parameters in the crop models, could be promising under future climate change conditions, resulting in increased yields and low inter-annual yield variability. In contrast, other genotypes could result in substantial yield declines. The most favorable climate-zone-specific barley ideotypes were further proposed, having combinations of several key genetic traits in terms of phenology, leaf growth, photosynthesis, drought tolerance, and grain formation. For both Boreal and Mediterranean climatic zones, barley ideotypes under future climatic conditions should have a longer reproductive growing period, lower leaf senescence rate, larger radiation use efficiency or maximum assimilation rate, and higher drought tolerance. Such characteristics can produce substantial positive impacts on yields under contrasting conditions. Moreover, barley ideotypes should have a low photoperiod and high vernalization sensitivity for the Boreal climatic zone; for the Mediterranean, in contrast, it should have a low photoperiod and low vernalization sensitivity. The drought-tolerance trait is more beneficial for the Mediterranean than for the Boreal climatic zone. Our study demonstrates a sound approach to design future barley ideotypes based on an ensemble of well-tested, diverse crop models and on integration of knowledge from multiple disciplines. The robustness of model-aided ideotypes design can be further enhanced by continuously improving crop models and enhancing information exchange between modellers, agro-meteorologists, geneticists, physiologists, and plant breeders.

Molecular Dissection of Seedling Salinity Tolerance in Rice (Oryza sativa L.) Using a High-Density GBS-Based SNP Linkage Map.

BackgroundSalinity is one of the many abiotic stresses limiting rice production worldwide. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated to salinity tolerance. However, due to large confidence interval for the position of QTLs, utility of reported QTLs and the associated markers has been limited in rice breeding programs. The main objective of this study is to construct a high-density rice genetic map for identification QTLs and candidate genes for salinity tolerance at seedling stage.ResultsWe evaluated a population of 187 recombinant inbred lines (RILs) developed from a cross between Bengal and Pokkali for nine traits related to salinity tolerance. A total of 9303 SNP markers generated by genotyping-by-sequencing (GBS) were mapped to 2817 recombination points. The genetic map had a total map length of 1650 cM with an average resolution of 0.59 cM between markers. For nine traits, a total of 85 additive QTLs were identified, of which, 16 were large-effect QTLs and the rest were small-effect QTLs. The average interval size of QTL was about 132 kilo base pairs (Kb). Eleven of the 85 additive QTLs validated 14 reported QTLs for shoot potassium concentration, sodium-potassium ratio, salt injury score, plant height, and shoot dry weight. Epistatic QTL mapping identified several pairs of QTLs that significantly contributed to the variation of traits. The QTL for high shoot K+ concentration was mapped near the qSKC1 region. However, candidate genes within the QTL interval were a CC-NBS-LRR protein, three uncharacterized genes, and transposable elements. Additionally, many QTLs flanked small chromosomal intervals containing few candidate genes. Annotation of the genes located within QTL intervals indicated that ion transporters, osmotic regulators, transcription factors, and protein kinases may play essential role in various salt tolerance mechanisms.ConclusionThe saturation of SNP markers in our linkage map increased the resolution of QTL mapping. Our study offers new insights on salinity tolerance and presents useful candidate genes that will help in marker-assisted gene pyramiding to develop salt tolerant rice varieties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0125-2) contains supplementary material, which is available to authorized users.

Experimental Validation of Evolutionarily Conserved Genes Regulating Hypoxia Adaption in Drosophila and Humans

Hypoxia tolerance is regulated by polygenic mechanisms in metazoan organisms. The following study was performed to determine whether such polygenic mechanisms are shared evolutionarily between organisms like Drosophila and humans. Using a generalized linear mixed model we identified significant allele frequency differences between three independently evolved hypoxia‐tolerant populations and normoxic control populations of Drosophila. Around 50% of the ~3,800 SNP variants are clustered in 66 distinct genomic regions that contain genes that are differentially expressed when hypoxia‐tolerant and normoxic populations were compared. In addition, using genome‐wide SNP data from four high‐altitude human populations (i.e., Sherpas, Tibetans, Ethiopians, and Andeans), we found that several human orthologs of the genes under selection in flies are also likely under positive selection in all four high‐altitude human populations, suggesting that these conserved genes and pathways may regulate hypoxia tolerance in both flies and humans. Currently we have experimentally evaluated the role of these candidate genes in hypoxia tolerance in flies using RNAi‐mediated knockdown. We found that down‐regulation of several candidate genes’ expression, such as pyd, significantly enhanced survival in severe hypoxia in flies. Our results demonstrated that fundamental genetic mechanisms regulating hypoxia tolerance have indeed remained conserved throughout evolution. Such mechanisms may help us to develop novel therapeutic strategies to treat hypoxia‐related diseases in humans.Support or Funding InformationThis work was supported by the following grants from National Institute of Health: Training in Oxygen in Health and Disease Grant T32HL094282 to ARJ; 5P01HD32573 to GGH; and P50 GM081892 to KPW.

Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses.

Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.

Identification of Putative Candidate Genes for Water Stress Tolerance in Canola (Brassica napus).

Drought stress can directly inhibit seedling establishment in canola (Brassica napus), resulting in lower plant densities and reduced yields. To dissect this complex trait, 140 B. napus accessions were phenotyped under normal (0.0 MPa, S0) and water-stressed conditions simulated by polyethylene glycol (PEG) 6000 (−0.5 MPa, S5) in a hydroponic system. Phenotypic variation and heritability indicated that the root to shoot length ratio was a reliable indicator for water stress tolerance. Thereafter, 66 accessions (16 water stress tolerant, 34 moderate and 16 sensitive lines) were genotyped using 25,495 Brassica single nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) identified 16 loci significantly associated with water stress response. Two B. napus accessions were used for RNA sequencing, with differentially-expressed genes under normal and water-stressed conditions examined. By combining differentially-expressed genes detected by RNA sequencing with significantly associated loci from GWAS, 79 candidate genes were identified, of which eight were putatively associated with drought tolerance based on gene ontology of Arabidopsis. Functional validation of these genes may confirm key drought-related genes for selection and breeding in B. napus. Our results provide insight into the genetic basis of water stress tolerance in canola.