Candidate Genes For Response Research Articles

Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress

Potassium (K+) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K+ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K+ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K+ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.

Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance

BackgroundAlfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement.ResultAn RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant ‘Halo’ and salt intolerant ‘Vernal’. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m− 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for ‘Halo’, 34 and 50 for ‘Vernal’, respectively. In root tissue, ‘Halo’ maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for ‘Vernal’. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in ‘Halo’ compared to ‘Vernal’ under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress.ConclusionThe identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance.

The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses

The WRKY genes are one of the largest families of transcription factors (TFs) and play a crucial role in certain processes in plants including stress signaling, regulation of transcriptional reprogramming associated with stress responses, and other regulatory networks. This study aims to investigate the WRKY gene family in the C3 model plant, Oryza sativa L., using a genome-wide in silico expression analysis. Firstly, 104 WRKY TF family members were identified, and then their molecular properties and expression signatures were analyzed systematically. In silico spatio-temporal and hormonal expression profiling revealed the roles of OsWRKY genes and their dynamism in diverse developmental tissues and hormones, respectively. Comparative mapping between OsWRKY genes and their synteny with C4 panicoid genomes showed the evolutionary insights of the WRKY TF family. Interactions of OsWRKY coding gene sequences represented the complexity of abiotic stress (AbS) and their molecular cross-talks. The expression signature of 26 novel candidate genes in response to stresses exhibited the putative involvement of individual and combined AbS (CAbS) responses. These novel findings unravel the in-depth insights into OsWRKY TF genes and delineate the plant developmental metabolisms and their functional regulations in individual and CAbS conditions.

Genetic mapping and identification of a QTL determining tolerance to freezing stress in Fragaria vesca L.

Extreme cold and frost cause significant stress to plants which can potentially be lethal. Low temperature freezing stress can cause significant and irreversible damage to plant cells and can induce physiological and metabolic changes that impact on growth and development. Low temperatures cause physiological responses including winter dormancy and autumn cold hardening in strawberry (Fragaria) species, and some diploid F. vesca accessions have been shown to have adapted to low-temperature stresses. To study the genetics of freezing tolerance, a F. vesca mapping population of 143 seedlings segregating for differential responses to freezing stress was raised. The progeny was mapped using ‘Genotyping-by-Sequencing’ and a linkage map of 2,918 markers at 851 loci was resolved. The mapping population was phenotyped for freezing tolerance response under controlled and replicated laboratory conditions and subsequent quantitative trait loci analysis using interval mapping revealed a single significant quantitative trait locus on Fvb2 in the physical interval 10.6 Mb and 15.73 Mb on the F. vesca v4.0 genome sequence. This physical interval contained 896 predicted genes, several of which had putative roles associated with tolerance to abiotic stresses including freezing. Differential expression analysis of the 896 QTL-associated gene predictions in the leaves and crowns from ‘Alta’ and ‘NCGR1363’ parental genotypes revealed genotype-specific changes in transcript accumulation in response to low temperature treatment as well as expression differences between genotypes prior to treatment for many of the genes. The putative roles, and significant interparental differential expression levels of several of the genes reported here identified them as good candidates for the control of the effects of freezing tolerance at the QTL identified in this investigation and the possible role of these candidate genes in response to freezing stress is discussed.

Phylogeny, gene structure and GATA genes expression in different tissues of solanaceae species

GATA proteins are a group of transcriptional regulators that can detect and bind to GATA motifs by zinc finger domain. The plant GATA family is one of the most significant TFs involved in light-responsive development, nitrogen metabolism, and phyto-hormone signaling. In this study, 20 potatoes and 22 tomato GATA genes were selected. The chromosomal locations, gene structures, phylogenetic tree, and the expression during developmental stages of 42 GATA transcription factors (TFs) in Solanaceae species were analyzed to further investigate the functions of these factors. Also, Gene duplication and synteny between the tomato and potato genomes were also analyzed to provide insights into their evolutionary characteristics. Furthermore, genome evolution of potato and tomato using orthologous and paralogous identification was studied. The results of chromosomal localization revealed that 20 SlGATA genes of tomato were located on 12 chromosomes, except on chromosomes 9 and 11. In potato, all 22 StGATA genes were located on 12 chromosomes. Our results indicated that gene duplication may play an important role in genome expansion of potato and tomato. So far, a complete analysis combining evolutionary analysis and expression of the GATA TFs in the Solanaceae species of tomato and potato has not been reported. A comparative phylogenetic analysis of the GATA factor zinc finger domain sequences in potato and tomato revealed four subfamilies. The conserved motifs and gene structure in most genes in each group was similar, according to the grouping of GATA TFs in phylogenetic tree. The analysis of cis -elements showed that SlGATA26a/26b and StGATA26a/26b can be suggested as candidate genes in response to abiotic and biotic stresses. SlGATA26a/26b and StGATA26a/26b genes were expressed in root, shoot, and inflorescence. Altogether, our resultsshowed diverse roles for StGATA and SlGATA genes under abiotic and biotic stresses. Utilization of cis -elements prediction can faciliate potato and tomato improvement. • GATA proteins are a group of transcriptional regulators that can detect and bind to GATA motifs by zinc finger domain. • We surveyed the phylogenetic relationships, gene structures, chromosomal locations, gene duplications, and genes expression of 42 GATA TFs in three tissue types of tomato and potato. • Our results provide insights into the functional differences, evolutionary relationships and expression profiles of GATA transcription factors in Solanaceae species.

Differential gene expression reveals candidate genes for osmotic stress response in faba bean (Vicia faba L.) involved in different molecular pathways

Drought and salinity are the most important environmental constraints affecting faba bean (Vicia faba L.) development and crop yield in Tunisia and other Mediterranean countries. Through using different strategies, associating in silico analysis of gene expression and qRT-PCR, this study aims at identifying key genes of faba bean molecular pathways potentially involved in salt and drought response. The impact of these stresses on several physiological and biochemical parameters were investigated in two genotypes (Bachar and Giza 3). To uncover abiotic stress-related genes and better understand the mechanisms of salt and drought stress tolerance in faba bean, a total of 25 faba bean genes were identified through in silico analysis. These genes were associated with important cellular processes such as transcription regulation, signal transport, kinases, phytohormonal signaling, and defense/stress responses. Most of the studied candidates were expressed at various levels in different organs including leaves, roots, flowers, stems, cotyledons, and seeds suggesting a potential role in the growth and development of faba bean plants. Furthermore, qRT-PCR was used to study gene expression profiles in leaves and roots of Bachar and Giza 3 plants under salt and drought stresses, and ABA treatment. The results showed that selected transcripts were differentially expressed under various treatments in both genotypes suggesting their important roles in abiotic stress tolerance responses. The osmotic-responsive genes identified in this study may be considered as potential candidates with a further application as stress selection markers for the creation of faba bean stress-tolerant varieties in various breeding programs.

Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Camellia sinensis (L.) Kuntze

Cold and drought are two of the most severe threats affecting the growth and productivity of the tea plant, limiting its global spread. Both stresses cause osmotic changes in the cells of the tea plant by decreasing their water potential. To develop cultivars that are tolerant to both stresses, it is essential to understand the genetic responses of tea plant to these two stresses, particularly in terms of the genes involved. In this study, we combined literature data with interspecific transcriptomic analyses (using Arabidopsis thaliana and Solanum lycopersicum) to choose genes related to cold tolerance. We identified 45 stress-inducible candidate genes associated with cold and drought responses in tea plants based on a comprehensive homologous detection method. Of these, nine were newly characterized by us, and 36 had previously been reported. The gene network analysis revealed upregulated expression in ICE1-related cluster of bHLH factors, HSP70/BAM5 connected genes (hexokinases, galactinol synthases, SnRK complex, etc.) indicating their possible co-expression. Using qRT-PCR we revealed that 10 genes were significantly upregulated in response to both cold and drought in tea plant: HSP70, GST, SUS1, DHN1, BMY5, bHLH102, GR-RBP3, ICE1, GOLS1, and GOLS3. SnRK1.2, HXK1/2, bHLH7/43/79/93 were specifically upregulated in cold, while RHL41, CAU1, Hydrolase22 were specifically upregulated in drought. Interestingly, the expression of CIP was higher in the recovery stage of both stresses, indicating its potentially important role in plant recovery after stress. In addition, some genes, such as DHN3, bHLH79, PEI54, SnRK1.2, SnRK1.3, and Hydrolase22, were significantly positively correlated between the cold and drought responses. CBF1, GOLS1, HXK2, and HXK3, by contrast, showed significantly negative correlations between the cold and drought responses. Our results provide valuable information and robust candidate genes for future functional analyses intended to improve the stress tolerance of the tea plant and other species.

Single nucleotide polymorphisms from candidate genes associated with nematode resistance and resilience in Corriedale and Pampinta sheep in Argentina.

Selective breeding of genetically resistant animals is considered a promising strategy to face the problem of nematode resistance to anthelmintics and mitigate concerns about the presence of chemical residues in animal food products and the environment. Gastrointestinal nematode resistance is a complex, multifactorial trait related to host immunity. However, the mechanisms underlying host resistance and response to infection remain to be fully elucidated. In this context, the objective of this study was to provide insight into the chromosomal regions determining nematode resistance and resilience in Corriedale and resistance in Pampinta sheep breeds. A total of 170 single nucleotide polymorphisms (SNP) from 76 candidate genes for immune response were studied in 624 Corriedale and 304 Pampinta animals. Lambs underwent artificial or natural challenges with infective larvae mainly from Haemonchus contortus. Fecal egg counts, estimated breeding values for fecal egg counts, and rate of packed cell volume change and FAMACHA© score change over the challenge were used, when available, as indicators of host parasite resistance or resilience. Phenotype-genotype association studies were conducted and significance values obtained were adjusted for multiple testing errors. Eight SNPs, located on OARs 3, 6, 12, and 20, reached significance in Corriedale sheep under artificial challenge. Those SNP represent allelic variants from the MHC-Ovine Lymphocyte Antigen-DRA, two C-type lectin domain families, the Interleukin 2 receptor β, the Toll-like receptor 10, the Mannan binding lectin serine peptidase 2, and the NLR family, CARD domain containing 4 genes. On Pampinta lambs under natural challenge, we found three significant SNPs, located in the TIMP metallopeptidase inhibitor 3, the FBJ murine osteosarcoma viral oncogene homolog, and the Interleukin 20 receptor alpha genes, on OARs 3, 7, and 8, respectively. The results obtained herein confirm genomic regions previously reported as associated with nematode resistance in other sheep breeds, reinforcing their role in host response to parasites. These findings contribute to gain knowledge on parasite resistance and resilience in Corriedale sheep and report for the first time SNPs associated with resistance to gastrointestinal parasite infections in Pampinta breed.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BackgroundSpecific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits.ResultsSNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117).ConclusionsAccurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Transcriptome profile of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies

Sunki Maravilha' and 'Sunki Tropical' are citrus plants with different drought tolerance strategies. `Sunki Tropical' is considered as another rootstock alternative for use in drought prone areas, however, its genetic expression profiles regarding response to water deficit, are still unknown. In this study, the transcriptome of the ‘Sunki Maravilha’ and ‘Sunki Tropical’ rootstocks under control were analyzed by RNA-seq technique using the Illumina HiSeq-2500. A total of 109,114.164 reads were produced and mapped against the Citrus sinensis reference genome (version 1.1). 3.607 transcripts showed significant variation in expression between the water deficit and control treatments with 739 genes up-regulated and 2868 down-regulated during water deficit imposition. The differentially expressed genes (DEGs) identified are involved in more than 100 biological processes and molecular functions whereas most enriched for the function of oxidoreductase, protein phosporilation, transcriptional regulation, ligation processes and response to oxidative stress. DEGs related to the biosynthesis of ABA (Abscisic Acid), redox system, cell wall mechanism, root development, transcription factors (TFs) and kinase proteins (KPs), were also identified. This work lays the basic foundation for further investigation of the specific functions of genes in citrus rootstocks, Sunki Maravilha’ and Sunki Tropical’, with different strategies of survival under water deficit and also provides candidate genes for engineering or breeding of citrus plants aiming drought tolerance.

Comparative Leaf Proteomics of Brassica napus Genotypes with Distinctive Levels of Early Cold Acclimation

Rapeseed/canola (Brassica napus L.) is considered amongst the “big four” oilseed crops with varying degrees of cold tolerance. Differential protein expression of cold acclimated young leaves of two canola genotypes, Sari Gul (spring type cold-sensitive) and Zarfam (winter type cold-tolerant), were determined via two dimensional polyacrylamide gel electrophoresis. Seedling leaves were cold acclimated by temperature regime and collected before and after cold treatment at 4 and − 4 °C after 24 h, proteins were isolated and separated on 2-DE. Gel analysis of 651 protein spots revealed that 19 protein spots were significantly different between the two conditions in response to early cold acclimation. Following nanoflow liquid chromatography–tandem mass spectrometry, 19 protein sequences were identified in gel spots, which were reported for the first time in response to early cold acclimation in B. napus and nearly half of them were associated with various aspects of chloroplast physiology; suggesting that the cold stress response of B. napus is achieved, at least partly, by regulation of chloroplast function. Our work has provided novel insights into the plant response to cold stress and should pave the way for future studies towards functional analysis of candidate genes in cold response.

Integration of anthracnose resistance loci and RLK and NBS‐LRR‐encoding genes in the Phaseolus vulgaris L. genome

AbstractThe most effective strategy to manage bean anthracnose (ANT), caused by Colletotrichum lindemuthianum, is the use of resistant cultivars. There are more than 20 ANT resistance genes that have been identified and mapped in common bean (Phaseolus vulgaris L.) chromosomes. Moreover, quantitative resistance loci (QRLs) have been described through genome‐wide association studies (GWAS). Identification of pathogen‐responsive genes and proteins on a molecular level provides a better understanding of metabolic pathways involved in ANT resistance. In this study, we investigated typical resistance proteins located close to ANT resistance loci in the common bean reference genome. Among them, we checked for proteins with nucleotide‐binding and leucine‐rich repeat (NBS‐LRR) domains and kinase domains since most resistance genes encode proteins with these domains. In addition, proteins with kinase domains are known to operate as pattern‐recognition receptors that recognize pathogen‐associated molecular patterns (PAMPs) and activate an immune response. Based on the common bean reference genome (Version 2.1), the regions 500‐kb upstream and downstream of the physical position of each ANT resistance locus were considered for a candidate gene search. Thus, an integrated map of ANT resistance loci and candidate genes (encoding defense response‐related proteins) was constructed. This map contains candidate genes for all ANT resistance genes and QRLs previously described in the literature. A total of 256 NBS‐LRR proteins and 200 protein kinases were detected. The functions of the identified candidate genes in ANT response should be validated and studies should be performed to understand how they interact with metabolic pathways.

Transcriptome Profiling of Gold Queen Hami Melons under Cold Stress

Hami melon (Cucumis melo L. var. inodorus Jacq) is an important horticultural crop but susceptible to chilling injury during low temperature storage. To characterize the gene expression profiles of Gold Queen Hami melon under the cold stress and discover the key cold stress-induced genes, five cDNA libraries, C0 (control), C12 (control for 12 d), C24 (control for 24 d), L12 (cold treatment at 0.5°C for 12 d) and L24 (cold treatment at 0.5°C for 24 d), were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. A total of 6479 and 7914 differentially expressed genes (DEGs) in L12 and L24 compared with C0 were respectively detected. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses identified the relevant biological functions and metabolic pathways of these differentially expressed genes. In addition, a diverse range of cold response candidate genes were mainly obtained from starch and sucrose metabolism, pentose phosphate pathway and glycolysis/gluconeogenesis, such as genes encoding sucrose-phosphate synthase, α-amylase, β-amylase, sucrose synthase and glucose-6-phosphate dehydrogenase. Various transcription factors with divergent expression patterns were identified. Finally, quantitative real time polymerase chain reaction (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. This study provides valuable information for further studies on cold response mechanisms and genetic improvement of cold tolerance in Gold Queen Hami melons.

Individual-based dendrogenomic analysis of forest dieback driven by extreme droughts

Droughts driven by global change are triggering worldwide forest dieback, a phenomenon that is predicted to worsen. We combined genome-wide single nucleotide polymorphisms (SNPs) and dendrochronological approaches to assess genetically-based individual tree vulnerability to past extreme droughts that caused massive mortality of coihue (Nothofagus dombeyi (Mirb.) Blume) forests in northern Patagonia, Argentina. We collected fresh leaves and wood cores from pairs of trees, one with a healthy crown (HC) and another with a partially affected crown (PA), at four sites impacted by droughts in 1998, 2008, and 2014. We used dendrochronological techniques to estimate parameters in terms of growth trends due to drought and genomic analysis to assess the relationship of genomic variation with water stress. While 5155 neutral loci did not differentiate PA from HC trees, a set of 33 adaptive SNPs did, 8 of which were related to water stress. Association analysis between genomic variants and dendrophenotypic traits yielded 6 SNPs that were associated with a growth measure as resilience to cope with drought. Our preliminary results indicate that susceptibility to drought in N. dombeyi could be determined at the genomic level. The combination of these approaches provides a framework for the identification and analysis of candidate genes for stress response in non-model species.

The identification of six risk genes for ovarian cancer platinum response based on global network algorithm and verification analysis.

Ovarian cancer is the most lethal gynaecological cancer, and resistance of platinum‐based chemotherapy is the main reason for treatment failure. The aim of the present study was to identify candidate genes involved in ovarian cancer platinum response by analysing genes from homologous recombination and Fanconi anaemia pathways. Associations between these two functional genes were explored in the study, and we performed a random walk algorithm based on reconstructed gene‐gene network, including protein‐protein interaction and co‐expression relations. Following the random walk, all genes were ranked and GSEA analysis showed that the biological functions focused primarily on autophagy, histone modification and gluconeogenesis. Based on three types of seed nodes, the top two genes were utilized as examples. We selected a total of six candidate genes (FANCA, FANCG, POLD1, KDM1A, BLM and BRCA1) for subsequent verification. The validation results of the six candidate genes have significance in three independent ovarian cancer data sets with platinum‐resistant and platinum‐sensitive information. To explore the correlation between biomarkers and clinical prognostic factors, we performed differential analysis and multivariate clinical subgroup analysis for six candidate genes at both mRNA and protein levels. And each of the six candidate genes and their neighbouring genes with a mutation rate greater than 10% were also analysed by network construction and functional enrichment analysis. In the meanwhile, the survival analysis for platinum‐treated patients was performed in the current study. Finally, the RT‐qPCR assay was used to determine the performance of candidate genes in ovarian cancer platinum response. Taken together, this research demonstrated that comprehensive bioinformatics methods could help to understand the molecular mechanism of platinum response and provide new strategies for overcoming platinum resistance in ovarian cancer treatment.

Convergent molecular evolution among ash species resistant to the emerald ash borer.

Recent studies show that molecular convergence plays an unexpectedly common role in the evolution of convergent phenotypes. We exploited this phenomenon to find candidate loci underlying resistance to the emerald ash borer (EAB; Agrilus planipennis), the USA’s most costly invasive forest insect to date, within the pan-genome of ash trees (the genus Fraxinus). We show that EAB-resistant taxa occur within three independent phylogenetic lineages. In genomes from these resistant lineages, we detect 53 genes with evidence of convergent amino acid evolution. Gene tree reconstruction indicates that for 48 of these candidates, the convergent amino acids are more likely to have arisen via independent evolution than by another process, such as hybridisation or incomplete lineage sorting. Seven of the candidate genes have putative roles connected to the phenylpropanoid biosynthesis pathway and 17 relate to herbivore recognition, defence signalling or programmed cell death. Evidence for loss-of-function mutations among these candidates is more frequent in susceptible species, than in resistant ones. Our results on evolutionary relationships, variability in resistance, and candidate genes for defence response within the ash genus could inform breeding for EAB resistance, facilitating ecological restoration in areas this beetle has invaded.

Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

BackgroundCommon vetch (Vicia sativa L.) is an important self-pollinating annual forage legume and is of interest for drought prone regions as a protein source to feed livestock and human consumption. However, the development and production of common vetch are negatively affected by drought stress. Plants have evolved common or distinct metabolic pathways between the aboveground and underground in response to drought stress. Little is known regarding the coordinated response of aboveground and underground tissues of common vetch to drought stress.ResultsOur results showed that a total of 30,427 full-length transcripts were identified in 12 samples, with an average length of 2278.89 bp. Global transcriptional profiles of the above 12 samples were then analysed via Illumina-Seq. A total of 3464 and 3062 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Gene Ontology (GO) enrichment analyses identified that the dehydrin genes and Δ1-pyrroline-5-carboxylate synthase were induced for the biosynthesis of proline and water conservation. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that the DEGs were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism, and various drought response candidate genes were also identified. Abscisic acid (ABA; the AREB/ABF-SnRK2 pathway) regulates the activity of AMY3 and BAM1 to induce starch degradation in leaves and increase carbon export to roots, which may be associated with the drought stress responses in common vetch. Among the co-induced transcription factors (TFs), AREB/ABF, bHLH, MYB, WRKY, and AP2/ERF had divergent expression patterns and may be key in the crosstalk between leaves and roots during adaption to drought stress. In transgenic yeast, the overexpression of four TFs increased yeast tolerance to osmotic stresses.ConclusionThe multipronged approach identified in the leaves and roots broadens our understanding of the coordinated mechanisms of drought response in common vetch, and further provides targets to improve drought resistance through genetic engineering.

Transcriptome profiling of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies

Transcriptome profiling of drought responsive candidate genes in varieties of citrus rootstocks with different tolerance strategies

In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice.

Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.

Revision of the barley WRKY gene family phylogeny and expression analysis of the candidate genes in response to drought

The WRKY belongs to an important plant specific transcription factor families which are involved in response to various environmental stresses, as well as in growth and developmental processes. In the present report, a genome-wide identification and characterization of WRKY gene family in barley led to revision of HvWRKYs to 93 members. The phylogenetic tree was also reconstructed based on the full-length WRKY protein sequences in barley and Arabidopsis. HvWRKYs were classified into three major groups (I, II, and III) and group II was further divided to 5 subgroups (a to e). HvWRKYs were named after this classification. Interestingly, some specific motifs were discovered in subgroups IIa, IIb, and III. Analyzing the available microarray data revealed eight candidate WRKY genes which were up-regulated under drought and salinity stresses compared to the optimum conditions at seedling stage in barley. Expression profiles of these WRKY genes were validated by quantitative real-time PCR. All the investigated candidate genes (HvWRKY_IIc2, HvWRKY_III11, HvWRKY_IIb2, HvWRKY_IId4, HvWRKY_III23, HvWRKY_IIa5 and HvWRKY_IIc19) except for HvWRKY_I8 were significantly up-regulated by drought stress at the seedling stage in drought-tolerant genotype, indicating their role in drought tolerance. We hope the presented information would be helpful toward achieving drought tolerant cultivars through genetic engineering or molecular breeding.