Vulgaris Genome Research Articles

Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.)

BackgroundSquamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.ResultsIn this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.ConclusionIn this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.

Genome-wide characterization of the glutathione S-transferase gene family in Phaseolus vulgaris reveals insight into the roles of their members in responses to multiple abiotic stresses

Glutathione S-transferases (GSTs) are a class of multifunctional enzymatic antioxidants that play a significant role in several aspects of plant physiology, including growth, development, and cellular protection from biotic and abiotic stressors. A total of 59 GST genes were found in Phaseolus vulgaris genome, which were categorized into 11 distinct classes according to their evolutionary connection and the existence of conserved structural domains and motifs. Gene duplication analysis revealed that the evolution of the members of the GST gene family in P. vulgaris was driven by both segmental and tandem duplication events. Analysis of the expression profiles of identified PvGST genes using the available transcriptome data demonstrated notable expression patterns and organ specificity of many genes throughout several developmental stages and under drought or salinity. Subsequent RT-qPCR analysis of several drought-responsive or salinity-responsive candidate genes showed that PvGSTF4 was up-regulated solely by drought, PvGSTU11 was up-regulated only by salinity, and PvGSTU3, PvGSTU12, PvGSTU13, PvGSTU14, PvGSTU16, PvGSTT1, and PvGSTZ2 were up-regulated by both salt and drought. The up-regulated PvGSTs under drought and/or salinity might enable P. vulgaris to adapt to stressful environments. These candidate genes could be explored in genetic engineering programs for development of stress-tolerant P. vulgaris varieties.

GATA transcription factor in common bean: A comprehensive genome-wide functional characterization, identification, and abiotic stress response evaluation

The GATA transcription factors (TFs) have been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance to abiotic stress has not yet been studied in the common bean. This study analyzed the functional identity of the GATA gene family in the P. vulgaris genome under different abiotic and phytohormonal stress. The GATA gene family was systematically investigated in the P. vulgaris genome, and 31 PvGATA TFs were identified. The study found that 18 out of 31 PvGATA genes had undergone duplication events, emphasizing the role of gene duplication in GATA gene expansion. All the PvGATA genes were classified into four significant subfamilies, with 8, 3, 6, and 13 members in each subfamily (subfamilies I, II, III, and IV), respectively. All PvGATA protein sequences contained a single GATA domain, but subfamily II members had additional domains such as CCT and tify. A total of 799 promoter cis-regulatory elements (CREs) were predicted in the PvGATAs. Additionally, we used qRT-PCR to investigate the expression profiles of five PvGATA genes in the common bean roots under abiotic conditions. The results suggest that PvGATA01/10/25/28 may play crucial roles in regulating plant resistance against salt and drought stress and may be involved in phytohormone-mediated stress signaling pathways. PvGATA28 was selected for overexpression and cloned into N. benthamiana using Agrobacterium-mediated transformation. Transgenic lines were subjected to abiotic stress, and results showed a significant tolerance of transgenic lines to stress conditions compared to wild-type counterparts. The seed germination assay suggested an extended dormancy of transgenic lines compared to wild-type lines. This study provides a comprehensive analysis of the PvGATA gene family, which can serve as a foundation for future research on the function of GATA TFs in abiotic stress tolerance in common bean plants.

Genome-wide characterization of the GPAT gene family in bean (Phaseolus vulgaris L.) and expression analysis under abiotic stress and melatonin

AbstractGPAT (sn-Glycerol-3-phosphate-1-O-acyltransferase) is a key enzyme in the biosynthesis of membrane lipids. Two kinds of GPATs are involved in the production of glycerolipids. While sn-1-GPATs are responsible for creating lysophosphatidic acid, sn-2-GPATs generate monoacylglycerol. GPAT genes of beans (Phaseolus vulgaris) have never been investigated before. This study aimed to assess the expression profiles of GPAT genes in common bean leaves under drought and salt stress and apply bioinformatics tools to the genome-wide analysis of GPAT gene family members. In the P. vulgaris genome, PvGPAT genes with molecular weights ranging from 50.2 to 60.4 kDa, amino acid counts ranging from 376 to 539, theoretical isoelectric points ranging from 8.41 to 9.46, and instability indices ranging from 31.84 to 51.38 were found. Based on the gene structure analysis, the expected number of exons and introns was between 2 and 12. The GPAT proteins from Arabidopsis thaliana, Glycine max, Vitis vinifera, Cicer arietinum, Lens culinaris, and P. vulgaris were analyzed phylogenetically. GPAT proteins of G. max and A. thaliana are evolutionarily related to those of beans. The PvGPAT4/PvGPAT10 and PvGPAT7/PvGPAT12 gene pairs were detected to be segmentally duplicated. In this work, qRT-PCR was performed on six PvGPAT genes, and the effects of salt, drought, and melatonin treatments on bean GPAT genes were studied. The role of melatonin in the response to salt and drought stress was investigated at the gene expression level. The findings of the present study will shed light on GPAT gene family members in beans and provide insight for future functional research.

Genome-wide identification and comparative analysis of the Amino Acid Transporter (AAT) gene family and their roles during Phaseolus vulgaris symbioses

Amino acid transporters (AATs) are essential integral membrane proteins that serve multiple roles, such as facilitating the transport of amino acids across cell membranes. They play a crucial role in the growth and development of plants. Phaseolus vulgaris, a significant legume crop, serves as a valuable model for studying root symbiosis. In this study, we have conducted an exploration of the AAT gene family in P. vulgaris. In this research, we identified 84 AAT genes within the P. vulgaris genome sequence and categorized them into 12 subfamilies based on their similarity and phylogenetic relationships with AATs found in Arabidopsis and rice. Interestingly, these AAT genes were not evenly distributed across the chromosomes of P. vulgaris . Instead, there was an unusual concentration of these genes located toward the outer edges of chromosomal arms. Upon conducting motif analysis and gene structural analysis, we observed a consistent presence of similar motifs and an intron-exon distribution pattern among the subfamilies. When we analyzed the expression profiles of PvAAT genes, we noted tissue-specific expression patterns. Furthermore, our investigation into AAT gene expression under rhizobial and mycorrhizal symbiotic conditions revealed that certain genes exhibited high levels of expression. Specifically, ATLa5 and LHT2 was notably upregulated under both symbiotic conditions. These findings point towards a potential role of AATs in the context of rhizobial and mycorrhizal symbiosis in P. vulgaris, in addition to their well-established regulatory functions.

Genome-wide Analysis and Functional Identification of KCS Gene Family under Drought and Salt Stresses in Phaseolus vulgaris L

β-ketoacyl-CoA synthase (KCS) is an important enzyme that catalyzes the biosynthesis of very-long-chain fatty acids (VLCFAs). In this study, the genome-wide analysis and functional characterization of the KCS gene family members in common bean (Phaseolus vulgaris L.) plants were conducted, and the response of the identified gene family to abiotic stresses was evaluated. In this study, 19 KCS genes were identified and characterized in the P. vulgaris genome. The molecular weights of these KCS proteins ranged from 49.14 kDa to 60.57 kDa, their amino acid lengths varied from 437 to 534, and their pI values ranged from 8.81 to 9.47, indicating a basic nature. Segmental and tandem duplications were observed in the Pvul-KCS gene family. Phylogenetic analysis revealed that Pvul-KCS proteins clustered into three main groups with Arabidopsis thaliana and Glycine max species. Comparative mapping analysis was also conducted with A. thaliana and G. max. Expression profile comparisons indicated that these genes had different expression levels in common bean varieties and played a role in the plant’s response to biotic and abiotic stresses. This study provides important insights into the biological functions of KCS genes in Phaseolus vulgaris and offers valuable information for improving drought and salt stress tolerance in common beans.

CRK12: A Key Player in Regulating the Phaseolus vulgaris-Rhizobium tropici Symbiotic Interaction.

Cysteine-rich receptor-like kinases (CRKs) are a type of receptor-like kinases (RLKs) that are important for pathogen resistance, extracellular reactive oxygen species (ROS) signaling, and programmed cell death in plants. In a previous study, we identified 46 CRK family members in the Phaseolus vulgaris genome and found that CRK12 was highly upregulated under root nodule symbiotic conditions. To better understand the role of CRK12 in the Phaseolus-Rhizobia symbiotic interaction, we functionally characterized this gene by overexpressing (CRK12-OE) and silencing (CRK12-RNAi) it in a P. vulgaris hairy root system. We found that the constitutive expression of CRK12 led to an increase in root hair length and the expression of root hair regulatory genes, while silencing the gene had the opposite effect. During symbiosis, CRK12-RNAi resulted in a significant reduction in nodule numbers, while CRK12-OE roots showed a dramatic increase in rhizobial infection threads and the number of nodules. Nodule cross sections revealed that silenced nodules had very few infected cells, while CRK12-OE nodules had enlarged infected cells, whose numbers had increased compared to controls. As expected, CRK12-RNAi negatively affected nitrogen fixation, while CRK12-OE nodules fixed 1.5 times more nitrogen than controls. Expression levels of genes involved in symbiosis and ROS signaling, as well as nitrogen export genes, supported the nodule phenotypes. Moreover, nodule senescence was prolonged in CRK12-overexpressing roots. Subcellular localization assays showed that the PvCRK12 protein localized to the plasma membrane, and the spatiotemporal expression patterns of the CRK12-promoter::GUS-GFP analysis revealed a symbiosis-specific expression of CRK12 during the early stages of rhizobial infection and in the development of nodules. Our findings suggest that CRK12, a membrane RLK, is a novel regulator of Phaseolus vulgaris-Rhizobium tropici symbiosis.

Chromosome-level genome assembly of Hydractinia symbiolongicarpus.

Hydractinia symbiolongicarpus is a pioneering model organism for stem cell biology, being one of only a few animals with adult pluripotent stem cells (known as i-cells). However, the unavailability of a chromosome-level genome assembly has hindered a comprehensive understanding of global gene regulatory mechanisms underlying the function and evolution of i-cells. Here, we report the first chromosome-level genome assembly of H. symbiolongicarpus (HSymV2.0) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The final assembly is 483 Mb in total length with 15 chromosomes representing 99.8% of the assembly. Repetitive sequences were found to account for 296 Mb (61%) of the total genome; we provide evidence for at least two periods of repeat expansion in the past. A total of 25,825 protein-coding genes were predicted in this assembly, which include 93.1% of the metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) gene set. 92.8% (23,971 genes) of the predicted proteins were functionally annotated. The H. symbiolongicarpus genome showed a high degree of macrosynteny conservation with the Hydra vulgaris genome. This chromosome-level genome assembly of H. symbiolongicarpus will be an invaluable resource for the research community that enhances broad biological studies on this unique model organism.

Genome-Wide Analysis and Characterization of the PIF Gene Family Under Salt and Drought Stress in Common Beans (Phaseolus vulgaris L.)

The purpose of this study was to identify and describe members of the phytochrome-interacting factors (PIFs) gene family including the basic helix loop helix (bHLH) binding site in Phaseolus vulgaris plants, as well as to investigate their responses to salt and drought stress. Various tools of in silico approaches were used to identify five Pvul-PIF gene families in the P. vulgaris genome. This gene family contained 324 to 726 amino acids and has molecular weights ranging from 35.11 kDa to 77.67 kDa. The theoretical isoelectric points range from 6.03 (Pvul-PIF-3.3) to 8.30 (Pvul-PIF-3.2). Pvul-PIF proteins were shown to be clustered in three main groups with Arabidopsis thaliana, Populus trichocarpa, Solanum lycopersicum, Zea mays, Arachis hypogaea L., Oryza sativa, Vitis vinifera, Glycine max, and Phaseolus vulgaris species as a result of the phylogenetic study. Segmental duplication was detected between Pvul-PIF-3.2, Pvul-PIF-3.3 and Pvul-PIF-3.1 genes, Pvul-PIF-4.1 and Pvul-PIF-4.2 genes and Pvul-PIF-3.3 and Pvul-PIF-3.1 genes. When the expression patterns of the Pvul-PIF genes were examined, it was observed that they had different levels of expression under salt and drought stress and that they may be involved in specific biological and molecular processes in response to different abiotic and biotic stresses. The results of this research, which were established for the first time in response to salt and drought stress in P. vulgaris of the PIF gene family, will be a valuable source of knowledge and additional information in the fields of plant biotechnology, agricultural biotechnology, and molecular biology.

Phenotypic, Anatomical, and Diel Variation in Sugar Concentration Linked to Cell Wall Invertases in Common Bean Pod Racemes under Water Restriction.

The common bean (Phaseolus vulgaris L.) pod wall is essential for seed formation and to protect seeds. To address the effect of water restriction on sugar metabolism in fruits differing in sink strength under light–dark cycles, we used plants of cv. OTI at 100% field capacity (FC) and at 50% FC over 10 days at the beginning of pod filling. Water restriction intensified the symptoms of leaf senescence. However, pods maintained a green color for several days longer than leaves did. In addition, the functionality of pods of the same raceme was anatomically demonstrated, and no differences were observed between water regimes. The glucose and starch concentrations were lower than those of sucrose, independent of pod wall size. Remarkably, the fructose concentration decreased only under water restriction. The cell wall invertase activity was twofold higher in the walls of small pods than in those of large ones in both water regimes; similar differences were not evident for cytosolic or vacuolar invertase. Using bioinformatics tools, six sequences of invertase genes were identified in the P. vulgaris genome. The PvINVCW4 protein sequence contains substitutions for conserved residues in the sucrose-binding site, while qPCR showed that transcript levels were induced in the walls of small pods under stress. The findings support a promising strategy for addressing sink strength under water restriction.

Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (Phaseolus vulgaris L.).

The hard-to-cook defect in common beans is dictated by the ability to achieve cell separation during cooking. Hydrolysis of pectin methyl-esters by the pectin methyl-esterase (PME) enzyme influences cell separation. However, the contributions of the PME enzyme and the cell wall to the hard-to-cook defect have not been studied using molecular tools. We compared relevant molecular processes in fast- and slow-cooking bean varieties to understand the mechanisms underpinning the hard-to-cook defect. A PME spectrophotometric assay showed minor differences in enzyme activity between varieties. Meanwhile, a PME HMMER search in the P. vulgaris genome unveiled 113 genes encoding PMEs and PME inhibitors (PMEIs). Through RNA sequencing, we compared the gene expression of the PME-related genes in both varieties during seed development. A PME (Phvul010g080300) and PMEI gene (Phvul005g007600) showed the highest expression in the fast- and slow-cooking beans, respectively. We further identified 2132 differentially expressed genes (DEGs). Genes encoding cell-wall-related enzymes, mainly glycosylphosphatidylinositol mannosyltransferase, xyloglucan O-acetyltransferase, pectinesterase, and callose synthase, ranked among the top DEGs, indicating novel relations to the hard-to-cook defect. Gene ontology mapping revealed hydrolase activity and protein phosphorylation as functional categories with the most abundant upregulated DEGs in the slow-cooking bean. Additionally, the cell periphery contained 8% of the DEGs upregulated in the slow-cooking bean. This study provides new insights into the role of pectin methyl-esterase-related genes and novel cell wall processes in the occurrence of the hard-to-cook defect.

The state of Medusozoa genomics: current evidence and future challenges.

Medusozoa is a widely distributed ancient lineage that harbors one-third of Cnidaria diversity divided into 4 classes. This clade is characterized by the succession of stages and modes of reproduction during metagenic lifecycles, and includes some of the most plastic body plans and life cycles among animals. The characterization of traditional genomic features, such as chromosome numbers and genome sizes, was rather overlooked in Medusozoa and many evolutionary questions still remain unanswered. Modern genomic DNA sequencing in this group started in 2010 with the publication of the Hydra vulgaris genome and has experienced an exponential increase in the past 3 years. Therefore, an update of the state of Medusozoa genomics is warranted. We reviewed different sources of evidence, including cytogenetic records and high-throughput sequencing projects. We focused on 4 main topics that would be relevant for the broad Cnidaria research community: (i) taxonomic coverage of genomic information; (ii) continuity, quality, and completeness of high-throughput sequencing datasets; (iii) overview of the Medusozoa specific research questions approached with genomics; and (iv) the accessibility of data and metadata. We highlight a lack of standardization in genomic projects and their reports, and reinforce a series of recommendations to enhance future collaborative research.

Comparative genomic identification and characterization of npcRNA homologs in Proteus vulgaris

Proteus vulgaris is a rod-shaped Gram-negative bacterium known to be the member of Enterobacteriaceae that is able to cause disease in human being. Generally, non-protein-coding RNAs (npcRNAs) do not code for proteins, but they play a vital role in gene regulation at the RNA level including pathogenicity. The present study aims at elucidating homologous npcRNAs from other bacteria in Proteus vulgaris. A comparative genomic analysis was carried out to identify npcRNA homolog of other Enterobacteriaceae pathogens in Proteus vulgaris. A total of 231 npcRNAs previously reported in Salmonella typhi, Salmonella typhimurium and Escherichia coli were screened using BLASTn tool against Proteus vulgaris genome. Interestingly, 33 npcRNAs are homologs to Proteus vulgaris. Northern blot analysis of 6 out of 33 npcRNA candidates confirmed their expression and showed that most of them are differentially expressed during lag, exponential and stationary growth phases. This study is the first approach of identification and characterization of npcRNAs in P. vulgaris. Hence, this could be a pioneer study to further validate the regulatory functions of these npcRNAs to fill the gaps in understanding of the pathogenicity of P. vulgaris.

Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris.

The online version contains supplementary material available at 10.1007/s12298-021-01052-9.

Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris).

Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.

Identification and Characterization of SRS Genes in Phaseolus vulgaris Genome and Their Responses Under Salt Stress.

SHI-Related Sequence (SRS) transcription factors comprise a protein family with important roles in growth and development. However, the genome-wide study of the SRS protein family has not yet been carried out in the common bean. For this reason, the SRS family has been characterized in depth at both gene and protein levels and several bioinformatics methods have been used. As a result, 10 SRS genes have been identified and their proteins have been phylogenetically categorized into three major groups within the common bean. By investigating duplications that play a major role in the development of gene families, 19 duplication events have been identified in the SRS family (18 segmental and 1 tandem). In addition, using available RNAseq data, comparative expression analysis of Pvul-SRS genes was performed and expression changes in Pvul-SRS-1, 2, 4, 6, 7, and 10 genes were observed under both salt and drought stress. Five Pvul-SRS genes were selected based on RNAseq data (Pvul-SRS-1, 2, 4, 6, and 10) and screened with RT-qPCR in two common bean cultivars (Yakutiye 'salt-resistant' and Zulbiye 'salt-susceptible' cv.). These genes also showed different levels of expression between two common bean cultivars under salt stress conditions and this may explain the responses of Pvul-SRS genes against abiotic stress. In summary, this work is the first study in which in silico identification and characterization of Pvul-SRS genes have been examined at gene expression level. The results could therefore provide the basis for future studies of functional characterization of Pvul-SRS genes.

Impact of transposable elements on genome size variation between two closely related crustacean species

Identifying and quantifying genome size variation among species and understanding the underlying causes is a long-standing objective in evolutionary biology. Here, we investigated the basis of genome size variation between two closely related species of terrestrial isopods: Armadillidium vulgare and Armadillidium nasatum. The two species diverged 25 million years ago and the A. vulgare genome is ~500 megabases larger than the A. nasatum genome (1.7 vs. 1.2 gigabases, respectively). Our analyses indicated that genome size difference is essentially attributed to transposable elements (TEs). We found that the deletion rate may be slightly higher in A. nasatum than in A. vulgare, but it is unlikely to explain the observed genome size difference. As the two genomes largely share the same TE families, differential transpositional activity also contributes to the observed variation. Analyses of TE expression suggested that the cumulative expression level of all expressed TEs was higher in A. nasatum than in A. vulgare. Assuming TE expression level is a good proxy for TE transpositional activity, our results suggest that the two species may have recently been experiencing different TE transposition dynamics. Overall, our results illustrate the important impact TEs can have on genome structure and evolution between closely related species.

Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States.

Tamarix spp. (saltcedar) were introduced from Asia to the southern United States as windbreak and ornamental plants and have spread into natural areas. This study determined differential gene expression responses to water deficit (WD) in seedlings of T. chinensis and T. ramosissima from established invasive stands in New Mexico and Montana, respectively. A reference de novo transcriptome was developed using RNA sequences from WD and well-watered samples. Blast2GO analysis of the resulting 271,872 transcripts yielded 89,389 homologs. The reference Tamarix (Tamaricaceae, Carophyllales order) transcriptome showed homology with 14,247 predicted genes of the Beta vulgaris subsp. vulgaris (Amaranthaceae, Carophyllales order) genome assembly. T. ramosissima took longer to show water stress symptoms than T. chinensis. There were 2068 and 669 differentially expressed genes (DEG) in T. chinensis and T. ramosissima, respectively; 332 were DEG in common between the two species. Network analysis showed large biological process networks of similar gene content for each of the species under water deficit. Two distinct molecular function gene ontology networks (binding and transcription factor-related) encompassing multiple up-regulated transcription factors (MYB, NAC, and WRKY) and a cellular components network containing many down-regulated photosynthesis-related genes were identified in T. chinensis, in contrast to one small molecular function network in T. ramosissima.

Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm

BackgroundCommon bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits.ResultsWe conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland).ConclusionsThis study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.

Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments.

The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs.