scholarly journals Genome-wide in silico identification, characterization and transcriptional analysis of the family of growth-regulating factors in common bean (Phaseolus vulgaris L.) subjected to polyethylene glycol-induced drought stress

2017 ◽  
Vol 69 (1) ◽  
pp. 5-14 ◽  
Author(s):  
İlker Büyük ◽  
Sümer Aras
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
In Silico ◽  
Expression Patterns ◽  
Transcriptional Analysis ◽  
Genome Wide ◽  
The Common ◽  
Root Tissues

According to most recent findings, growth regulating factors (GRFs) are plant-specific transcription factors (TFs) that play important roles in many processes, including abiotic and biotic stress response mechanisms. Completion of the common bean (Phaseolus vulgaris) genome project has provided researchers with the opportunity to identify all GRF genes in this species. With this aim, a genome-wide in silico study was performed and 10 GRF proteins (called PhvGRFs) were identified in the common bean genome. Conserved and mandatory motifs (QLQ and WRC) were confirmed in all identified PhvGRFs and two segmental duplication events were determined. Most of the PhvGRFs were found to be more similar to Arabidopsis thaliana GRFs than to Zea mays GRFs in a phylogenetic tree. According to the expression analysis of 10 PhvGRFs, inversely related expression patterns were observed in the roots of Yakutiye and Zulbiye cultivars based on their capacity to adopt to drought stress. After drought treatment of the Zulbiye cultivar, a drought-sensitive common bean cultivar, PhvGRF1, PhvGRF2, PhvGRF3, PhvGRF5, PhvGRF6, PhvGRF9 and PhvGRF10 genes were upregulated 2- to 4-fold in root tissues, as compared to the untreated control. The trend of PhvGRF1, PhvGRF2, PhvGRF3, PhvGRF5, PhvGRF6, PhvGRF7, PhvGRF9 and PhvGRF10 genes showed a consistent decline of 2- to 6-fold in root tissues of the drought-tolerant Yakutiye cultivar subjected to 24 h of drought stress. We demonstrated that the expression patterns of the identified PhvGRFs correlated with the drought-stress response in a cultivar-specific manner in the common bean. We suggest that members of the GRF family can also be used for genetic engineering applications in the common bean.

scholarly journals Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sadhana Singh ◽  
Himabindu Kudapa ◽  
Vanika Garg ◽  
Rajeev K. Varshney
Keyword(s):  
Drought Stress ◽  
Candidate Genes ◽  
Developmental Stages ◽  
Biological Activities ◽  
Expression Patterns ◽  
Genome Wide ◽  
Legume Crops ◽  
Root Tissues ◽  
Semi Arid ◽  
Comprehensive Study

Abstract Background Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. Results In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.)

Genomics ◽  
2020 ◽  
Vol 112 (6) ◽  
pp. 4536-4546
Author(s):  
Semih Erdogmus ◽  
Duygu Ates ◽  
Seda Nemli ◽  
Bulent Yagmur ◽  
Tansel Kaygisiz Asciogul ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Phaseolus Vulgaris L ◽  
Genome Wide ◽  
The Common

scholarly journals Differential proteomic analysis of drought stress response in leaves of common bean (Phaseolus vulgaris L.)

2013 ◽  
Vol 78 ◽  
pp. 254-272 ◽  
Author(s):  
Tanja Zadražnik ◽  
Kristin Hollung ◽  
Wolfgang Egge-Jacobsen ◽  
Vladimir Meglič ◽  
Jelka Šuštar-Vozlič
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Proteomic Analysis ◽  
Phaseolus Vulgaris L

Genome-wide in silico analysis of SOD genes in common bean (Phaseolus vulgaris L.)

2020 ◽  
Vol 23 (3) ◽  
pp. 241-251
Author(s):  
Silviany Angelica Fernandes Silva ◽  
Fláive Loyze Baldassarini Silva ◽  
Alessandra Ferreira Ribas ◽  
Silvia Graciele Hülse de Souza ◽  
Tiago Benedito dos Santos
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
In Silico ◽  
In Silico Analysis ◽  
Phaseolus Vulgaris L ◽  
Genome Wide ◽  
Silico Analysis

scholarly journals Drought Stress Response in Agricultural Plants: A Case Study of Common Bean (Phaseolus vulgaris L.)

2020 ◽  
Author(s):  
Aleš Sedlar ◽  
Marjetka Kidrič ◽  
Jelka Šuštar-Vozlič ◽  
Barbara Pipan ◽  
Tanja Zadražnik ◽  
...  
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Phaseolus Vulgaris L ◽  
Agricultural Plants

scholarly journals Genetic characterization at the species and symbiovar level of indigenous rhizobial isolates nodulating Phaseolus vulgaris in Greece

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Evdoxia Efstathiadou ◽  
Georgia Ntatsi ◽  
Dimitrios Savvas ◽  
Anastasia P. Tampakaki
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Phylogenetic Affiliation ◽  
Rhizobial Inoculation ◽  
Rhizobial Species ◽  
The Common ◽  
First Time ◽  
Of Greece ◽  
Rhizobial Isolates

AbstractPhaseolus vulgaris (L.), commonly known as bean or common bean, is considered a promiscuous legume host since it forms nodules with diverse rhizobial species and symbiovars. Most of the common bean nodulating rhizobia are mainly affiliated to the genus Rhizobium, though strains belonging to Ensifer, Pararhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia have also been reported. This is the first report on the characterization of bean-nodulating rhizobia at the species and symbiovar level in Greece. The goals of this research were to isolate and characterize rhizobia nodulating local common bean genotypes grown in five different edaphoclimatic regions of Greece with no rhizobial inoculation history. The genetic diversity of the rhizobial isolates was assessed by BOX-PCR and the phylogenetic affiliation was assessed by multilocus sequence analysis (MLSA) of housekeeping and symbiosis-related genes. A total of fifty fast-growing rhizobial strains were isolated and representative isolates with distinct BOX-PCR fingerpriniting patterns were subjected to phylogenetic analysis. The strains were closely related to R. anhuiense, R. azibense, R. hidalgonense, R. sophoriradicis, and to a putative new genospecies which is provisionally named as Rhizobium sp. I. Most strains belonged to symbiovar phaseoli carrying the α-, γ-a and γ-b alleles of nodC gene, while some of them belonged to symbiovar gallicum. To the best of our knowledge, it is the first time that strains assigned to R. sophoriradicis and harbored the γ-b allele were found in European soils. All strains were able to re-nodulate their original host, indicating that they are true microsymbionts of common bean.

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