Muhammad Waqas1, Muhammad Tehseen Azhar1, Iqrar Ahmad Rana2, Farrukh Azeem3, Muhammad Amjad Ali4, Muhammad Amjad Nawaz5, Gyuhwa Chung6, Rana Muhammad Atif7,8,9. 1. Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan. 2. Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan. 3. Department of Bioinformatics and Biotechnology, GC University, Faisalabad, Pakistan. 4. Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan. 5. Education Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation. 6. Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea. 7. Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan. dratif@uaf.edu.pk. 8. Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan. dratif@uaf.edu.pk. 9. Center for Advanced Studies in Agriculture & Food Security, University of Agriculture, Faisalabad, Pakistan. dratif@uaf.edu.pk.
Abstract
BACKGROUND: WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. OBJECTIVE: In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. METHODS: For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. RESULTS: We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways. CONCLUSION: This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.
BACKGROUND: WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. OBJECTIVE: In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. METHODS: For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. RESULTS: We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways. CONCLUSION: This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.