Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)

Mondal, T K and Maheshwari, P and Kummari, D and Palakolanu, S R and Nagasai Tejaswi, U. and Nagaraju, M. and Rajasheker, G. and Jawahar, G. and Jalaja, N. and Rathnagiri, P. and Kavi Kishor, P. B. (2019) Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench). PLOS ONE (TSI), 14 (9). pp. 1-27. ISSN 1932-6203

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Abstract

Members of the plant Heme Activator Protein (HAP) or NUCLEAR FACTOR Y (NF-Y) are trimeric transcription factor complexes composed of the NF-YA, NF-YB and NF-YC subfamilies. They bind to the CCAAT box in the promoter regions of the target genes and regulate gene expressions. Plant NF-Ys were reported to be involved in adaptation to several abiotic stresses as well as in development. In silico analysis of Sorghum bicolor genome resulted in the identification of a total of 42 NF-Y genes, among which 8 code for the SbNF-YA, 19 for SbNF-YB and 15 for the SbNF-YC subunits. Analysis was also performed to characterize gene structures, chromosomal distribution, duplication status, protein subcellular localizations, conserved motifs, ancestral protein sequences, miRNAs and phylogenetic tree construction. Phylogenetic relationships and ortholog predictions displayed that sorghum has additional NF-YB genes with unknown functions in comparison with Arabidopsis. Analysis of promoters revealed that they harbour many stress-related cis-elements like ABRE and HSE, but surprisingly, DRE and MYB elements were not detected in any of the subfamilies. SbNF-YA1, 2, and 6 were found upregulated under 200 mM salt and 200 mM mannitol stresses. While NF-YA7 appeared associated with high temperature (40˚C) stress, NF-YA8 was triggered by both cold (4˚C) and high temperature stresses. Among NF-YB genes, 7, 12, 15, and 16 were induced under multiple stress conditions such as salt, mannitol, ABA, cold and high temperatures. Likewise, NF-YC 6, 11, 12, 14, and 15 were enhanced significantly in a tissue specific manner under multiple abiotic stress conditions. Majority of the mannitol (drought)-inducible genes were also induced by salt, high temperature stresses and ABA. Few of the high temperature stress-induced genes are also induced by cold stress (NF-YA2, 4, 6, 8, NF-YB2, 7, 10, 11, 12, 14, 16, 17, NF-YC4, 6, 12, and 13) thus suggesting a cross talk among them. This work paves the way for investigating the roles of diverse sorghum NF-Y proteins during abiotic stress responses and provides an insight into the evolution of diverse NF-Y members.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Sorghum
Subjects:	Mandate crops > Sorghum Others > Genetics and Genomics
Depositing User:	Mr Arun S
Date Deposited:	14 Feb 2020 08:38
Last Modified:	14 Feb 2020 08:38
URI:	http://oar.icrisat.org/id/eprint/11374
Official URL:	https://doi.org/10.1371/journal.pone.0222203
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	PBK is thankful to the CSIR, New Delhi for providing Research Grant and CSIR-Emeritus Fellowship. Maheshwari acknowledges the financial support from the CSIR, New Delhi, for Research Associateship. Jawahar acknowledges the financial support from UGC, New Delhi. RG acknowledges the financial support from DST-SERB, New Delhi. We thank Dr. Prashanth Suravajhala, BISR, Jaipur for his critical comments.
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