Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits

Moin, M and Bommineni, P R and Tyagi, W (2024) Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits. BMC Genomics (TSI), 25. pp. 1-23. ISSN 1471-2164

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Abstract

Background Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented. Results In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and nonmetal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet. Conclusions The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.

Item Type:	Article
Divisions:	Global Research Program - Accelerated Crop Improvement
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Pearl millet, Phospholipases, PLD, Grain quality, Rancidity
Subjects:	Mandate crops > Millets > Pearl Millet
Depositing User:	Mr Nagaraju T
Date Deposited:	12 Aug 2024 04:05
Last Modified:	12 Aug 2024 04:05
URI:	http://oar.icrisat.org/id/eprint/12778
Official URL:	https://link.springer.com/article/10.1186/s12864-0...
Projects:	UNSPECIFIED
Funders:	Novo Nordisk Foundation
Acknowledgement:	The authors express their gratitude to Dr Shashi Kumar Gupta, the pearl millet breeder at ICRISAT for generously supplying the pearl millet (ICMB-863 and ICMB-95222) seeds required for generating expression data. Ms A Tejaswi is acknowledged for her valuable assistance in generating synteny plots. Mr N Kedarinath is acknowledged for maintaining pearl millet plants and collecting tissue samples. The authors also express their gratitude towards Dr P Sudhakar and Dr K Yogendra for their inputs in experimental design. All the authors have read and approved the manuscript.
Links:	Google Scholar

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