Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

Abstract

Rice bran, a by-product after milling, is a rich source of phytonutrients like oryzanols, tocopherols, tocotrienols, phytosterols, and dietary fibers. Moreover, exceptional properties of the rice bran oil make it unparalleled to other vegetable oils. However, a lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) causes rancidity and 'stale flavor' in the oil, and thus limits the rice bran usage for human consumption. To improve the rice bran quality, sequence based allele mining at OsPLDα1 locus (3.6 Kb) was performed across 48 accessions representing 11 wild Oryza species, 8 accessions of African cultivated rice, and 7 Oryza sativa cultivars. From comparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDα1 locus. Phylogenetic analysis revealed 20 OsPLDα1 cDNA variants which further translated into 12 protein variants. The O. officinalis protein variant, when compared to Nipponbare, showed maximum variability comprising 22 amino acid substitutions and absence of two peptides and two β-sheets. Further, expression profiling indicated significant differences in transcript abundance within as well as between the OsPLDα1 variants. Also, a new OsPLDα1 transcript variant having third exon missing in it, Os01t0172400-06, has been revealed. An O. officinalis accession (IRGC101152) had lowest gene expression which suggests the presence of novel allele, named as OsPLDα1-1a (GenBank accession no. MF966931). The identified novel allele could be further deployed in the breeding programs to overcome rice bran rancidity in elite cultivars.

Overexpression of OsNAR2.1 by OsNAR2.1 promoter increases drought resistance by increasing the expression of OsPLDα1 in rice

“…Rice PLD mediates the production of signaling molecules phosphatidic acid (Phosphatidic acid, PA) through hydrolyzing phospholipids, resulting in the reorganization of components of biochemical membranes. Studies in Arabidopsis and rice indicate that PLD is involved in lipid metabolism and signal transduction processes in plants under various stress conditions, with significant biological effects [ 62 ].…”

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

“…In pearl millet, the presence of PLD-alpha1 members is also notably higher, with a total of three (PgPLD-alpha1-1, PgPLD-alpha1-5, and PgPLD-alpha1-7) in contrast to rice which has only one (OsPLD-alpha1, Os01t0172400 ). It is also important to note that rice also undergoes rancidity in bran mediated by OsPLD-alpha1 [ 58 ]. The protein alignment analysis of OsPLD-alpha1 with PgPLD isoforms showed the highest resemblance with PgPLD-alpha1-1 and PgPLD-alpha1-5 proteins.…”

Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza

“…These accessions were initially procured from International Rice Research Institute (IRRI), Philippines and National Rice Research Institute (NRRI), Cuttack, India and are being actively maintained at Punjab Agricultural University, Ludhiana. Standard agronomic practices were followed to raise the crop, as reported previously 51 . Voucher specimens for all accessions used currently have been deposited in the herbarium of National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India.…”

“…The Wizard® SV PCR Clean-Up System (Promega, USA) as per the manufacturer’s protocol was followed to purify the DNA fragments from remaining 25 μl PCR product. The nucleotide sequence information of the PCR products was generated as described previously 51 .…”