Novel Cis-acting Regulatory Elements in Wild Oryza Species Impart Improved Rice Bran Quality by Lowering the Expression of Phospholipase D Alpha1 Enzyme (OsPLDα1)

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2019 Oct 24

PMID 31642040

Citations 3

Authors

Amandeep Kaur

Kumari Neelam

Ai Kitazumi

Karminderbir Kaur

Priti Sharma

Gurjit Singh Mangat

Benildo G de Los Reyes

Darshan Singh Brar

Kuldeep Singh

Affiliations

Soon will be listed here.

Abstract

Rice bran oil is good quality edible oil, rich in antioxidants and comprised typically of oleic-linoleic type fatty acids. However, presence of a highly lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) increases free fatty acid content in the oil which further leads to stale flavor and rancidity of the oil, making it unfit for human consumption. In this study, we compared the upstream regions of OsPLDα1 orthologs across 34 accessions representing 5 wild Oryza species and 8 cultivars, to uncover sequence variations and identify cis-elements involved in differential transcription of orthologs. Alignment of the upstream sequences to the Nipponbare OsPLDα1 reference sequence revealed the presence of 39 SNPs. Phylogenetic analysis showed that all the selected cultivars and wild species accessions are closely related to the reference except for three accessions of O. rufipogon (IRGC89224, IRGC104425, and IRGC105902). Furthermore, using exon-specific qRT-PCR, OsPLDα1 expression patterns in immature grains indicated significant differences in transcript abundance between the wild species accessions. In comparison to the control, lowest gene expression was observed in IRGC89224 accession (0.20-fold) followed by IRGC105902 (0.26-fold) and IRGC104425 (0.41-fold) accessions. In-silico analysis of the OsPLDα1 promoter revealed that the copy number variations of CGCGBOXAT, GT1CONSENSUS, IBOXCORE, NODCON2GM, OSE2ROOTNODULE, SURECOREATSULTR11, and SORLIP1AT cis-elements play an important role in the transcriptional activities of orthologous genes. Owing to the presence of ARFAT and SEBF elements only in the IRGC89224 accession, which had the lowest gene expression as well, these putative upstream regulatory sequences have been identified as novel cis-elements which may act as repressors in regulating the OsPLDα1 gene expression. The accessions identified with low OsPLDα1 expressions could be further deployed as potential donors of ideal OsPLDα1 allele for transfer of the desired trait into elite rice cultivars.

Citing Articles

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

Kaur K, Neelam K, Singh J, Malik P, Singh K Sci Rep. 2023; 13(1):830.

PMID: 36646847 PMC: 9842635. DOI: 10.1038/s41598-023-28053-w.

Targeting -Regulatory Elements for Rice Grain Quality Improvement.

Ding Y, Zhu J, Zhao D, Liu Q, Yang Q, Zhang T Front Plant Sci. 2021; 12:705834.

PMID: 34456947 PMC: 8385297. DOI: 10.3389/fpls.2021.705834.

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

Kaur A, Neelam K, Kaur K, Kitazumi A, de Los Reyes B, Singh K Sci Rep. 2020; 10(1):6571.

PMID: 32313086 PMC: 7170842. DOI: 10.1038/s41598-020-62649-w.

References

Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q . Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet. 2008; 40(11):1370-4. DOI: 10.1038/ng.220. View

Brar D, Khush G . Alien introgression in rice. Plant Mol Biol. 1997; 35(1-2):35-47. View

Schmittgen T, Livak K . Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008; 3(6):1101-8. DOI: 10.1038/nprot.2008.73. View

Rosas U, Mei Y, Xie Q, Banta J, Zhou R, Seufferheld G . Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS. Nat Commun. 2014; 5:3651. PMC: 3997802. DOI: 10.1038/ncomms4651. View

Kieffer M, Neve J, Kepinski S . Defining auxin response contexts in plant development. Curr Opin Plant Biol. 2009; 13(1):12-20. DOI: 10.1016/j.pbi.2009.10.006. View

Thomson M, Edwards J, Septiningsih E, Harrington S, McCouch S . Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics. 2006; 172(4):2501-14. PMC: 1456415. DOI: 10.1534/genetics.105.050500. View

Feussner I, Wasternack C . The lipoxygenase pathway. Annu Rev Plant Biol. 2002; 53:275-97. DOI: 10.1146/annurev.arplant.53.100301.135248. View

Pappan K, Qin W, Dyer J, Zheng L, Wang X . Molecular cloning and functional analysis of polyphosphoinositide-dependent phospholipase D, PLDbeta, from Arabidopsis. J Biol Chem. 1997; 272(11):7055-61. DOI: 10.1074/jbc.272.11.7055. View

Civan P, Craig H, Cox C, Brown T . Three geographically separate domestications of Asian rice. Nat Plants. 2016; 1:15164. PMC: 4900444. DOI: 10.1038/nplants.2015.164. View

10.

Venter M, Botha F . Promoter analysis and transcription profiling: Integration of genetic data enhances understanding of gene expression. Physiol Plant. 2004; 120(1):74-83. DOI: 10.1111/j.0031-9317.2004.0209.x. View

11.

Li G, Xue H . Arabidopsis PLDzeta2 regulates vesicle trafficking and is required for auxin response. Plant Cell. 2007; 19(1):281-95. PMC: 1820954. DOI: 10.1105/tpc.106.041426. View

12.

Shamloo-Dashtpagerdi R, Razi H, Aliakbari M, Lindlof A, Ebrahimi M, Ebrahimie E . A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis. J Theor Biol. 2014; 364:364-76. DOI: 10.1016/j.jtbi.2014.09.038. View

13.

McGee J, Roe J, Sweat T, Wang X, Guikema J, Leach J . Rice phospholipase D isoforms show differential cellular location and gene induction. Plant Cell Physiol. 2003; 44(10):1013-26. DOI: 10.1093/pcp/pcg125. View

14.

Yoon D, Kang K, Kim H, Ju H, Kwon S, Suh J . Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet. 2006; 112(6):1052-62. DOI: 10.1007/s00122-006-0207-4. View

15.

Nemhauser J, Mockler T, Chory J . Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol. 2004; 2(9):E258. PMC: 509407. DOI: 10.1371/journal.pbio.0020258. View

16.

Soliman K, Jorgensen R, Allard R . Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci U S A. 1984; 81(24):8014-8. PMC: 392284. DOI: 10.1073/pnas.81.24.8014. View

17.

Pappan K, Zheng S, Wang X . Identification and characterization of a novel plant phospholipase D that requires polyphosphoinositides and submicromolar calcium for activity in Arabidopsis. J Biol Chem. 1997; 272(11):7048-54. DOI: 10.1074/jbc.272.11.7048. View

18.

Chapman E, Estelle M . Mechanism of auxin-regulated gene expression in plants. Annu Rev Genet. 2009; 43:265-85. DOI: 10.1146/annurev-genet-102108-134148. View

19.

Testerink C, Munnik T . Phosphatidic acid: a multifunctional stress signaling lipid in plants. Trends Plant Sci. 2005; 10(8):368-75. DOI: 10.1016/j.tplants.2005.06.002. View

20.

Pappan K, Chapman K, Wang X . Substrate selectivities and lipid modulation of plant phospholipase D alpha, -beta, and -gamma. Arch Biochem Biophys. 1998; 353(1):131-40. DOI: 10.1006/abbi.1998.0640. View