Identification of QTL-Based Polymorphic Genes As Salt-Responsive Potential Candidates Through Mapping with Two Reference Genomes in Rice

Overview

Journal Plants (Basel)

Date 2020 Feb 15

PMID 32054112

Citations 1

Authors

Buddini Abhayawickrama

Dikkumburage Gimhani

Nisha Kottearachchi

Venura Herath

Dileepa Liyanage

Prasad Senadheera

Affiliations

Soon will be listed here.

Abstract

Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of , , , and were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.

Citing Articles

Pharmaceutical, food potential, and molecular data of Gomes: a systematic review.

Nunes V, Silva-Mann R, Souza J, Calazans C Genet Resour Crop Evol. 2022; 69(2):525-543.

PMID: 35068695 PMC: 8764503. DOI: 10.1007/s10722-021-01319-w.

References

Fujiwara T, Beachy R . Tissue-specific and temporal regulation of a beta-conglycinin gene: roles of the RY repeat and other cis-acting elements. Plant Mol Biol. 1994; 24(2):261-72. DOI: 10.1007/BF00020166. View

Li C, Shen H, Wang T, Wang X . ABA Regulates Subcellular Redistribution of OsABI-LIKE2, a Negative Regulator in ABA Signaling, to Control Root Architecture and Drought Resistance in Oryza sativa. Plant Cell Physiol. 2015; 56(12):2396-408. DOI: 10.1093/pcp/pcv154. View

Xu F, Park M, Kitazumi A, Herath V, Mohanty B, Yun S . Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. BMC Genomics. 2012; 13:497. PMC: 3522565. DOI: 10.1186/1471-2164-13-497. View

Xue T, Wang D, Zhang S, Ehlting J, Ni F, Jakab S . Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis. BMC Genomics. 2008; 9:550. PMC: 2612031. DOI: 10.1186/1471-2164-9-550. View

Santi L, Wang Y, Stile M, Berendzen K, Wanke D, Roig C . The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J. 2003; 34(6):813-26. DOI: 10.1046/j.1365-313x.2003.01767.x. View

Conesa A, Gotz S . Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008; 2008:619832. PMC: 2375974. DOI: 10.1155/2008/619832. View

Menkens A, Schindler U, Cashmore A . The G-box: a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins. Trends Biochem Sci. 1995; 20(12):506-10. DOI: 10.1016/s0968-0004(00)89118-5. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Kotchoni S, Jimenez-Lopez J, Gao D, Edwards V, Gachomo E, Margam V . Modeling-dependent protein characterization of the rice aldehyde dehydrogenase (ALDH) superfamily reveals distinct functional and structural features. PLoS One. 2010; 5(7):e11516. PMC: 2902511. DOI: 10.1371/journal.pone.0011516. View

10.

Gupta B, Huang B . Mechanism of salinity tolerance in plants: physiological, biochemical, and molecular characterization. Int J Genomics. 2014; 2014:701596. PMC: 3996477. DOI: 10.1155/2014/701596. View

11.

Mishra S, Singh B, Panda K, Singh B, Singh N, Misra P . Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm. Rice (N Y). 2016; 9(1):15. PMC: 4811800. DOI: 10.1186/s12284-016-0083-8. View

12.

Naveed S, Zhang F, Zhang J, Zheng T, Meng L, Pang Y . Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses. Sci Rep. 2018; 8(1):6505. PMC: 5916932. DOI: 10.1038/s41598-018-24946-3. View

13.

Jain M, Moharana K, Shankar R, Kumari R, Garg R . Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol J. 2014; 12(2):253-64. DOI: 10.1111/pbi.12133. View

14.

Islam M, Ontoy J, Subudhi P . Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice ( L.). Plants (Basel). 2019; 8(2). PMC: 6409918. DOI: 10.3390/plants8020033. View

15.

Golldack D, Li C, Mohan H, Probst N . Tolerance to drought and salt stress in plants: Unraveling the signaling networks. Front Plant Sci. 2014; 5:151. PMC: 4001066. DOI: 10.3389/fpls.2014.00151. View

16.

Hossain M, Bassel G, Pritchard J, Sharma G, Ford-Lloyd B . Trait Specific Expression Profiling of Salt Stress Responsive Genes in Diverse Rice Genotypes as Determined by Modified Significance Analysis of Microarrays. Front Plant Sci. 2016; 7:567. PMC: 4853522. DOI: 10.3389/fpls.2016.00567. View

17.

Shobbar Z, Oane R, Gamuyao R, De Palma J, Malboobi M, Karimzadeh G . Abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. New Phytol. 2008; 178(1):68-79. DOI: 10.1111/j.1469-8137.2007.02365.x. View

18.

Nguyen T, Moon S, Nguyen V, Gho Y, Nalini Chandran A, Soh M . Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage. Plant Mol Biol. 2016; 92(1-2):71-88. DOI: 10.1007/s11103-016-0496-1. View

19.

Zong W, Tang N, Yang J, Peng L, Ma S, Xu Y . Feedback Regulation of ABA Signaling and Biosynthesis by a bZIP Transcription Factor Targets Drought-Resistance-Related Genes. Plant Physiol. 2016; 171(4):2810-25. PMC: 4972276. DOI: 10.1104/pp.16.00469. View

20.

Xing Z, Tan F, Hua P, Sun L, Xu G, Zhang Q . Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet. 2003; 105(2-3):248-257. DOI: 10.1007/s00122-002-0952-y. View