Transcriptome Landscape of Perennial Wild Cicer Microphyllum Uncovers Functionally Relevant Molecular Tags Regulating Agronomic Traits in Chickpea

Overview

Journal Sci Rep

Specialty Science

Date 2016 Sep 30

PMID 27680662

Citations 14

Authors

Rishi Srivastava

Deepak Bajaj

Ayushi Malik

Mohar Singh

Swarup K Parida

Affiliations

Soon will be listed here.

Abstract

The RNA-sequencing followed by de-novo transcriptome assembly identified 11621 genes differentially xpressed in roots vs. shoots of a wild perennial Cicer microphyllum. Comparative analysis of transcriptomes between microphyllum and cultivated desi cv. ICC4958 detected 12772 including 3242 root- and 1639 shoot-specific microphyllum genes with 85% expression validation success rate. Transcriptional reprogramming of microphyllum root-specific genes implicates their possible role in regulating differential natural adaptive characteristics between wild and cultivated chickpea. The transcript-derived 5698 including 282 in-silico polymorphic SSR and 127038 SNP markers annotated at a genome-wide scale exhibited high amplification and polymorphic potential among cultivated (desi and kabuli) and wild accessions suggesting their utility in chickpea genomics-assisted breeding applications. The functional significance of markers was assessed based on their localization in non-synonymous coding and regulatory regions of microphyllum root-specific genes differentially expressed predominantly in ICC 4958 roots under drought stress. A high-density 490 genic SSR- and SNP markers-anchored genetic linkage map identified six major QTLs regulating drought tolerance-related traits, yield per plant and harvest-index in chickpea. The integration of high-resolution QTL mapping with comparative transcriptome profiling delineated five microphyllum root-specific genes with non-synonymous and regulatory SNPs governing drought-responsive yield traits. Multiple potential key regulators and functionally relevant molecular tags delineated can drive translational research and drought tolerance-mediated chickpea genetic enhancement.

Citing Articles

A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea.

Thakro V, Malik N, Basu U, Srivastava R, Narnoliya L, Daware A Plant Physiol. 2022; 191(3):1884-1912.

PMID: 36477336 PMC: 10022645. DOI: 10.1093/plphys/kiac550.

Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes.

Singh G, Gudi S, Amandeep , Upadhyay P, Shekhawat P, Nayak G Front Plant Sci. 2022; 13:1035878.

PMID: 36438090 PMC: 9682257. DOI: 10.3389/fpls.2022.1035878.

An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea.

Jain M, Bansal J, Singh Rajkumar M, Garg R Commun Biol. 2022; 5(1):1106.

PMID: 36261617 PMC: 9581958. DOI: 10.1038/s42003-022-04083-4.

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses.

Singh R, Singh C, Ambika , Chandana B, Mahto R, Patial R Front Genet. 2022; 13:905771.

PMID: 36035111 PMC: 9416867. DOI: 10.3389/fgene.2022.905771.

Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea ( L.).

Jha U, Nayyar H, Palakurthi R, Jha R, Valluri V, Bajaj P Front Plant Sci. 2021; 12:655103.

PMID: 34381469 PMC: 8350164. DOI: 10.3389/fpls.2021.655103.

References

Garg R, Sahoo A, Tyagi A, Jain M . Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.). Biochem Biophys Res Commun. 2010; 396(2):283-8. DOI: 10.1016/j.bbrc.2010.04.079. View

Jain M . Next-generation sequencing technologies for gene expression profiling in plants. Brief Funct Genomics. 2011; 11(1):63-70. DOI: 10.1093/bfgp/elr038. View

Singh R, Sharma P, Varshney R, Sharma S, Singh N . Chickpea improvement: role of wild species and genetic markers. Biotechnol Genet Eng Rev. 2011; 25:267-313. DOI: 10.5661/bger-25-267. View

Parida S, Verma M, Yadav S, Ambawat S, Das S, Garg R . Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Front Plant Sci. 2015; 6:645. PMC: 4543896. DOI: 10.3389/fpls.2015.00645. View

Varshney R, Song C, Saxena R, Azam S, Yu S, Sharpe A . Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol. 2013; 31(3):240-6. DOI: 10.1038/nbt.2491. View

Abbo S, Berger J, Turner N . Viewpoint: Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Funct Plant Biol. 2020; 30(10):1081-1087. DOI: 10.1071/FP03084. View

Rushton P, Somssich I, Ringler P, Shen Q . WRKY transcription factors. Trends Plant Sci. 2010; 15(5):247-58. DOI: 10.1016/j.tplants.2010.02.006. View

Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi A . High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci Rep. 2015; 5:13387. PMC: 4548218. DOI: 10.1038/srep13387. View

Kang J, Hwang J, Lee M, Kim Y, Assmann S, Martinoia E . PDR-type ABC transporter mediates cellular uptake of the phytohormone abscisic acid. Proc Natl Acad Sci U S A. 2010; 107(5):2355-60. PMC: 2836657. DOI: 10.1073/pnas.0909222107. View

10.

Ray S, Dansana P, Giri J, Deveshwar P, Arora R, Agarwal P . Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct Integr Genomics. 2010; 11(1):157-78. DOI: 10.1007/s10142-010-0187-y. View

11.

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

12.

Chen L, Song Y, Li S, Zhang L, Zou C, Yu D . The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta. 2011; 1819(2):120-8. DOI: 10.1016/j.bbagrm.2011.09.002. View

13.

Zahaf O, Blanchet S, De Zelicourt A, Alunni B, Plet J, Laffont C . Comparative transcriptomic analysis of salt adaptation in roots of contrasting Medicago truncatula genotypes. Mol Plant. 2012; 5(5):1068-81. DOI: 10.1093/mp/sss009. View

14.

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

15.

Kujur A, Bajaj D, Saxena M, Tripathi S, Upadhyaya H, Gowda C . Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Res. 2013; 20(4):355-74. PMC: 3738162. DOI: 10.1093/dnares/dst015. View

16.

Hiremath P, Kumar A, Penmetsa R, Farmer A, Schlueter J, Chamarthi S . Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J. 2012; 10(6):716-32. PMC: 3465799. DOI: 10.1111/j.1467-7652.2012.00710.x. View

17.

Thudi M, Bohra A, Nayak S, Varghese N, Shah T, Penmetsa R . Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One. 2011; 6(11):e27275. PMC: 3216927. DOI: 10.1371/journal.pone.0027275. View

18.

Bhardwaj J, Chauhan R, Swarnkar M, Chahota R, Singh A, Shankar R . Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC Genomics. 2013; 14:647. PMC: 3853109. DOI: 10.1186/1471-2164-14-647. View

19.

Jhanwar S, Priya P, Garg R, Parida S, Tyagi A, Jain M . Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol J. 2012; 10(6):690-702. DOI: 10.1111/j.1467-7652.2012.00712.x. View

20.

Moumeni A, Satoh K, Kondoh H, Asano T, Hosaka A, Venuprasad R . Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress. BMC Plant Biol. 2011; 11:174. PMC: 3268746. DOI: 10.1186/1471-2229-11-174. View