Transcriptional and Genetic Characteristic of Chimera Pea Generation Via Double Ethyl Methanesulfonate-induced Mutation Revealed by Transcription Analysis

Overview

Journal Front Plant Sci

Date 2024 Oct 16

PMID 39411652

Authors

Jinglei Hu

Mingxia Liu

Dongxia Wang

Yunlong Liang

Yuan Zong

Yun Li

Dong Cao

Baolong Liu

Affiliations

Soon will be listed here.

Abstract

Ethyl methanesulfonate (EMS)-induced mutagenesis is a prominent method for generating plant mutants, often resulting in chimera plants; however, their transcriptional and genetic characteristic remain elusive. In this investigation, chimera pea ( L.) specimens, labeled GY1 and GY2, exhibiting a distinctive phenotype with yellow and green leaves were meticulously cultivated via sequential double EMS mutagenesis. The observed color disparity between the yellow and green leaves was attributed to a significant reduction in chlorophyll content coupled with heightened lutein levels in both chimeric variants. Transcriptome profiling revealed the enrichment of differentially expressed genes in both GY1 and GY2, specifically implicating Kyoto Encyclopedia of Genes and Genomes pathways linked to amino acid biosynthesis and ribosome development, alongside Gene Ontology (GO) biological processes linked with stress response mechanisms. Few structural genes associated with chlorophyll and lutein biosynthesis exhibited discernible differential expression. Despite these functional similarities, distinctive nuances were evident between specimens, with GY1 exhibiting enrichment in GO pathways related to chloroplast development and GY2 showing enrichment for ribosome development pathways. Single-nucleotide polymorphism (SNP) analysis uncovered a shared pool of 599 and 598 polymorphisms in the yellow and green leaves of GY1 and GY2, respectively, likely stemming from the initial EMS mutagenesis step. Further investigation revealed an increased number of unique SNPs in the yellow leaves following the second EMS application, whereas the green leaves exhibited sparse and unique SNP occurrences, suggestive of potential evasion from secondary mutagenesis. This inherent genetic variability underpins the mechanism underlying the formation of chimera plants. Predominant base mutations induced by EMS were characterized by G/A and C/T transitions, constituting 74.1% of the total mutations, aligning with established EMS mutation induction paradigms. Notably, genes encoding the eukaryotic translation initiation factor eIIso4G and the ubiquitin ligase RKP, known to modulate leaf color in model plants, harbored two SNPs in the yellow leaves of both GY1 and GY2, implicating their putative role in the yellow leaf phenotype. Collectively, this study provides novel insights into the transcriptional and genetic characteristics of chimera plants via EMS-induced mutagenesis.

References

Rojas M, Ruwe H, Miranda R, Zoschke R, Hase N, Schmitz-Linneweber C . Unexpected functional versatility of the pentatricopeptide repeat proteins PGR3, PPR5 and PPR10. Nucleic Acids Res. 2018; 46(19):10448-10459. PMC: 6212717. DOI: 10.1093/nar/gky737. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Lellis A, Allen M, Aertker A, Tran J, Hillis D, Harbin C . Deletion of the eIFiso4G subunit of the Arabidopsis eIFiso4F translation initiation complex impairs health and viability. Plant Mol Biol. 2010; 74(3):249-63. PMC: 2938417. DOI: 10.1007/s11103-010-9670-z. View

Kong W, Wang L, Cao P, Li X, Ji J, Dong P . Identification and genetic analysis of EMS-mutagenized wheat mutants conferring lesion-mimic premature aging. BMC Genet. 2020; 21(1):88. PMC: 7430028. DOI: 10.1186/s12863-020-00891-x. View

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View

Dufil G, Bernacka-Wojcik I, Armada-Moreira A, Stavrinidou E . Plant Bioelectronics and Biohybrids: The Growing Contribution of Organic Electronic and Carbon-Based Materials. Chem Rev. 2021; 122(4):4847-4883. PMC: 8874897. DOI: 10.1021/acs.chemrev.1c00525. View

Sega G . A review of the genetic effects of ethyl methanesulfonate. Mutat Res. 1984; 134(2-3):113-42. DOI: 10.1016/0165-1110(84)90007-1. View

Liao Y, Smyth G, Shi W . featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2013; 30(7):923-30. DOI: 10.1093/bioinformatics/btt656. View

Wang X, An Y, Xu P, Xiao J . Functioning of PPR Proteins in Organelle RNA Metabolism and Chloroplast Biogenesis. Front Plant Sci. 2021; 12:627501. PMC: 7900629. DOI: 10.3389/fpls.2021.627501. View

10.

Daniell H, Lin C, Yu M, Chang W . Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016; 17(1):134. PMC: 4918201. DOI: 10.1186/s13059-016-1004-2. View

11.

Yu G, Wang L, Han Y, He Q . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284-7. PMC: 3339379. DOI: 10.1089/omi.2011.0118. View

12.

Ilag L, Kumar A, Soll D . Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis. Plant Cell. 1994; 6(2):265-75. PMC: 160432. DOI: 10.1105/tpc.6.2.265. View

13.

Kim D, Paggi J, Park C, Bennett C, Salzberg S . Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019; 37(8):907-915. PMC: 7605509. DOI: 10.1038/s41587-019-0201-4. View

14.

Koboldt D, Larson D, Wilson R . Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection. Curr Protoc Bioinformatics. 2015; 44:15.4.1-17. PMC: 4278659. DOI: 10.1002/0471250953.bi1504s44. View

15.

Yan W, Deng X, Yang C, Tang X . The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice. Front Plant Sci. 2021; 12:579675. PMC: 8025102. DOI: 10.3389/fpls.2021.579675. View

16.

Zhu P, Zeng M, Lin Y, Tang Y, He T, Zheng Y . Variability in Leaf Color Induced by Chlorophyll Deficiency: Transcriptional Changes in Bamboo Leaves. Curr Issues Mol Biol. 2024; 46(2):1503-1515. PMC: 10888276. DOI: 10.3390/cimb46020097. View

17.

Minoche A, Dohm J, Himmelbauer H . Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 2011; 12(11):R112. PMC: 3334598. DOI: 10.1186/gb-2011-12-11-r112. View

18.

Bailey M, Ivanauskaite A, Grimmer J, Akintewe O, Payne A, Osborne R . The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation. Nat Commun. 2021; 12(1):251. PMC: 7801604. DOI: 10.1038/s41467-020-20506-4. View

19.

Matile P, Hortensteiner S, Thomas H . CHLOROPHYLL DEGRADATION. Annu Rev Plant Physiol Plant Mol Biol. 2004; 50:67-95. DOI: 10.1146/annurev.arplant.50.1.67. View

20.

Tsyganov V, Belimov A, Borisov A, Safronova V, Georgi M, Dietz K . A chemically induced new pea (Pisum sativum) mutant SGECdt with increased tolerance to, and accumulation of, cadmium. Ann Bot. 2007; 99(2):227-37. PMC: 2802999. DOI: 10.1093/aob/mcl261. View