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Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat

Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nu...

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Autores principales: Xu, Wenjing, Li, Yingchun, Li, Yajing, Liu, Chun, Wang, Yanxia, Xia, Guangmin, Wang, Mengcheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8226224/
https://www.ncbi.nlm.nih.gov/pubmed/34178040
http://dx.doi.org/10.3389/fgene.2021.682324
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author Xu, Wenjing
Li, Yingchun
Li, Yajing
Liu, Chun
Wang, Yanxia
Xia, Guangmin
Wang, Mengcheng
author_facet Xu, Wenjing
Li, Yingchun
Li, Yajing
Liu, Chun
Wang, Yanxia
Xia, Guangmin
Wang, Mengcheng
author_sort Xu, Wenjing
collection PubMed
description Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.
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spelling pubmed-82262242021-06-26 Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat Xu, Wenjing Li, Yingchun Li, Yajing Liu, Chun Wang, Yanxia Xia, Guangmin Wang, Mengcheng Front Genet Genetics Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock. Frontiers Media S.A. 2021-06-11 /pmc/articles/PMC8226224/ /pubmed/34178040 http://dx.doi.org/10.3389/fgene.2021.682324 Text en Copyright © 2021 Xu, Li, Li, Liu, Wang, Xia and Wang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Xu, Wenjing
Li, Yingchun
Li, Yajing
Liu, Chun
Wang, Yanxia
Xia, Guangmin
Wang, Mengcheng
Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat
title Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat
title_full Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat
title_fullStr Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat
title_full_unstemmed Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat
title_short Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat
title_sort asymmetric somatic hybridization affects synonymous codon usage bias in wheat
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8226224/
https://www.ncbi.nlm.nih.gov/pubmed/34178040
http://dx.doi.org/10.3389/fgene.2021.682324
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