Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat

Frontiers in Genetics

Yanxia Wang¹  Wenjing Xu²  Yingchun Li²  Guangmin Xia²  Yajing Li²  Mengcheng Wang²  Chun Liu² 

[1] Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China;The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China;

关键词: introgression line;    genomic shock;    synonymous codon usage bias;    somatic hybridization;    wheat;   

DOI  :  10.3389/fgene.2021.682324

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown