1. The non-random patterns of genetic variation induced by asymmetric somatic hybridization in wheat
- Author
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Guangmin Xia, Yujie Ji, Zhen Xiao, Yanxia Wang, Shiting Feng, Xiaoping Wang, Mengcheng Wang, and Chun Liu
- Subjects
0106 biological sciences ,0301 basic medicine ,Somatic cell ,Plant Science ,Biology ,01 natural sciences ,Genome ,03 medical and health sciences ,INDEL Mutation ,lcsh:Botany ,Genetic variation ,Allele ,Common wheat ,Indel ,Triticum ,Sequence Deletion ,Genetics ,Expressed Sequence Tags ,Expressed sequence tag ,food and beverages ,Genetic Variation ,Nucleotide substitution ,Introgression line ,Insertion and deletion ,Chromatin ,lcsh:QK1-989 ,Somatic fusion ,Genomic shock ,030104 developmental biology ,010606 plant biology & botany ,Research Article - Abstract
Background Asymmetric somatic hybridization is an efficient crop breeding approach by introducing several exogenous chromatin fragments, which leads to genomic shock and therefore induces genome-wide genetic variation. However, the fundamental question concerning the genetic variation such as whether it occurs randomly and suffers from selection pressure remains unknown. Results Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Both nucleotide substitutions and indels (insertions and deletions) had lower frequencies in coding sequences than in un-translated regions. The frequencies of nucleotide substitutions and indels were both comparable between chromosomes with and without introgressed fragments. Nucleotide substitutions distributed unevenly and were preferential to indel-flanking sequences, and the frequency of nucleotide substitutions at 5′-flanking sequences of indels was obviously higher in chromosomes with introgressed fragments than in those without exogenous fragment. Nucleotide substitutions and indels both had various frequencies among seven groups of allelic chromosomes, and the frequencies of nucleotide substitutions were strongly negatively correlative to those of indels. Among three sets of genomes, the frequencies of nucleotide substitutions and indels were both heterogeneous, and the frequencies of nucleotide substitutions exhibited drastically positive correlation to those of indels. Conclusions Our work demonstrates that the genetic variation induced by asymmetric somatic hybridization is attributed to both whole genomic shock and local chromosomal shock, which is a predetermined and non-random genetic event being closely associated with selection pressure. Asymmetric somatic hybrids provide a worthwhile model to further investigate the nature of genomic shock induced genetic variation. Electronic supplementary material The online version of this article (10.1186/s12870-018-1474-3) contains supplementary material, which is available to authorized users.
- Published
- 2018