Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/<i>Ambylopyrum muticum</i> introgression lines

Coombes, Benedict; Fellers, John P.; Grewal, Surbhi; Rusholme‐Pilcher, Rachel; Hubbart-Edwards, Stella; Yang, Caiyun; Joynson, Ryan; King, Ian P.; King, Julie; Hall, Anthony

doi:10.1101/2021.11.16.468825

Cited by 6 publications

(6 citation statements)

References 87 publications

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“…On the other hand, mRNAseq analysis of six introgression lines of Triticum aestivum/ Ambylopyrum muticum showed that the expression of Ambylopyrum muticum genes introduced into the wheat genome is reduced compared to wheat orthologs without corresponding compensation of the expression of homoeologous wheat genes [18]. This directly indicates the possibility of mutual epigenetic influences between alien chromatin and chromatin of the resident genome and can serve as an explanation for all the phenomena described above.…”

Section: Facts Of the Variability Of The Recipient Genome Of Hybrid O...mentioning

confidence: 82%

Significance of introgression hybridization for extension of genetic variability in recipient genome

Аntonyuk

Shpylchyn

Martynenko

et al. 2022

NRPBE

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Alien chromatin (introgressions) can be incorporated into the wheat genome either through recombination or through translocation. Lines of introgressive origin may not contain identified alien chromatin, although they appear to be changed relative to the original wheat sample by some characteristics that are registered at different levels of phenotype assessment. It has been shown numerous facts of the variability of the recipient genome of hybrid origin. They can be caused by irregular behavior of chromosomes in mitoses of somatic cells with hybrid genome, and DNA changes. Wide phenotypic variability was observed among the progeny of hybrid genomes up to appearance of phenotypic novelties. The study of DNA profiles using several methods revealed the presence of numerous genetic and epigenetic changes, including deletions, changes in gene expression, changes in the methylation pattern, and activation of retrotransposons in the recipient genome. When these changes were not directly related to alien fragments, they are considered as possible mechanisms of extension of genetic variability intra genome of hybrid origin. Transcriptomic analysis of lines of hybrid origin and parental plants using the RNA-seq analyses showed that the change of expression affected a different number of genes. The change in the expression of alien genes occurred in the direction of down-regulation, upregulation was typical for wheat genes. Phenotypic variability during introgressive hybridization can be accompanied by attenuation of the expression of an alien gene when it enters the recipient genome. That may be a consequence of the interaction between the alien gene and the genetic environment of the host genome. Today there is a lot of evidence that these mechanisms are epigenetic, which include DNA methylation, histone modification, the involvement of small RNAs in the regulation of gene expression, and the involvement of transposons. Moreover, none of these mechanisms act independently, but are a component of events, the results of which can be a change in gene expression and the appearance of a new phenotype that is not related to the expression of an alien gene.

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Section: Facts Of the Variability Of The Recipient Genome Of Hybrid O...mentioning

confidence: 82%

Significance of introgression hybridization for extension of genetic variability in recipient genome

Аntonyuk

Shpylchyn

Martynenko

et al. 2022

NRPBE

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“…In addition to comparison of expression patterns among homoeoalleles, the differential expression analysis at the whole genome level between the parents and SHW lines performed to characterize the expression changes of the genes between different genomic backgrounds, revealed the large-scale repression of the D subgenome genes. The introgression of chromosomal segments from species in the secondary and tertiary gene pools has resulted in transcriptomic changes in both wheat [60][61][62][63] and other polyploid species 64,65 . Specifically, transcriptomic analysis of wheat × Ambylopyrum muticum introgression lines indicated the suppressed expression of genes in the introgressed segments 60 .…”

Section: Discussionmentioning

confidence: 99%

Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat

et al. 2023

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Synthetic hexaploid wheat (SHW) lines are created as pre-breeding germplasm to diversify the D subgenome of hexaploid wheat and capitalize upon the untapped genetic diversity of the Aegilops tauschii gene pool. However, the phenotypes observed in the Ae. tauschii parents are not always recovered in the SHW lines, possibly due to inter-subgenome interactions. To elucidate this post-polyploidization genome reprogramming phenomenon, we performed RNA-seq of four SHW lines and their corresponding tetraploid and diploid parents, across ten tissues and three biological replicates. Homoeologue expression bias (HEB) analysis using more than 18,000 triads suggests massive suppression of homoeoalleles of the D subgenome in SHWs. Comparative transcriptome analysis of the whole-genome gene set further corroborated this finding. Alternative splicing analysis of the high-confidence genes indicates an additional layer of complexity where all five splice events are identified, and retained intron is predominant. Homoeologue expression upon resynthesis of hexaploid wheat has implications to the usage and handling of this germplasm in breeding as it relates to capturing the effects of epistatic interaction across subgenomes upon polyploidization. Special considerations must be given to this germplasm in pre-breeding activities to consider the extent of the inter-subgenome interactions on gene expression and their impact on traits for crop improvement.

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“…However, it is important to note that their efficiency is dependent on their density across the wheat genome and small introgressions existing between two KASP markers could have gone undetected. With the reducing cost of DNA sequencing, we envisage that the next improvement in characterization of such introgressions, with the potential to give higher resolution, would be low‐coverage whole genome resequencing of wheat–wild relative introgression lines as has been recently demonstrated (Coombes et al., 2021).…”

Section: Discussionmentioning

confidence: 99%

Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines

et al. 2022

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Many wild‐relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)‐based arrays and molecular markers have been widely used to characterize wheat–wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP‐based Kompetitive allele‐specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome‐ and polymerase chain reaction (PCR)‐amplicon‐based sequencing of the wild species. But chromosome‐specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome‐specific markers were used to recharacterize previously genotyped wheat–Am. muticum doubled haploid (DH) introgression lines. The chromosome‐specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.

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Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines

Cited by 6 publications

References 87 publications

Significance of introgression hybridization for extension of genetic variability in recipient genome

Significance of introgression hybridization for extension of genetic variability in recipient genome

Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat

Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines

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