Short Tandem Repeats in plants: Genomic distribution and function prediction

Zhu, Lin; Wu, Hui; Li, Huayang; Tang, Heng; Zhang, Li; Xu, Hua; Fangchan, Jiao; Wang, Nian; Yang, Long

doi:10.1016/j.ejbt.2020.12.003

Cited by 13 publications

(14 citation statements)

References 36 publications

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“…Trinucleotide repeat expansions are highly mutagenic structures that have been associated with degenerative diseases in humans (Nageshwaran and Festenstein 2015), especially when present in coding regions, where they can have significant impacts on protein structure (Figura et al 2015), such as in the case of Huntington's disease (Shacham et al 2019). Trinucleotide repeat expansions have also been implicated in temperaturesensitivity adaptation in Arabidopsis thaliana (Tabib et al 2016), though remain largely unstudied in the plant kingdom (Zhu et al 2021). The paralog of Glyma.20G085100, Glyma.10G13440, contains a similar number of trinucleotide copies (six) as is widely found in low-protein individuals (five).…”

Section: Discussionmentioning

confidence: 99%

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Marsh

Petereit

et al. 2022

Theor Appl Genet

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Key message The major soy protein QTL, cqProt-003, was analysed for haplotype diversity and global distribution, and results indicate 304 bp deletion and variable tandem repeats in protein coding regions are likely causal candidates. Abstract Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait-associated region within a 173 kb linkage block was identified, and variants in the region were characterized, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the second exon of gene Glyma.20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304 bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximize protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterization and modification.

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Section: Discussionmentioning

confidence: 99%

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Marsh

Petereit

et al. 2022

Theor Appl Genet

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“…Further studies to evaluate additional Panicum species from diverse habitats across Australia could confirm the utility of this approach. In addition to the techniques presented, other molecular tools, including whole or partial genome sequencing 49 , high resolution melt curve analysis 50 , short tandem repeats (STR) 51 , or some combination of the above, may prove useful for rapid and refined species differentiation through estimation of other genetic parameters.…”

Section: Discussionmentioning

confidence: 99%

Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding

Chen

Zhu²,

Loukopoulos

et al. 2021

Sci Rep

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Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.

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“…Trinucleotide repeat expansions are highly mutagenic structures that have been associated with degenerative diseases in humans (Nageshwaran and Festenstein 2015), especially when present in coding regions, where they can have significant impacts on protein structure (Figura et al 2015), such as in the case of Huntington's disease (Shacham et al 2019). Trinucleotide repeat expansions have also been implicated in temperature-sensitivity adaptation in Arabidopsis thaliana (Tabib et al 2016), though remain largely unstudied in the plant kingdom (Zhu et al 2021). Our finding may represent the first case of causal short tandem repeat variation in a coding region underlying phenotypic effect in soybean.…”

Section: Discussionmentioning

confidence: 99%

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Marsh

Petereit

et al. 2021

Preprint

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Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait associated region within a 173 kb linkage block was identified and variants in the region were characterised, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the third exon of gene 20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximise protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterisation and modification.

show abstract

Short Tandem Repeats in plants: Genomic distribution and function prediction

Cited by 13 publications

References 36 publications

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding

Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

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