Insertion of a solo LTR retrotransposon associates with spur mutations in ‘Red Delicious’ apple (Malus × domestica)

Han, Mengxue; Sun, Qibao; Zhou, Jinjun; Qiu, Huarong; Guo, Jing; Lu, Lijuan; Mu, Wenlei; Sun, Jun

doi:10.1007/s00299-017-2160-x

Cited by 22 publications

(15 citation statements)

References 39 publications

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“…Therefore, apple sports are therefore an excellent starting point to study epigenetics in plants. Although some sports might be the result of genetic changes (such as mutations induced by transposable elements 302 , others might vary only at the epigenetic level and more specifically at the DNA methylation level.…”

Section: Epigenetics: Scratching the Surfacementioning

confidence: 99%

Apple whole genome sequences: recent advances and new prospects

Peace¹,

Bianco²,

Troggio³

et al. 2019

Hortic Res

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In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple ( Malus domestica ). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

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Section: Epigenetics: Scratching the Surfacementioning

confidence: 99%

Apple whole genome sequences: recent advances and new prospects

Peace¹,

Bianco²,

Troggio³

et al. 2019

Hortic Res

View full text Add to dashboard Cite

show abstract

“…They have been successfully applied in the studies of plant genetic diversity and QTL mapping [48]. Furthermore, some RIPs have been proved as a causal mutation to change the plant phenotype [49][50][51]. It is believed that SINE of RIPs are "nearly ideal" genetic markers to facilitate plant breeding [52].…”

Section: Discussionmentioning

confidence: 99%

An 192 bp ERV insertion in the first intron of TLR6 acts as an enhancer to increase TLR6 and TLR1 expression

Wang

Chen

Muráni

et al. 2020

Preprint

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Background Toll-like receptors (TLRs) play important roles in building innate immune and inducing adaptive immune responses. Associations of the TLR gene polymorphisms with diseases susceptibility, which are the basis of molecular breeding for disease resistant animals, have been reported extensively. Retrotransposon insertion polymorphisms (RIPs) were developed recently as a new type of molecular marker having great potential in population genetics and quantitative trait locus (QTL) mapping analysis. In this study, bioinformatics prediction combined with the PCR-based amplification was employed to screen for RIPs in porcine TLR genes. Their population distribution and impact on gene activity and phenotype of one RIP was further evaluated. Results Totally, five RIPs, located at the 3' flank of TLR3, 5' flank of TLR5, intron 1 of TLR6, intron 1 of TLR7, and 3' flank of TLR8 respectively, were identified. These RIPs were detected in different breeds with an uneven distribution among them. By using the dual luciferase activity assay a 192 bp endogenous retrovirus (ERV) in the intron 1 of TLR6 was proven to act as an enhancer increasing the activities of TLR6 promoter and multiple mini-promoters. Furthermore, the real-time quantitative polymerase chain reaction (qPCR) analysis demonstrated that the ERV insertion significantly enhances the mRNA expressions of TLR6, the neighboring gene TLR1, and the downstream genes MyD88 (Myeloid differentiation factor 88), Rac1 (Rac family small GTPase 1 ), TIRAP (TIR domain containing adaptor protein), Tollip (Toll interacting protein) of TLR signaling pathway and the inflammatory factors IL6 (Interleukin 6), IL8 (Interleukin 8), and TNFα (Tumor necrosis factor alpha) in 30-day piglet tissues. In addition, the serum IL-6 and TNFα were also significantly upregulated by ERV insertion. Conclusions Overall, five RIPs were identified in several TLRs, and the 192 bp ERV insertion in the first intron of TLR6 can improve the expressions of TLR6, TLR1, their downstream genes, and the inflammatory factors by acting as an enhancer affecting the regulation of TLR pathways, which may be applicable in the molecular breeding of disease resistant animals.

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“…They have been successfully applied in the studies of plant genetic diversity and QTL mapping [46]. Furthermore, some RIPs have been proved as a causal mutation to change the plant phenotype [47][48][49]. It is believed that SINE of RIPs are "nearly ideal" genetic markers to facilitate plant breeding [50].…”

Section: Discussionmentioning

confidence: 99%

An 192 bp ERV Insertion in the First Intron of TLR6 Acts as an Enhancer to Increase TLR6 and TLR1 Expression

Wang

Chen

Muráni

et al. 2020

Preprint

View full text Add to dashboard Cite

BackgroundToll-like receptors (TLRs) play important roles in building innate immune and inducing adaptive immune responses. Associations of the TLR gene polymorphisms with diseases susceptibility, which are the basis of molecular breeding for disease resistant animals, have been reported extensively. Retrotransposon insertion polymorphisms (RIPs) were developed recently as a new type of molecular marker having great potential in population genetics and quantitative trait locus (QTL) mapping analysis. In this study, bioinformatics prediction combined with the PCR-based amplification was employed to screen for RIPs in porcine TLR genes. Their population distribution and impact on gene activity and phenotype of one RIP was been further evaluated. ResultsThe results showed that five RIPs, located at the 3' flank of TLR3, 5' flank of TLR5, intron 1 of TLR6, intron 1 of TLR7, and 3' flank of TLR8 respectively, was identified. These RIPs were detected in different breeds with an uneven distribution among them. By using the dual luciferase activity assay a 192 bp endogenous retrovirus (ERV) in the intron 1 of TLR6 was proven to act as an enhancer increasing the activities of TLR6 promoter and multiple mini-promoters. Furthermore, the real-time quantitative polymerase chain reaction (qPCR) analysis demonstrated that the ERV insertion significantly enhances the mRNA expressions of TLR6, the neighboring gene TLR1, and the downstream genes MyD88 (Myeloid differentiation factor 88), Rac1 (Rac family small GTPase 1), TIRAP (TIR domain containing adaptor protein), Tollip (Toll interacting protein) of TLR signaling pathway and the inflammatory factors IL6 (Interleukin 6), IL8 (Interleukin 8), and TNFα (Tumor necrosis factor alpha) in 30-day piglet tissues. In addition, the serum IL-6 and TNFα was also significantly upregulated by ERV insertion. ConclusionsOverall, five RIPs were been identified in several TLRs, and the 192 bp ERV insertion in the first intron of TLR6 can improve the expressions of TLR6, TLR1, their downstream genes, and the inflammatory factors by acting as an enhancer affecting the regulation of TLR pathways, which may be applicable in the molecular breeding of disease resistant animals.

show abstract

Insertion of a solo LTR retrotransposon associates with spur mutations in ‘Red Delicious’ apple (Malus × domestica)

Cited by 22 publications

References 39 publications

Apple whole genome sequences: recent advances and new prospects

Apple whole genome sequences: recent advances and new prospects

An 192 bp ERV insertion in the first intron of TLR6 acts as an enhancer to increase TLR6 and TLR1 expression

An 192 bp ERV Insertion in the First Intron of TLR6 Acts as an Enhancer to Increase TLR6 and TLR1 Expression

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