EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1that are associated with annuality and winter hardiness

Frerichmann, Sebastian Leo Max; Kirchhoff, Martin; Müller, Andreas E.; Scheidig, Axel J.; Jung, Christian; Kopisch‐Obuch, Friedrich J.

doi:10.1186/1471-2229-13-52

Cited by 36 publications

(24 citation statements)

References 58 publications

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“…EcoTILLING is shown to be a fast, convenient, and effective method for detecting SNPs in genes of haploid species, such as fungus. The method has been widely adapted for many crop species [43][44][45]. Having established EcoTILLING for C. sativus, we expect that it can be similarly adapted for many microorganisms.…”

Section: Resultsmentioning

confidence: 99%

EcoTILLING in Cochliobolus sativus Isolates Reveals Polymorphisms in the XYL1 and XYL2

Jawhar¹,

Bj²,

Albaterni³

et al. 2018

J Plant Biochem Physiol

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The fungus Cochliobolus sativus is a cereal pathogen that in addition to its role in plant disease has potential industrial applications. It has been shown to be an efficient producer of xylanase. The enzyme breaks down hemicellulose and therefore identification of isolates with high xylanase activity is one target for enhancing biofuel production. Genetic variants of XYL1 and XYL2 genes were found to be associated with altered xylanase activity. However, although these two major genes have been described, relatively little is known about the patterns of xylanase gene diversity in this pathogen. In this work, we have developed a low-cost EcoTILLING method for singlenucleotide polymorphism (SNP) and small indel discovery in XYL1 and XYL2 genes from fungal isolates that is suitable for most laboratories. The approach utilizes self-extracted single-strand-specific nucleases and standard agarose gel electrophoresis for polymorphism discovery. Gene-specific primer pairs were used to optimize enzymatic mismatch cleavage and polymorphism discovery on a panel of 56 C. sativus isolates. Based on the nucleotide polymorphisms detected, these isolates were organized into four haplotype groups. These haplotype groups were found to correlate with differences in xylanase production. Seven novel nucleotide variation was confirmed by sequencing. The discovered polymorphisms serve as genome specific markers for screening of additional C. sativus isolates. The ability of rapid and low-cost genotypic methods to categorize xylanase production may be of value in both basic research and industrial settings.

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Section: Resultsmentioning

confidence: 99%

EcoTILLING in Cochliobolus sativus Isolates Reveals Polymorphisms in the XYL1 and XYL2

Jawhar¹,

Bj²,

Albaterni³

et al. 2018

J Plant Biochem Physiol

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“…The sequence variations (Substitutions and Indels) were detected by using ‘Multalin’ software (http://multalin.toulouse.inra.fr/multalin/, Corpet (1988). The SNP frequency was calculated using the formula: (Total number of SNPs detected / total length of the screened fragment) X 1000 (Frerichmann et al ., 2013). PARSESNP (Taylor and Greene, 2003) was used to analyze and display the variation in gene sequences, and SIFT (Sorting intolerant from tolerant; Sim et al ., 2012) was used to predict the deleterious variations for protein functions.…”

Section: Methodsmentioning

confidence: 99%

MutS-Homolog2silencing generates tetraploid meiocytes in tomato (Solanum lycopersicum)

Sarma

Pandey

Ravi

et al. 2017

Preprint

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SUMMARYMSH2 is the core protein of MutS-homolog family involved in recognition and repair of the errors in the DNA. While other members of MutS-homolog family reportedly regulate mitochondrial stability, meiosis, and fertility, MSH2 is believed to participate mainly in mismatch repair. The search for polymorphism in MSH2 sequence in tomato accessions revealed both synonymous and nonsynonymous SNPs; however, SIFT algorithm predicted that none of the SNPs influenced MSH2 protein function. The silencing of MSH2 gene expression by RNAi led to phenotypic abnormalities in highly-silenced lines, particularly in the stamens with highly reduced pollen formation. MSH2 silencing exacerbated formation of UV-B induced thymine dimers and blocked light-induced repair of the dimers. The MSH2 silencing also affected the progression of male meiosis to a varying degree with either halt of meiosis at zygotene stage or formation of diploid tetrads. The immunostaining of male meiocytes with centromere localized CENPC (Centromere protein C) protein antibody showed the presence of 48 univalent along with 24 bivalent chromosomes suggesting abnormal tetraploid meiosis. The mitotic cells of root tips of silenced lines showed diploid nuclei but lacked intervening cell plates leading to cells with syncytial nuclei. Thus we speculate that tetraploid pollen mother cells may have arisen due to the fusion of syncytial nuclei before the onset of meiosis. It is likely that in addition to Mismatch repair (MMR), MSH2 may have an additional role in regulating ploidy stability.

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“…This technique is now applied to rice, maize, lotus, poplar , Brassica, zebrafish, Drosophila, Caenorhabditis and human , indicating its broad applicability. The implication of ECO-TILLING to identify potential novel functional alleles in the known and candidate genes/transcription factors (TFs) regulating qualitative and quantitative agronomic traits by association/genetic mapping is well-documented for expediting the genetic enhancement of crop plants (Mejlhede et al, 2006;Barkley and Wang, 2008;Ibiza et al, 2010;Negrao et al, 2011;Yu et al, 2012;Frerichmann et al, 2013). ECO-TILLING usually employs a mismatchspecific CEL-I nuclease to cleave the PCR amplified fragments at the site of heteroduplex formation involving nucleotide (SNP-allelic) polymorphism.…”

Section: Eco-tillingmentioning

confidence: 99%

Tilling and Eco-Tilling - A Reverse Genetic Approach for Crop Improvement

Khan¹,

Abidi²,

Bhat³

et al. 2018

Int.J.Curr.Microbiol.App.Sci

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EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1that are associated with annuality and winter hardiness

Cited by 36 publications

References 58 publications

EcoTILLING in Cochliobolus sativus Isolates Reveals Polymorphisms in the XYL1 and XYL2

EcoTILLING in Cochliobolus sativus Isolates Reveals Polymorphisms in the XYL1 and XYL2

MutS-Homolog2silencing generates tetraploid meiocytes in tomato (Solanum lycopersicum)

Tilling and Eco-Tilling - A Reverse Genetic Approach for Crop Improvement

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