Mutation scanning of peach floral genes

BackgroundMutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM) analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I.ResultsHRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA.ConclusionsNatural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.

• Publication year

  2011

• Venue

  BMC Plant Biology

• Publication date

  2011-05-23

• Fields of study

  Biology, Agricultural and Food Sciences, Medicine

• Identifiers
  DOI 10.1186/1471-2229-11-96PMID 21605436PMCID 3120741
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• BRAFV600E detection in melanoma is highly improved by COLD-PCR.

  2011cited by this paper
• Comparison of gene order in the chromosome region containing a TERMINAL FLOWER 1 homolog in apricot and peach reveals microsynteny across angiosperms

  2010influential reference
• Reverse genetics techniques: engineering loss and gain of gene function in plants.

  2010cited by this paper
• A cost-effective high-resolution melting approach using the EvaGreen dye for DNA polymorphism detection and genotyping in plants.

  2010cited by this paper
• Genetic variation, population structure and linkage disequilibrium in peach commercial varieties

  2010cited by this paper
• Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations

  2010cited by this paper
• NEATTILL: A simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications

  2010cited by this paper
• Comparative analysis of pyrosequencing and QMC‐PCR in conjunction with high resolution melting for KRAS/BRAF mutation detection

  2010cited by this paper
• Engineering Melon Plants with Improved Fruit Shelf Life Using the TILLING Approach

  2010cited by this paper
• Quick-multiplex-consensus (QMC)-PCR followed by high-resolution melting: a simple and robust method for mutation detection in formalin-fixed paraffin-embedded tissue

  2010influential reference
• Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations

  2009cited by this paper
• A PLENA-like gene of peach is involved in carpel formation and subsequent transformation into a fleshy fruit

  2009cited by this paper
• High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology

  2009cited by this paper
• A Modified TILLING Method for Wheat Breeding

  2009cited by this paper
• COLD-PCR-enhanced high-resolution melting enables rapid and selective identification of low-level unknown mutations.

  2009cited by this paper
• Mutation scanning and genotyping by high-resolution DNA melting analysis in olive germplasm.

  2009cited by this paper
• Replacing PCR with COLD-PCR enriches variant DNA sequences and redefines the sensitivity of genetic testing

  2009cited by this paper
• MNU-induced mutant pools and high performance TILLING enable finding of any gene mutation in rice

  2008influential reference
• Reducing the content of nornicotine in tobacco via targeted mutation breeding

  2008influential reference
• High‐throughput amplicon scanning of the TP53 gene in breast cancer using high‐resolution fluorescent melting curve analyses and automatic mutation calling

  2008cited by this paper
• Replacing PCR with COLD-PCR enriches variant DNA sequences and redefines the sensitivity of genetic testing

  2008cited by this paper
• Endonucleolytic mutation analysis by internal labeling (EMAIL)

  2008influential reference
• High resolution melting analysis of almond SNPs derived from ESTs

  2008cited by this paper
• PpAG1, a homolog of AGAMOUS, expressed in developing peach flowers and fruit

  2006cited by this paper
• Spidey: a tool for mRNA-to-genomic alignments.

  2001cited by this paper
• Inbreeding and Coancestry of Freestone Peach Cultivars of the Eastern United States and Implications for Peach Germplasm Improvement

  1985cited by this paper
• BMC Medical Genetics BioMed Central Research article High-throughput mutational analysis of TOR1A in primary dystonia

  year unknowncited by this paper

• Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus

  2022cites this paper
• The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L.

  2018cites this paper
• Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities

  2017cites this paper
• Haplotype analysis of the germacrene A synthase gene and association with cynaropicrin content and biological activities in Cynara cardunculus

  2017cites this paper
• Mutation Detection by Analysis of DNA Heteroduplexes in TILLING Populations of Diploid Species

  2017cites this paper
• QMC-PCRx: a novel method for rapid mutation detection

  2017cites this paper
• MRSA Methicillin-Resistant Staphylococcus aureus MBC Minimum bactericidal concentration MIC Minimal inhibitory concentration MAF Minor allele frequency

  2017cites this paper
• High-Resolution DNA Melting Analysis in Plant Research.

  2016cites this paper
• Induced Mutations and Crop Improvement

  2015cites this paper
• HRM analysis of chloroplast and mitochondrial DNA revealed additional genetic variability in Prunus

  2015cites this paper
• EMS mutagenesis and qPCR-HRM prescreening for point mutations in an embryogenic cell suspension of grapevine

  2014cites this paper
• Allele Discovery Platform (ADP) in Papaya (Carica papaya L.)

  2014cites this paper
• Nonsense-mediated decay of sucrose synthase 1 mRNA with induced premature chain termination codon during cold acclimation in winter wheat

  2014cites this paper
• A DNA marker assay based on high-resolution melting curve analysis for distinguishing species of the Festuca–Lolium complex

  2014cites this paper
• Characterization of Peach TFL1 and Comparison with FT/TFL1 Gene Families of the Rosaceae

  2013cites this paper
• Gene Identification: Reverse Genetics

  2013cites this paper
• High Resolution Melting Analysis Is a More Sensitive and Effective Alternative to Gel-Based Platforms in Analysis of SSR – An Example in Citrus

  2012cites this paper
• Temperature-Tolerant COLD-PCR Eliminates Temperature Stringency and Enables Robust Mutation Enrichment

  2012cites this paper
• Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment.

  2012cites this paper
• Development of TILLING by sequencing platform towards enhanced leaf yield in tobacco

  2012cites this paper
• Targeted mutation breeding of horticultural plants

  2012cites this paper
• Characterization of the Genetic Diversity of Peach Cultivars in Taif by RAPD-PCR

  2011cites this paper