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Related Concept Videos

Pedigree Analysis01:35

Pedigree Analysis

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Trihybrid Crosses02:27

Trihybrid Crosses

Trihybrid Crosses
Some of Mendel’s crosses examined three pairs of contrasting characteristics. Such a cross is called a trihybrid cross. A trihybrid cross is a combination of three individual monohybrid crosses. For example, plant height (tall vs. short), seed shape (round vs. wrinkled), and seed color (yellow vs. green).
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Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.

Jeffrey B Endelman1, Moctar Kante2, Hannele Lindqvist-Kreuze2

  • 1Department of Plant & Agroecosystem Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.

The Plant Genome
|June 18, 2024
PubMed
Summary
This summary is machine-generated.

A new potato genotyping assay (DArTag) offers a cost-effective method for genetic analysis, improving marker accuracy for breeding. This technology aids in selecting superior potato varieties for enhanced agricultural outcomes.

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Area of Science:

  • Plant genetics and breeding
  • Genomics and bioinformatics
  • Agricultural science

Background:

  • Mid-density targeted genotyping-by-sequencing (GBS) provides a balance of cost and genomic information for plant breeding.
  • Developing efficient and accurate genotyping tools is crucial for accelerating crop improvement.

Purpose of the Study:

  • To develop and validate a targeted genotyping-by-sequencing (GBS) assay for potato (Solanum tuberosum L.) using DArTag technology.
  • To assess the performance of the DArTag assay against existing SNP arrays and evaluate its utility for genomic selection and imputation in polyploid populations.

Main Methods:

  • Development of a 2.5K and later 4K targeted GBS assay for potato using DArTag technology.
  • Selection of markers from the potato Infinium SNP array to maximize genome coverage and polymorphism.
  • Comparison of DArTag and SNP array platforms using dendrograms and quantitative agreement metrics (RMSE).
  • Evaluation of marker imputation accuracy using the R package polyBreedR with linkage analysis and random forest methods.

Main Results:

  • DArTag and SNP array platforms produced equivalent dendrograms, with 83% of common markers showing good quantitative agreement (RMSE < 0.5).
  • Marker imputation using linkage analysis in polyploid populations achieved a significantly lower RMSE (0.15) compared to random forest (0.42).
  • DArTag markers successfully tracked targets for key potato traits, including disease resistance (potato virus Y, golden cyst nematode, potato wart) and agronomic traits (maturity, tuber shape).

Conclusions:

  • The potato DArTag assay is a cost-effective and transformative technology for potato breeding and genetics.
  • The assay is suitable for genomic selection in clonal evaluation trials and can be coupled with imputation for training populations.
  • The DArTag technology is publicly available, facilitating its adoption in potato research and breeding programs worldwide.