Genetics Trihybrid Cross Problem
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Questions and Answers

What is the name of the molecular marker technique that combines RFLP and RAPD methods?

  • RAPD
  • RFLP
  • PCR
  • AFLP (correct)

What is the purpose of using oligonucleotide adapters in AFLP?

  • To amplify the entire genome
  • To ligate to the ends of DNA fragments (correct)
  • To increase the length of DNA fragments
  • To decrease the specificity of the restriction enzymes

What is the characteristic of AFLP that makes it a DNA fingerprinting technique?

  • It involves the display of a set of DNA fragments from a specific DNA sample (correct)
  • It uses a large set of genetic primers
  • It requires prior knowledge of the DNA sequence
  • It involves sequencing of the entire genome

What is the purpose of using radioactively labelled primers in AFLP?

<p>To visualize the amplified fragments (D)</p> Signup and view all the answers

What is the typical number of restriction enzymes used in AFLP?

<p>Two (B)</p> Signup and view all the answers

What is the characteristic of AFLP that makes it different from other molecular marker techniques?

<p>It produces fingerprints without prior sequence knowledge (C)</p> Signup and view all the answers

What was the main objective of the Human Genome Project?

<p>To identify and map all the genes in the human DNA. (C)</p> Signup and view all the answers

What is the term for individuals that have the same form of a gene?

<p>Monomorphic (D)</p> Signup and view all the answers

When was the Human Genome Project formally launched?

<p>1990 (C)</p> Signup and view all the answers

What is the approximate number of genes in the human DNA?

<p>20,000-25,000 (B)</p> Signup and view all the answers

In a three-point cross, how many loci are involved?

<p>Three (D)</p> Signup and view all the answers

What is the purpose of a test cross?

<p>To identify the genotype of an individual with unknown genotype (D)</p> Signup and view all the answers

What was the duration of the Human Genome Project?

<p>13 years (D)</p> Signup and view all the answers

What type of sequence is used as an STS?

<p>EST (B)</p> Signup and view all the answers

Which company acquired 454 in 2007?

<p>Roche (C)</p> Signup and view all the answers

What was the Human Genome Project?

<p>A project to sequence the human genome (D)</p> Signup and view all the answers

What is unique about the DNA library construction in the 454 sequencing system?

<p>It uses spray method to break DNA samples into small fragments. (C)</p> Signup and view all the answers

What is another term for a three-point cross?

<p>Trihybrid cross (B)</p> Signup and view all the answers

What is the purpose of Emulsion PCR in the Roche 454 system?

<p>To amplify DNA samples. (C)</p> Signup and view all the answers

How are recombination frequencies calculated in a three-point cross?

<p>As we did before for one pair of loci (A)</p> Signup and view all the answers

When was the 454 sequencing system launched?

<p>2005 (A)</p> Signup and view all the answers

What is the significance of the Human Genome Project?

<p>It was one of the great feats of exploration in history (A)</p> Signup and view all the answers

What is the primary goal of short read alignment?

<p>To map reads back to human reference (C)</p> Signup and view all the answers

Which of the following de novo assembly strategies uses a DeBruijn graph algorithm?

<p>Velvet (A)</p> Signup and view all the answers

What is the product of the assembly step in the genomic DNA sequencing process?

<p>Contigs (A)</p> Signup and view all the answers

In comparative assembly, what is the purpose of merging assemblies?

<p>To combine assemblies from multiple genomes (B)</p> Signup and view all the answers

What is gene prediction in the context of genome annotation?

<p>Identifying elements on a genome (C)</p> Signup and view all the answers

What is the primary difference between structural and functional annotation in genome annotation?

<p>Identifying elements versus attaching biological information (C)</p> Signup and view all the answers

Which of the following is NOT a de novo assembly strategy?

<p>Genomic DNA (C)</p> Signup and view all the answers

What is the purpose of finishing reads in the genomic DNA sequencing process?

<p>To verify the assembly (A)</p> Signup and view all the answers

What is one of the main applications of whole genome sequencing?

<p>Predicting disease susceptibility based on gene sequence variation (B)</p> Signup and view all the answers

What is the primary advantage of Next Generation Sequencing?

<p>Faster and cheaper sequencing of entire genomes (C)</p> Signup and view all the answers

What is the primary purpose of paired-end sequencing?

<p>To determine the orientation of genomic fragments (D)</p> Signup and view all the answers

What is a challenge in Next Generation Sequencing?

<p>The difficulty of assembling genomic fragments (B)</p> Signup and view all the answers

What type of sequencing produces short reads?

<p>Next Generation Sequencing (B)</p> Signup and view all the answers

Which company is associated with the 454 FLX sequencing platform?

<p>Roche (B)</p> Signup and view all the answers

Flashcards

Monomorphic trait

A genetic trait that is found in most individuals within a population.

Polymorphic trait

A genetic trait that has multiple variations within a population.

Three-point cross

A technique to study the inheritance of three genes by observing the frequency of recombinant offspring.

Recombination frequency

The frequency at which recombination occurs between two genes on a chromosome.

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Human Genome Project (HGP)

An international research project aimed at sequencing the entire human genome which was completed in 2003.

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Genome

The complete set of genetic instructions in an organism.

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Genome sequencing

The process of determining the sequence of DNA bases in a genome.

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Next-Generation Sequencing (NGS)

Techniques that allow for rapid and cost-effective sequencing of entire genomes, producing short DNA sequences called reads.

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454 sequencing

A sequencing technology that uses emulsion PCR to amplify DNA fragments on beads and detect the sequence by a spray method.

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Illumina sequencing

A sequencing technology that uses a different DNA library preparation and amplification method compared to 454 sequencing.

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AFLP (Amplified Fragment Length Polymorphism)

A PCR-based molecular marker technique that combines RFLP and RAPD methods for DNA fingerprinting.

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RFLP (Restriction Fragment Length Polymorphism)

A technique used to identify genetic variations by cutting DNA with restriction enzymes and analyzing the resulting fragments.

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RAPD (Random Amplified Polymorphic DNA)

A technique used to identify genetic variations by amplifying random DNA fragments using PCR.

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Genome Assembly

A technique used to assemble a genome from short DNA sequence reads.

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Genome Annotation

A process of identifying the functional elements within a genome, including genes, regulatory elements, and other features.

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Comparative Assembly

The use of multiple genomes from related species to improve the accuracy and completeness of genome assembly.

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Structural annotation

The process of identifying and characterizing coding and non-coding regions within a genome.

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Functional annotation

The process of assigning biological information to identified genomic elements, such as gene function and regulatory elements.

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Bowtie

A short read alignment tool used in genome assembly.

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Velvet

A de novo genome assembly strategy that uses a graph-based approach.

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SSAKE

A de novo genome assembly strategy that uses a greedy algorithm.

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Edena

A de novo genome assembly strategy that uses a combination of greedy and graph approaches.

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Artifacts

A common problem in genome assembly, where errors are introduced during the sequencing process.

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Artifact Removal

The process of removing errors or artifacts from a genome assembly.

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Short read alignment

The process of determining the order of DNA bases in a genome from short read data.

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Divergent regions

Regions in a genome that show differences between closely related species.

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Study Notes

Genetics and Genomics

  • Monomorphic and polymorphic are two types of genetic traits that can be identified through a three-point cross, which involves studying the inheritance of three genes that affect different traits, such as tail length, fur color, and whisker length.
  • Recombination frequencies can be calculated for each pair of loci in a three-point cross, similar to a dihybrid cross.

Human Genome Project

  • The Human Genome Project (HGP) was an international research project that aimed to sequence and map all the genes in the human genome, completed in 2003.
  • The project's goals included identifying and mapping around 20,000-25,000 genes, determining the sequences of the 3 billion chemical base pairs that make up human DNA, and storing the information in databases.
  • The HGP also aimed to develop more efficient technologies for data analysis, allow private sector access to the information and technologies, and sequence the genomes of other medically important organisms.

Next-Generation Sequencing (NGS)

  • NGS platforms, such as 454, Illumina, ABI's Solid, and Roche's 454 FLX, enable the sequencing of entire genomes in a few days at a very low cost.
  • NGS produces high-throughput data in the form of short reads, which can be used for various applications, including evolutionary studies, personalized medicine, and disease-susceptibility prediction.

Genome Sequencing Technologies

  • 454 sequencing system uses a spray method to break DNA samples into small fragments, adds different adapters at both ends, and amplifies the DNA using emulsion PCR.
  • Illumina sequencing system uses a different method of DNA library preparation and amplification.

AFLP (Amplified Fragment Length Polymorphism)

  • AFLP is a PCR-based molecular marker technique that combines RFLP and RAPD methods.
  • AFLP involves the PCR amplification of genomic restriction fragments generated by specific restriction enzymes and oligonucleotide adapters.
  • AFLP produces a DNA fingerprint without prior sequence knowledge, using a limited set of genetic primers.

Genome Assembly and Annotation

  • Whole genome sequencing provides information about coding and non-coding parts of the genome.
  • Challenges in genome assembly and annotation include removal of artifacts, genome assembly, short read alignment, and annotation and validation.
  • De novo assembly strategies, such as SSAKE, Edena, and Velvet, are used to assemble genomes from short reads.

Comparative Assembly

  • Comparative assembly involves merging assemblies from multiple genomes to produce a more accurate and complete sequence.
  • Comparative assembly can be used to identify divergent regions between genomes.

Genome Annotation

  • Genome annotation is the process of attaching biological information to sequences, consisting of two main steps: identifying elements on the genome (structural annotation) and attaching biological information to these elements (functional annotation).

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Description

This quiz assesses understanding of genetics and inheritance patterns in a trihybrid cross problem, involving loci affecting tail length, fur color, and whisker length. It requires application of genetics principles to predict phenotypes and genotypes of offspring.

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