Midterm Exam 2 Flashcards by Anna Zimmerman

The main steps in a PCR reaction are, in order:

Denaturing of the target DNA, addition of primers (single stranded oligonucleotides), annealing of the primers to the DNA, and primer extension

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Having multiple copies of a gene may translate into a stronger phenotype but this is not always true.

True

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IF the presence of aroma was always associated with susceptibility to a disease, which of the following is a most likely explanation?

Pleiotropy

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The reason restriction enzymes are so useful is that they make cuts at specified intervals (e.g. every 20 bp for EcoRI) rather than at specific recognition sequences in the DNA.

False

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The presence of aroma in rice, according to the assigned paper, is due to

a premature stop codon in the BAD-2 gene

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The highest temperature (~94oC) in a PCR reaction is used for which of the following

Denaturing template DNA

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Reverse transcriptase is an enzyme that would most likely be used to create which type of DNA library?

cDNA

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A molecular marker that is linked to a gene controlling a trait of interest can be useful for marker assisted selection but not as a starting point for eventually cloning the gene of interest.

False

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A BAC contig is a set of non-overlapping BAC clones created by fragmenting a single sequence of interest into fragments of identical size and then cloning the fragments.

False

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Where do you think it is most likely to find SSR polymorphisms?

UTRs, introns, or intergenic DNA

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Molecular marker and morphological marker polymorphism data are both useful for genetic analysis, but molecular markers are more often used because they are more abundant.

True

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Silent, Missense, and Nonsense mutations can all be generated by SNP polymorphisms

True

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What is the relationship between restriction enzyme recognition sequence length and the average frequency (in terms of base pairs) at which that enzyme will cut in a sample of genomic DNA?

Shorter length = higher frequency

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For most sequencing techniques, PCR is a required pre-step, with the goal of amplifying the target DNA that will be sequenced.

True

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Which of the following suggests that the BAD2 gene is involved in fragrance in rice?

Sequence alignments of the fgr region between a non-fragrant and a fragrant variety revealed polymorphisms in the BAD2 gene.

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In most plants, a first step in learning how many genes determine a phenotype (either qualitative or quantitative) is to:

clone the genes determining the phenotype

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If a molecular marker is monomorphic (i.e. no polymorphism) in a particular cross, this indicates that the two parents have the same alleles at the marker locus.

True

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Mutations are rare and usually deleterious. However, genetic analysis requires abundant DNA polymorphisms. Where would you most likely expect to find abundant polymorphisms that do not lead to major effects on phenotype?

UTRs

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Non-coding regions of the genome may be more likely to be polymorphic than coding regions and thus more efficient for generating molecular markers. Which of the following is the most likely explanation for this observation?

Mutations are generally random events and since changes in the sequence of non-coding regions are less likely to cause changes in phenotype, these mutations will persist.

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In the “The gene for fragrance in rice” the authors found that 71% of rice genes were homologs to genes in Arabdopsis. The existence of homologs between two species suggests:

A common ancestor

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All rice varieties we know of today are cross-pollinated and originated in Asia

False

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Which of the following suggests that the BAD2 gene is involved in fragrance in rice?

Sequence alignments of the fgr region between a non-fragrant and a fragrant variety revealed polymorphisms in the BAD2 gene.

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There is not a conversion factor between linkage distance and physical distance. A distance of 1 centimorgan may correspond to 5 kb in one part of the chromosome and 500 kb in another part of the chromosome.

True

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cDNA libraries are different than gDNA libraries in that they contain only:

DNA sequences that can potentially be expressed

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In “The gene for fragrance in rice” paper, the authors conclude that the functional basis for the difference between aroma vs. non-aroma alleles is probably

a premature stop codon in the aromatic allele due to deletions which caused a frameshift mutation.

A key consideration in choosing a vector (for example, a plasmid or a bacterial artificial chromosome) for propagating and maintaining a population of DNA fragments is

the size of the DNA insert

The rice BAD (betaine aldehyde dehydrogenase) gene is part of ____ - a group of genes with similar sequence and function, which commonly arise as a result of gene or genome duplication events. A gene cluster

A gene family

If you wanted to study the inheritance of rice, you could assess aroma in the F2 generation and use a chi square test to determine the number of genes involved. However, you would not be able to determine the DNA basis of the aroma vs. non-aroma, using this method.

True

Which of the following is FALSE about the Sanger sequencing technique?

The reading frame of the gel starts at the longest fragment and ends at the shortest fragment

What makes TAQ polymerase so special and useful for PCR?

Works at high temperatures

Restriction enzymes:

Are isolated from bacteria, where they are part of a defense system against pathogens

Molecular marker polymorphisms are always within the coding regions of genes.

False

Rice is a model plant for the grasses because of its:

Small genome size, short generation time, amenability to genetic transformation, and economic importance

In the “The gene for fragrance in rice” the authors found that 71% of rice genes were homologs to genes in Arabdopsis. The existence of homologs between two species suggests:

A common ancestor

Genetic maps (also called linkage maps) are in units of kilo base pairs, while physical maps are in units of centimorgans.

False

A Simple Sequence Repeat (SSR) marker is based on

conserved sequences flanking a repeat motif sequence

The main reason why the corn genome is much bigger than the rice genome is that the corn genome contains more:

Transposable elements

According to the authors of “The gene for fragrance in rice” paper, there is no evidence that the BAD gene has pleiotropic effects on fragrance and stress tolerance. In other words, fragrance and stress tolerance seem to:

Not be determined by the same gene

Changes in DNA sequence that lead to new molecular marker alleles at a locus may not cause changes in phenotype.

True

In the PCR process which of the following determines what DNA sequence will be amplified by the polymerase?

primers

What is the role of vectors (e.g. plasmid or BAC) in DNA library preparation?

propagate and maintain DNA fragments generated by the restriction digestion

The Illumina HiSeq is based on the principle of ionic current modulation.

False

Which sequencing technique produces the longest reads?

Nanopore

In the Ilumina HiSeq, each DNA fragment results in:

2 short reads, one from the 3'end and another from the 5' end

Illumina sequencing is a better option for determining the correct sequence of recessive alleles due to loss-of-function mutations than Nanopore sequencing, because Nanopore sequencing requires simultaneous integration of phenotype and genotype.

False

In the Illumina Hiseq technique, it is essential that the DNA fragments are abundantly replicated in clusters because the fluorescence signal from one DNA molecule alone is not strong enough to be visualized. Which of the following plays an essential role in ensuring that the fragments are replicated in clusters?

Adaptors

The principle of sequencing by ionic current modulation is mainly based on the disruption of the ionic current being independent of the shape of the molecule (A, T, C or G) translocating through the pore.

False

Which of the following is FALSE about the Illumina HiSeq technique?

Fluorescent tags are added on the terminal phosphate of each nucleotide

If I wanted to look for polymorphisms between two protein sequences, which would be the best platform to do this?

BLASTp

If I wanted to find the DNA sequence of the Vrs1 gene in barley, which is the best platform to conduct this search?

NCBI Nucelotide

In a NCBI nucleotide entry, if you click on cds you will get:

The sequence of a gene, including introns (if the gene has introns and the sequence is from genomic DNA).

The plasmid libraries used for PACBio and Nanopore sequencing are unique in that the plasmid cloning sites have overhangs.

False

An Illumina sequencing library and a BAC library differ in that the Illumina library is used for the sequencing project and then is no longer available, whereas a BAC library can be conserved and re-used.

True

You are interested in aroma in mint and you know that the BAD2 gene is responsible for aroma in rice. You are wondering if there is a similar gene in mint. What can you do?

BLAST the BAD2 gene sequence against the mint genome sequence.

Which of these techniques is NOT based on the principle of sequencing by DNA synthesis?

Nanopore

In the PAC Bio sequencing technique:

The added nucleotides are fluorescence tagged from their phosphate terminal

If your goal was to get as much long-read genome sequence as possible at the best price and in the shortest possible time for your favorite plant, which of the following methods would you choose?

Pacific Biosciences (PAC Bio)

Which sequencing technique utilizes chain termination?

Sanger

In PAC Bio sequencing, having the fluorescence tag attached to the terminal phosphate of the nucleotide (instead of to the base of the nucleotide) allows for shorter reads.

False

Which of the sequencing techniques can, at least theoretically, easily be done in the middle of an isolated field?

Nanopore

Kary Mullis, who received a Nobel prize for his development of PCR, is a direct beneficiary of royalties from Nanopore sequencing because PCR technology is essential for this sequencing technique.

False

If I wanted to look for polymorphisms between two protein sequences, which would be the best platform to do this?

BLASTp

If I wanted to find the DNA sequence of the Vrs1 gene in barley, which is the best platform to conduct this search?

NCBI Nucleotide

In the Ilumina HiSeq, each DNA fragment results in:

2 short reads, one from the 3'end and another from the 5' end

In the PAC Bio sequencing technique:

The added nucleotides are fluorescence tagged from their phosphate terminal

Which of these techniques is NOT based on the principle of sequencing by DNA synthesis?

Nanopore

In PAC Bio sequencing, having the fluorescence tag attached to the terminal phosphate of the nucleotide (instead of to the base of the nucleotide) allows for shorter reads.

False

Adaptors

Dideoxy nucleotides are feature of which sequencing technique:

Sanger

In assembling a genome based on short reads, which of the following is most true?

It is very useful to have a reference genome to anchor the fragments to

You are interested in aroma in mint and you know that the BAD2 gene is responsible for aroma in rice. You are wondering if there is a similar gene in mint. What can you do?

BLAST the BAD2 gene sequence against the mint genome sequence.

False

Which of these sequencing techniques does not require PCR to be done previous to sequencing?

Nanopore

In a NCBI nucleotide entry, if you click on cds you will get:

The sequence of a gene, including introns (if the gene has introns and the sequence is from genomic DNA).

Which of the sequencing techniques can, at least theoretically, easily be done in the middle of an isolated field?

Nanopore

In the “The gene for fragrance in rice” paper, the authors found many strong lines of evidence that the BAD2 gene is responsible for aroma in rice. However, additional experimentation is required to prove the causal effect of this gene on the phenotype. This could be done by:

Knocking out the BAD2 gene of a non-aromatic rice and observing a phenotypic change.

Which of the following is FALSE about the Illumina HiSeq technique?

Fluorescent tags are added on the terminal phosphate of each nucleotide

Which sequencing technique produces the longest reads?

Nanopore

Which sequencing technique utilizes chain termination?

Sanger

If your goal was to get as much long-read genome sequence as possible at the best price and in the shortest possible time for your favorite plant, which of the following methods would you choose?

Pacific Biosciences (PAC Bio)

The Illumina HiSeq is based on the principle of ionic current modulation.

False

Reporter genes are included in transgenic constructs in order to

provide a mechanism for localizing and/or quantifying gene expression.

A construct leading to low polyphenol oxidase activity in a diploid will be expected to show Mendelian inheritance if the transgenic plant is crossed with a variety that has high polyphenol oxidase activity.

True

Genome editing is a technology that requires information about target genes in order to make specific changes in them that will result in changes in phenotype

True

Introns are never included in transgene constructs because they do not have any function.

False

In both hemizygotes and homozygotes for the CP4 EPSPS gene, the EPSPS enzyme (susceptible to gyphosate) is still produced, even though they are resistant to the herbicide.

True

The RISC complex consists of

argonaute protein and a short (~ 21 nt) segment of RNA

Which of the following is an example of a reporter gene?

Green fluorescent protein (GFP)

The Tnos terminator sequence:

signals an end to transcription.

An example of a constitutive promoter is one that allows a transgene to:

be expressed in all tissues all the time.

In a TILLING population, the random mutations are a result of:

Errors in DNA replication and repair

Coincidentally, the gene conferring resistance to glyphosate herbicide was found in the same organism that provided the gene for green florescent protein.

False

Selectable markers (e.g. antibiotic resistance genes) are added to transgene constructs

to facilitate selection of cells that incorporated and are expressing the transgene

In the CRISPR acronym, the “P” stands for:

Palindromic

A chemical company puts the Roundup herbicide resistance gene into sugar beet. A sugar beet plant homozygous for the Roundup resistance gene cross-pollinates with an edible beet plant homozygous for the lack of the Roundup resistance gene. Assume Round-up resistance is dominant. You would expect the F2 of this cross to segregate

3 resistant: 1 susceptible

The RNA primers that initiate DNA replication are encoded by the same genes encoding miRNAs

False

If you use a promoter that is expressed only in floral tissue it would be best described as:

Tissue-specific

In the context of RNAi, Dicer will cleave

Double stranded RNA

The sentence: “In a diploid plant, once the CRISPR machinery is present in the genome, the edited sequence will be present in both homologous chromosomes.” applies:

Independent if the gene editing is conducted via transient or non-transient methods

The CRISPR-cas9 system is potentially more attractive to plant geneticists that ionizing radiation or chemical mutagenesis because:

It is a targeted mutation system that has a lower likelihood of effects on non-target genes.

The CRISPR-Cas9 gene editing system was developed based on a naturally occurring defense system in what type of organism:

Bacteria

A key element needed for the development of glyphosate-resistant crops is that there must be sufficient expression of the CP4 EPSPS enzyme to overcome the expression of the EPSPS enzyme, because:

The CP4 EPSPS transgenic plant contains both the EPSPS gene as well as the CP4 EPSPS gene.

Agrobacterium tumefaciens, it will automatically be introduced at the same position on homologous chromosomes.

False

RNAi can involve a range of mechanisms, including transcriptional inhibition, mRNA cleavage, and translational inhibition.

True

It has been reported in Arabdopsis that the heat shock protein (HSP) terminator increases transgene expression compared to other transgene terminators. This suggests that terminators are not generic sequences.

True

Which of the following type of RNAi is widely used experimentally to degrade specific mRNAs?

Small interfering (si)RNA

When using ionizing radiation to induce mutations, it is possible to increase the frequency of mutations by manipulating the radiation dosage.

True

In the CRISPR-Cas9 gene editing system, the role of the guide RNA is to:

Ensure that the target DNA is cut at a specific target site

The principal drawback to the Agrobacterium method of gene transformation is that all the transformed plants also have crown gall disease.

False

RNAi is triggered by the presence of ______ in the cytoplasm:

Doubled stranded RNA molecules

A _____ encodes a protein (enzyme) that allows the transformed cells to grow while the growth of the non-transformed cells is inhibited.

Selectable marker

Which of the following techniques leaves the gene intact and unaltered but leads to a mutant phenotype by targeting gene transcripts?

RNAi

A TILLING population is a population of individuals originated from an inbred line, all containing the same mutation.

False

Which method is the most specific for creating specific and targeted mutations?

CRISPR/Cas9

The “Arctic” apple was developed using which one of the following techniques?

RNAi

Which of the following transgenic plant examples presented in class involved multiple transgenes required to for the target phenotype?

EPSPS in soybean

Which of the following are the minimal requirements for a transgene construct?

promoter, coding region, and terminator

RNAi is considered a fairly precise method for gene silencing due to the partial/complete complementary base pairing between the target mRNA and the:

Guide RNA (single stranded miRNA or siRNA)

You produce a test-cross generation (e.g. F1 x homozygous recessive parent) of 100 plants. The cross history is as follows: A Roundup resistant homozygote was crossed with a non-Roundup resistant homozygote to produce an F1. Assume resistance to Roundup is dominant. What ratio of living: dead do you expect in the test-cross generation?

50 resistant: 50 susceptible

A genetic engineering technique that involves microprojectile bombardment of tissues with small particles coated with transgene DNA is known in the popular press as

the gene gun method

Which of the following best describes the key difference between transgenics and cisgenics?

Cisgenics involves non-sexual transfer of genes from the same or closely related species whereas transgenics involves non-sexual transfer of genes from species that are not sexually compatible

Reporter genes are often included in transgene constructs to:

Indicate the location and level of expression of the transgene

A key difference between transgenics and genome edits is that transgenic strategies involve transfer of a gene from one organism to another whereas genome editing involves altering the DNA sequence of the target organism

True

The insertion of a transgene into somatic tissues may be an interesting strategy in the varietal improvement of:

Bananas

Which of the following type of RNAi is widely used experimentally to degrade specific mRNAs?

small interfering (si)RNA

The CRISPR-Cas9 gene editing system can only be used to knock-out target genes; it cannot change or add functionality to existing genes.

False

Inducing mutations via mutagenic treatment is a generic method in that mutations are generated randomly in the target genome. However, some mutagens tend to cause specific types of changes – for example, chemical treatment with EMS usually induces a G:C to A:T SNP.

True

The nptII gene, which confers resistance to the antibiotic kanamycin, was used as a selectable marker in the EPSPS transgene construct. Thus, after transformation, EPSPS transgenic cells are selected by:

Kanamycin application

In both hemizygotes and homozygotes for the CP4 EPSPS gene, the EPSPS enzyme (susceptible to gyphosate) is still produced, even though they are resistant to the herbicide.

True

When inserting a transgene construct into the T-DNA of a Ti-plasmid for delivery via the Agro method, the right and left borders of the T-DNA are kept flanking the transgene construct because:

They contain sequences that are important for the integration of the transgene into the genome of the host plant

Which of the following best describes a transposable element?

a DNA sequence that can move to a new site in the genome

Transposable elements can play a major role in plant evolution by:

Creating new genes, modifying or re-programing existent genes, and even causing chromosomal arrangements

An example of a non-autonomous transposon would be a Class 1 transposon (retrotransposon) lacking the ability to encode ______ and a Class 2 transposon (DNA transposon) lacking the ability to encode ______ .

Reverse transcriptase | Transposase

In the case of codominance, heterozygous F2 plants can be phenotypically distinguished from homozygous F2 plants.

True

In the case of incomplete dominance, where one parent has red flowers, the other parent has white flowers and the F1 has pink flowers what will be the expected ratio of flower color in doubled haploids derived from the F1?

1 red: 1 white

Which of the following terms best describes the interaction of alleles at two loci?

Epistatis

The color of grapes is an example of a phenotype influenced by transposon activity. In black grapes, the transcription factor VvMybA1 upregulates anthocyanin production. In white grapes, a retrotransposon is inserted within the transcription factor sequence, causing a loss of function.

True

A ratio of 3:1 in a doubled haploid population could be diagnostic of two-locus epistasis.

True

Diploid plants with the same genome sizes will all have the same numbers of chromosomes.

False

Which of the following has been revealed by a deeper understanding of genome sequence and architecture?

More regulatory factors than anticipated

DNA methylation:

Decreases gene expression

Transposable elements in plants are

up to half of the DNA content in many nuclear genomes

Fragaria vesca (woodland strawberry) is 2n = 2x = 14. This plant is reported to have 35,000 genes, and a genome size of 240 Mb. Considering these facts, one could most reasonably conclude that

a portion of the genome does not consist of protein coding genes

Which of the following would be evidence of transposable element activity in a gene conferring kernel pigment color in maize?

colored sectors in a white kernel

“The gene for fragrance in rice” paper describes a classic example of dominant allele conferring “more” of a phenotype, in this case fragrance. In other words, rice varieties with at least one dominant allele at the BAD2 locus are more fragrant than varieties that are homozygous recessive at the BAD2 locus.

False

A _____ is an estimated DNA sequence comprised by contigs and gaps of estimated sizes.

Scaffold

A fundamental expectation underlying the F1 hybrid seed industry is that the F1 of the cross of two inbred parents is expected to be 100% heterozygous at the loci where the parents have alternative alleles.

True

In a perfect genetic/physical map, the number of pseudochromosomes is equal to the number of chromosomes in a given species.

True

If you were interested in identifying which genes are expressed in fruits vs. roots, which of the following approached would be most useful?

RNA sequencing (RNAseq)

If you were to obtain the complete nuclear genome of an organism, such as Fragaria vesca, would you expect to find genes encoding tRNAs and rRNAs? If yes, in what abundance?

Yes, and in abundance

If you cross two inbred parents, both low in cyanide, and observe high cyanide in the F1 and a 9:7 ratio of high to low cyanide in the F2, you might hypothesize that which of the following is responsible?

Epistasis

The C value paradox is best defined by which of the following statements?

Organisms of similar evolutionary complexity may vary significantly in genome size

DNA transposons move via an RNA intermediate whereas retrotransposons move via a DNA cut and paste mechanism

False

Class 1 transposable elements, also called retrotransposons, replicate their own sequence into another place in the genome, thus, leading to genome expansion. In contrast, Class 2 transposable elements move in the genome by a cut and paste mechanism: therefore, their activity does not lead to genome expansion.

False

Because transposable elements in plants can eliminate or alter gene function, they are usually

epigenetically silenced

In cases of incomplete dominance, heterozygous F2 plants can be phenotypically distinguished from homozygous F2 plants.

True

You are a geneticist working on okra. Knowing the Haldane cM distance between two loci in an ancestral diploid species and in a polyploid relative is most useful for potentially understanding which of the following?

Homoeology and synteny

Locus A determines flower color. The dominant allele produces an enzyme critical for pigment formation, which gives a red color. The recessive allele is non-functional and gives no color (white flowers). Knowing that the two alleles show partial dominance, what phenotypic ratio do you expect in the F2 from a cross between a plant with white flowers and one with red flowers, both completely homozygous?

1 red : 2 pink : 1 white

A common feature of the F2 epistatic ratios presented for two unlinked loci is that they all add up to

According to the classical “overdominance theory” for heterosis, it should be possible to develop an inbred with performance equal to the F1.

False

The number of transposable elements in and around genes is most likely to

Increase with time

In general, if genome sizes of flowering plants are compared to those of other organisms,

flowering plants show the greatest range in genome sizes

Which type of heterosis for grain yield in maize is most likely to be preferred in the hybrid seed business?

High parent heterosis

Epigenetic changes are heritable. They are, however, potentially reversible. That’s why it is very useful to know if a phenotype is due to epigenetics, but could be risky to depend on epigenetics for a phenotype because the phenotype could revert at some point in the future.

True

After years of research, Barbara McClintock discovered the role of transposons in colored kernels in maize. A small pigmented spot in a white kernel suggests that:

A transposon was excised late in kernel development

Which of the following plants would you expect to suffer the most from inbreeding depression?

Maize (cross pollinated)

What is the approximate number of genes one might expect in a diploid plant? For this question use the classical definition of a gene: a DNA sequence that codes for a mRNA that is translated to a protein, or that codes for a functional RNA (tRNA or rRNA).

30,000

There are two classical theories for the genetic basis of hybrid vigor. These are:

Overdominance and dispersed dominant genes

Flow cytometry is a technique used to:

Measure genome size

In the Fragaria genome sequencing paper, the authors

Chose a wild diploid species because of the small genome size

If a species is 2n = 2x = 14 and there is complete genome sequence information available, how many pseudochromosomes would you expect?

In addition to being cold tolerant, facultative type barleys do not require vernalization to flower because:

The VRN-H2 gene is completely deleted.

The two classical theories of heterosis are mutually exclusive in that according to one of the theories the F1 will always be superior to the parents and according to the other theory it is theoretically possible to accumulate all possible favorable alleles in a single homozygous plant

True

In the reading on sequencing the Fragaria genome, the authors show a diagram demonstrating that different types of genes are expressed in fruits and roots. (Technically speaking the part of the strawberry we usually eat is neither a fruit nor a berry, but that is a matter for another class). This means that if you eat a strawberry "fruit" you are eating the same genes (as DNA) that are present in a root, or for that matter, a leaf.

True

Transposable elements and their proliferation may help to explain the C value paradox

True

Gene ontology is a representation of:

Gene and gene product

Genes can be regulated:

All the answers are correct

We can always predict a phenotype directly from the coding sequence of gene.

False

Transposable elements are always very small and never exceed 21 nucleotides in length

False

Which of the following is true about the C-value?

C-value refers to a constant value. The term came up when scientists observed that within a species the genome size is quite constant.

In the woodland strawberry genome sequencing project, before extracting total RNA from roots and fruits and characterizing the transcriptomes of these tissues, the authors subjected plants to a wide array of environmental conditions in order to:

Maximize the number of mRNAs transcribed

In the case of complete dominance, the homozygous recessive condition always leads to less of a phenotype (e.g. less color, less aroma, fewer fertile florets per rachis node)

False

In the woodland strawberry genome sequencing project, some scaffolds were anchored to bins. Imagine two given scaffolds A and B that anchored to Bin X, which is between markers 1 and 2. One can say:

That scaffolds A and B are located somewhere between markers 1 and 2.

Which of the following is the best definition of a transcription factor, such as the functional allele (Nud) at the nud locus?

A gene that encodes a protein that binds to DNA, thus regulating gene expression.

Match the conceptual model with the intra-locus interaction: The dominant allele is functional and overrules the effect of the recessive allele, which is non-functional The dominant allele is functional and does not overrule the effect of the recessive allele, which is non-functional Both dominant and recessive alleles are functional and encode different functions

Complete dominance Incomplete (partial) dominance Codominance

Which of the following is most directly related to genes in chromatin being "switched on"?

More acetylation of histones

When alleles at a locus show overdominance:

The phenotypic value of the heterozygote is superior to both homozygous states.

What statement is FALSE about transcription factors?

They can only enhance the expression of another gene; they cannot repress expression of another gene.

Heterosis is most commonly observed in crosses involving parents that are

inbreds

Epistasis can be observed when considering alleles at just one locus.

False

In the context of genome sequencing, more coverage means:

More reads representing each part of the genome

Cyanide concentration in clover is an example of duplicate recessive epistasis. If a low cyanide plant AAbb is crossed with another low cyanide plant aaBB, and doubled haploids are produced from the F1, what is the phenotypic ration in the doubled haploid population?

1 high cyanide : 3 low cyanide

In hazelnuts, the S locus determines self-incompatibility and the alleles at the S locus usually show:

Codominance

Which of the following type of molecular marker will allow you to identify heterozygotes?

codominant

In the woodland strawberry genome sequencing project, the authors concluded that the species’ small genome size was, in large part, due to:

The absence of large duplications and the limited number of transposable elements

In the context of allelic interactions within a locus, a ___________ allele is often the result of mutations involving deletion, altered transcription (for example, a mutation in the promoter), or altered translation (for example, a premature stop codon).

Non-functional

Why was the woodland strawberry chosen over the cultivated strawberry as the representative of the genus Fragaria for genome sequencing?

It has a smaller genome, it is diploid and amenable to transformation, and it has synteny with other species of the Rosaceae family

In the woodland strawberry genome sequencing project, the authors observed strong syntenic relationships between woodland strawberry and Prunus. This suggests that woodland strawberry and Prunus:

Diverged at similar evolutionary time from a common ancestor.

Which statement below is FALSE about the dispersed dominant genes theory:

It implies that it is not possible to have inbreds with the same phenotypic value as the F1.

In domesticated barley varieties, vernalization requirement can be explained by a 2-locus epistatic model. According to the model presented in class, a winter type barley will flower when:

The VRN-H2 gene is not expressed, and, as a consequence, VRN-H1 gene determining meristem differentiation is expressed.

The metabolic pathway model explains the duplicate recessive epistasis observed in clover. According to the model, the alleles at both genes need to be functional because:

The enzyme produced by one gene is a precursor to the enzyme produced by the other gene.

In the woodland strawberry genome sequencing project, short reads were assembled de novo because there was not a reference genome for the Fragaria genus at the time. This type of assembly:

Requires the reads to overlap

possible to identify the allelic state of all individuals with a dominant marker.

False

A phenotype can be a result of all of the following: RNAi, chromatin remodeling, inter-locus interactions, intra-locus interactions, promoters, transcription factors, mRNA stability, protein modification, and possibly much more.

True

Consider two loci. One locus (C) controls fruit shape. A second locus (F) determines texture. CC and Cc = round; cc = spherical. FF and Ff = mushy; ff = firm. One parent is CCFF and the other parent is ccff. You score the two traits in 100 doubled haploid progeny derived from the F1 of this cross and record the following data:

Given the following data from a doubled haploid population derived from the F1 of the cross between parents QQZZ x qqzz, the two loci are definitely on the same chromosome. QQZZ QQzz qqZZ qqzz 40 10 10 40

True

The co-segregation of markers in a linkage map is usually caused by small population size (due to rare recombinants within the region of the markers).

True

Linkage maps can be useful for plant geneticists as a starting point for cloning genes.

True

In linkage maps based on different crosses within the same species, locus orders will usually be consistent but estimates of distance may vary.

True

If you read that two loci are 10 cM apart, this means that in every individual heterozygous at these loci, there will be 10 crossovers between the two loci.

False

Alleles at loci on the same chromosome will never show independent assortment

False

You are building a linkage map for your favorite plant species based on a doubled haploid population, and you come up with the linkage data below. What is your diagnosis of the data point in bold (marker allele in position 15 cM)? Chromosome Marker position (cM) Marker allele 1 1 A 1 5 A 1 10 A 1 15 B 1 20 A 1 25 A 1 30 A

It indicates a double crossover, which is rare within a 5 cM distance, thus this data point can considered missing data.

You read in a journal article that two loci are on the same chromosome according to a map made in a doubled haploid population. But when you calculate the % recombination between the two loci in an F2 population derived from the same cross it is 50%. Which of the following is the most likely explanation?

The authors of the journal article probably had more markers available to make their map than you did.

You observe that in a very large (n = 1000) F2 population derived from the cross of two completely homozygous parents, two specific combinations of traits are always inherited together: all purple-flowered progeny are susceptible to a fungal disease and all white-flowered progeny are resistant to the fungal disease. This is most likely a case of:

Pleiotropy

Alleles at loci on different chromosomes should always show independent assortment.

True

A linkage group is ~ 150 centiMorgans long. Loci at the opposite ends of this linkage group are expected to show close to what % recombination?

50%

If you calculate a recombination value of 30% between two loci and convert this value to centiMorgans (Haldane or Kosambi)

The cM value will be larger than the % recombination value

Which meiotic phenomenon would you hypothesize to be most related to the synaptonemal complex?

Crossing over

Assuming you have sufficient markers to generate a medium density linkage map with an average spacing of 3 cM in a species that is 2n = 2x = 30, how many linkage groups would you expect?

Mutation is the source of new alleles whereas recombination between linked loci, and independent assortment of alleles at un-linked loci, are sources of new combinations of alleles.

Crossovers occur only in the "dark matter" between protein coding genes, never within genes.

False

If you had sufficient SNP markers to provide complete genome coverage of all chromosomes - at an average density of 2 cM - in an allopolyploid species that is 2n = 6x = 42, how many linkage groups would you expect?

Loci “far enough” apart on same chromosome show independent assortment – due to “sufficient” crossovers between the loci in a population of individuals

True

An advantage of higher density linkage maps is that you can more accurately convert cM to Mb.

False

The Oregon Wolfe Barley doubled haploid population is a great choice for linkage mapping because:

It is very diverse (which means many recombination events can be identified ) and there are abundant genotype data.

You are offered a job as a tomato breeder, with primary responsibility for breeding a new variety of tomato with great flavor and long shelf life. Experience and data confirm that poor flavor and long shelf life are associated. Which of the following genetic phenomenon would offer you the greatest chance of success in your new job?

Flavor and shelf life are controlled by two tightly linked genes

What is the main purpose for applying a mapping function such as the Haldane or Kosambi function?

To adjust observed recombination fractions for double crossovers, so that calculated map distances (cM) are additive along the chromosome.

You have two different linkage mapping populations in the common bean. Which of the following is most likely (assuming that your data are excellent for both populations)?

The loci in the two maps will be in the same order for a given linkage group but distances between loci may vary

If a plant is 2n = 6x = 24 and there are sufficient polymorphic loci to make complete linkage maps of all chromosomes, there will be how many linkage groups?

The co-segregation of markers in a linkage map is usually caused by small population size (due to rare recombinants within the region of the markers).

True

Alleles at loci on the same chromosome will never show independent assortment

False

Linkage map data can be used in gene discovery. In QTL analysis, for example, marker positions obtained from linkage maps are associated with traits. This is often the first step in determining the location of a gene associated with a trait.

True

Crossing over can (but does not always) lead to observable recombination. A crossover will not lead to observable recombination when it occurs_____. (Mark all that apply)

Between two sister chromatids in a 100% heterozygous plant Between two sister chromatids in a doubled haploid plant Between two non-sister chromatids in a doubled haploid plant

It indicates a double crossover, which is rare within a 5 cM distance, thus this data point can considered missing data.

Crossing over is the basis of linkage mapping. Which type of crossover will be most informative for map construction?

Crossovers between polymorphic loci

Linkage maps can be useful for plant geneticists as a starting point for cloning genes.

True

Locus A determines tomato color and locus B determines tomato flavor. AA=red, aa=pink. BB=mild flavor, bb=strong flavor. The A and B loci are in a repulsion linkage, and have a recombination frequency of 1%. Color is easy to measure. Flavor is difficult and expensive to measure. What would the minimum (and affordable) doubled haploid population size you would need to have a reasonable probability of recovering 5 plants with red color and strong flavor?

500 plants

Consider two loci. One locus (Y) controls flower color. A second locus (F) determines flavor. YY and Yy = yellow; yy = white. FF and Ff = no flavor; ff = flavor. One parent is YYFF and the other parent is yyff. You cross the two parents, produce 100 doubled haploids from the F1 and score the two traits in the doubled haploid progeny. You record the following data: Yellow and no flavor: 46 individuals Yellow and flavor: 6 individuals White and no flavor: 4 individuals White and flavor: 44 individuals How many non-parental (aka recombinant) individuals are in the doubled haploid population?

Pleiotropy

Mutation is the source of new alleles and recombination is the source of new combinations of alleles.

True

Regions around the centromere are generally heterochromatic and therefore will have, on average, more Mb/cM than euchromatic regions with higher recombination rates.

True

In comparing linkage maps of the same chromosome in the same diploid species based on two different samples of 100 random F2 indviduals from the same cross, which of the following is the most likely?

Locus orders will the same but cM distances will vary

Alleles at loci on different chromosomes

will always show independent assortment

If there is 14% recombination between the N locus and the L locus; there is 39% recombination between the W locus and the N locus; and there is 48% recombination between the W and L loci, what is the most likely order of these loci in a linkage map?

WNL