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Plant Genetics: Quiz 3 – Flashcards

Tiffany Hanchett

7 July 2022

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A floral mutation in Arabidopsis. Causes the four whorls to be: sepals, petals, petals, sepals. In combination with ap3, the gene produces stamens, and alone it produces carpels. It represses ap2 by cleaving its miRNA. When absent, ap2 takes over its domain.

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ap2

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A floral mutation in Arabidopsis. Causes the four whorls to be: carpels, stamens, stamens, carpels. Alone this gene produces sepals, and in combination with ap3 it produces petals. When absent, ag takes over its domain. In ap3/ag double mutants, ap2 is the only gene left, and all four whorls are sepals. Using in situ hybridization, it is shown that ap2 is expressed in all four whorls, so it must have an inactive transcript in whorls 3 and 4, repressed by ag. It is an miRNA, and ag cleaves it.

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apetala 1 (ap1)

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A mutant in Arabidopsis where floral meristems are more like inflorescence meristems, producing a flower-in-a-flower phenotype. Instead of sepals there are leaf-like bracts, and instead of petals there is another flower, which also has bracts and other flowers within it. The gene is important for transition from an indeterminate inflorescence meristem to a determinate floral meristsem. It is dominant to Cal, with stronger bonding to enhancers.

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Arabidopsis

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The current model system, adopted in the 1980s. Individual seeds have 2 cells which give rise to the reproductive sytem. Outcrossing occurs at a rate of 10-4. Produces 50,000 seeds per plant in a 1.5 mL Eppendorf dube. You can grow 5 - 10 plants/cm². Generation time is 5 - 6 weeks. 10,000 seeds can germinate in a petri dish. You can make 20 - 30 crosses an hour, with each silique producing 20 seeds. Can self to produce M2 for selective screens. As the plant develops, the vegetative meristem is changed into an inflorescence meristem, reslting in bolting. The flower consists of four whorls: sepals, petals, stamens, and carpels.

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Backcross

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Sometimes a chi square test can fit more than one possible F2 segregation ratio for epistasis. In this case, cross the F1 to a double homozygous recessive.

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Bolting

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The development of a flower stalk in Arabidopsis. The flower stalk is indeterminate. Floral meristems differentiate from the buttress of the indeterminate inflorescence meristem. The floral meristem is determinate, terminating in differentiated organs.

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cal

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A single mutant of this gene has wild type phenotype. In a double ap1/cal mutant, the floral meristem is proliferated to look like a caulifower head. Has a similar sequence to ap1, and probably resulted from a gene duplication followed by divergence. Discovered with an enhancer screen. It is redundant of ap1, but is not identical.

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Carpel

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Can fuse to form a pistil. In pear they are fused at the base.

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Chemical mutagen

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A method of mutagenesis. Carcinogens. Seeds may be soaked in ethyl methane sulfonate (EMS), which causes base substitutions.

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Chi square (?²) test

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Used to test genetic ratios, to see if they fit with a model. Does not prove the fit of data: only indicates the probability of their fitting a ratio. Converts deviations from expected values into probabilities of inequalities occurring by chance. Takes into account sample size and number of variables. The p value is determined from the ?² and degrees of freedom using a table. If the p value is 0.05 or less, the null hypothesis is rejected: this takes a 5% chance of discarding a valid hypothesis. Must be used with numerical raw data, not percentages or ratios, and the expected frequency of any class cannot be less than 5. Can include the Yates correction.
² = ? ((observed - expected)² / expected)

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Chi square test of heterogeneity

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One cannot make crosses among plants with similar phenotype, and pool the data on offspring while doing a chi square. This is especially bad in heterogeneous populations in cross-pollinating crops: these crosses may have different segregation patterns, possibly due to other segregating loci. One must first determine if the segregation patterns of different crosses are homogenous, before pooling data for a chi square. If the population is too heterogeneous, more experiments need to be done; there may be a mutation which causes inviable embryos.

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Classic dihybrid

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A cross first made by Mendel. A cross of green wrinkled peas (AAbb) with yellow round peas (aaBB) to produce a green round F1 (AaBb), and a selfed F2 segregation ratio of 9 green round (A_B_):3 green wrinkled (A_bb):3 yellow round (aaB_):1 yellow wrinkled (aabb). The additive phenotype of a double mutant indicates the genes are on different genetic pathways, with no epistatic interactions. When F1 is backcrossed to aabb, it produces 1 green round (AaBb):1 green wrinkled (Aabb):1 yellow round (aaBb):1 yellow wrinkled (aabb).

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Classical mutagenesis

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Induction of mutations with chemical mutagens or radiation.

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Constitutive triple response (ctr)

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A mutant that responds as if ethylene is present, even in air. Phenotype is triple response. Wild type function of the gene is to repress triple response in the absence of ethylene, as a negative regulator of gene expression. The gene is epistatic to etr. It is uptream of ein, and downstream of etr. It is a repressor of triple response.

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Corn

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It was a model system early on. It is easy to manipulate, and easy to phenotype (especially kernels on a cob). There are large genetic resources, because Native Americans saved seed of exotic looking kernels. It is easy to make crosses with the monoecious flowers. There are 11 independent genes which control seed colour, all of which have the same enhancers, C and R. Generation time is long, with a maximum of 2 generations per year, using a greenhouse.

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Cytoplasmic male sterility (CMS)

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Mitochondrial genes which cause male sterility; they are inherited from the female parent. Can be caused by short-functioning of mitochondria. Sometimes the genes may be expressed only in the anther. Many forms of CMS have evolved independently.

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Degrees of freedom (df)

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The number of classes, minus 1. The p value is determined from the ?² and degrees of freedom using a table.

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Dominant and recessive epistasis

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Produces a dihybrid segregation of 13:3. A cross of white (D'D'CC) and white (DDcc) produces white F1 (D'D'Cc) and selfed F2 segregation of 13 white (D'_C_ + D'_cc + DDcc):3 red (DDC_).

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Dominant epistasis

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Produces a dihybrid segregation ratio of 12:3:1. A cross of white (D'D'AA) and yellow (DDaa) produces a white F1 (D'DAa), and a selfedd F2 segregation of 12 white (D'_A_ + D'aa):3 red (DDA_):1 yellow (DDaa).

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Dominant mutation

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When the wid type (DD), is crossed to a dwarf (D'D'), producing a dwarf F1 (D'D). When F1 is crossed to a wild type, there is a segregation of 1 dwarf (D'D):1 normal (DD). When F1 is selfed, there is a segregation of 3 dwarf (D'_):1 normal (DD).

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Duplicate dominant genes

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Produces a dihybrid segregation ratio of 15:1. A cross of red (E1E1E2E2) and white (e1e1e2e2) produces red F1 (E1e1E2e2), and a selfed F segregation of 15 red (E1_E2_ + E1_e2e2 + e1e1E2_):1 white (e1e1e2e2). A backcross of F1 to e1e1e2e2 produes 3 red (E1e1E2e2 + E1e1e2e2 + e1e1E2e2):1 white (e1e1e2e2).

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Duplicate gene with cumulative effect

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Additive mutation. Produces a dihybrid segergation ratio of 9:6:1. The double mutant has a different phenotype than either single mutant, through additive gene action. A cross of a dwarf (AAbb) and dwarf (aaBB) produces a normal F1 (AaBb), and a selfed F2 segregation of 9 normal (A_B_):6 dwarf (A_bb + aaB_):1 superdwarf (aabb). A backcross of F1 to aabb produces a segergation of 1 normal (AaBb):2 dwarf (Aabb + aaBb):1 superdwarf (aabb).

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Duplicate recessive genes

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Produces a dihybrid segregation ratio of 9:7. A cross of white (CCdd) with white (ccDD) produces a red F1 (CcDd), and a selfed F2 segregation of 9 red (C_D_):7 white (C_dd + ccD_ + ccdd). A backcross of F1 to ccdd produces a segregation of 1 red (CcDd):3 white (Ccdd + ccDd + ccdd).

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Enhancer screen

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A previously identified mutant is remutagenized. A second locus could be altered to increase the intensity of the original mutant phenotype. A new phenotype arises from a double mutant. Can find additional loci that act redundantly, interact with the original gene, or exist on a parallel pathway. You must determine that it is not a mutation in the same gene.

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Epistasis

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Interlocus interactions which mask the effect of one gene on another. Detectable as deviations from dihybrid 9:3:3:1 segregation ratios. Includes dominant epistasis (12:3:1), recessive epistasis (9:3:4), dominant and recessive epistasis (13:3), duplicate gene with cumulative effect (9:6:1), duplicate dominant genes (15:1), and duplicate recessive genes (9:7).

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Ethylene

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C₂H₄
Has a significant effect on germinating seeds, producing triple response: shortened hypocotyls and roots, thickened hypocotyl, and exaggerated curling of apical hook. There are ethylene insensitive mutants, constitutive triple response mutants, and ethylene receptor mutants. It is a plant hormone that triggers fruit ripening and leaf senescence.

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Ethylene insensitive (ein)

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A mutant that responds as if no ethylene is present, even in the presence of ethylene. Phenotype is elongated hypocotyl. Wildtype is important as a positive regulator of triple response. The gene is epistatic to etr. It is downstream of ctr.

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Ethylene receptor (etr)

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A mutation in the receptor of ethylene. Causes a phenotype similar to ethylene insensitive mutants. Phenotype is elongated hypocotyl. It is upstream of ctr.

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A restorer of fertility gene in beans which causes permanent restoration of fertility to male-sterile cytoplasm. It affects the replication of mitochondrial genome sub-circle.

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In situ hybridization

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A labelled antisense probe is added for a gene, and hybridized to tissue, where it fluoresces, showing where the gene is expressed.

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Leaky mutation

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Additive double mutant
Produces weak expression of a gene. Some product or signal is moving through the pathway at a reduced level. In a double mutant, the first mutation reduces quantity of product, and the second mutation reduces it further, producing a phenotype different from either single mutant. Produces additive phenotype. Use the strongest mutant phenotype in crosses, so that additivity can be interpreted properly. A_B_ are normal, A_bb and aaB_ are moderate dwarfs (50% off), and aabb are dwarfs (75% of).

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Leaves

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A leaf is the ground state of all floral organs: this is why an ap2/ag double mutant has leaves in all four whorls. Floral organs evolved from leaves. Unlike sepals, leaves have trichomes.

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When mutagenizing seed to find mutant phenotypes, the treated seed and plants grown from it. Produces M2. In Arabidopsis, if a mutation occurs in one of the seed cells which becomes the reproductive system, half the M1 plant will be heterozygous at the mutant locus.

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When mutagenizing seeds, the progeny of M1. In Arabidopsis, if a mutation occurred in M1 in one of the seed cells which becomes the reproductive system, then the M2 generation will be half segregating 4:0, and half segregating 3:1, assuming the mutation is recessive. Overall, segregation is 7:1 for any given trait. This ratio is beneficial, because it decreases the minimum population size in order to get at least 5 rare segregates when doing chi square tests

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Mendel

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His data were found to be too perfect, and very improbably to have occurred by chance. The probability of getting his data are 1 in 20,000 experiments. He might have been very lucky, or his results were cooked!

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Minimum population size

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The expected number for the smallest class must be at least 5 in order to do a chi square test. Ensures that the population is large enough for there to be enough rare segregates.

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Mitochondria

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Important for cytoplasmic male sterility.

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Morning glory

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Ipomoea purpurea
An annual, self-compatible vine with strikingly polymorphic flower colour, with eight common phenotypes. It is a weed in southern USA. Pigment in flowers is controlled by segregation at three loci: P (hue), W (distribution), and I (intensity). There is no linkage between these genes. At the P locus, blue (P_) is dominant to pink (pp). At the W locus, WW produces full colour and intensity is then controlled by the I locus, Ww produces light colour, and ww produces a white flower with rays of colour. At the I locus, dark (I_) is dominant to intense (ii), but is only expressed in WW flowers. Flower colour can influence pollinator behaviour and maternal out-crossing.

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Mutation

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We can only know the function of a gene by looking at how mutants have altered phenotype. Natural frequency of mutations varies for a gene, with some genes more mutable than others. Different mutations in one gene can cause different phenotypes. Mutations in different genes can cause the same phenotype.

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Null mutation

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No additivity double mutant. Produces no expression of the gene. The TATA box may be knocked out. The two single mutants have the same phenotype as a double mutant. A_B_ are normal, and A_bb, AaB_, and aabb are dwarfs.

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Phytochrome A (phyA)

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Allows plants to perceive far-red light. In darkness, germinating seeds produce a long, etiolated hypocotyl, but in the presence of far-red light, the hypocotyl is short. Mutation prevents seedlings from perceiving far-red light, resulting in a long hypocotyl in the light.

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pi/ag3

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A floral mutation in Arabidopsis. Causes the four whorls to be: sepals, sepals, carpels, carpels. In combination with ap2, this gene produces petals, and in combination with ag, it produces stamens. When absent, ap2 and ag remain alone. In an ap2/ag double mutant, ap3 is the only gene left, and all four whorls are leaves.

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Pistil

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May contain more than one carpel.

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Radiation

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A method of mutagenesis. The backbone of the DNA, causing chromosomal changes, inversions, deletions, and translocations. Induces mutations depending on dosage, but can be near 10^-4.

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Recessive epistasis

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Produces a dihybrid segregation ratio of 9:3:4. A cross of yellow (aaCC) and white (AAcc) produces a red F1 (AaCc), and a selfed F2 segregation of 9 red (A_C_):3 yellow (aaC_):4 white (A_cc + aacc).

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Recessive mutation

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When a wild type (DD) is crossed to a dwarf (dd), it produces a normal (Dd) F1. When F1 is crossed to the dwarf parent, it produces a segregation of 1 normal (Dd):1 dwarf (dd). When F1 is selfed, it produces a segergation of 3 normal (D_):1 dwarf (dd).

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Restorer of fertility (rf)

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A nuclear gene which is expressed only in male-sterile cytoplasm, acting to restore fertility to a plant with cytoplasmic male sterility.

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Rice

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Has five types of cytoplasmic male sterility. There is a polycistronic mRNA that is toxic to bacteria, but also suppresses male sterility. The rf gene Rf1A cleaves the transcript, so no toxin is produced. The rf gene Rf1B suppresses transcription of the transcript. The rf gene rf2 inactivates the toxin, but in heterozygotes it does not inactivate enough to completely suppress sterility.

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Sorghum

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The gene for cytoplasmic male sterility causes chimeric genes to form with unidentified reading frames within ATP9, causing short-functioning of ATP production. This does not harm most cells, but in the tapetum of the anthers, high respiratory needs to make pollen are not met, causing male sterility.

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spa1

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A mutation in this gene restores wild-type phenotype to phyA mutants. It is a repressor of light phenotype. Phytochrome A is inactive in the darkness, and spa1 degrades transcription factors promoting short hypocotyls. In the light, phytochrome A inactivates spa1, allowing for short hypocotyls. In a double mutant, spa1 cannot interact with transcription factors, promoting short hypocotyls.

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sup

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Superman
A floral mutation in Arabidopsis. It prevents ap3 from entering the fourth whorl. When absent, ap3 is in the fourth whorl, and whorls are: sepals, petals, stamens, lots of stamens with one small carpel.

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Suppressor screen

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A previously identified mutant is remutagenized. Phenotypes that reconstitute or approach wild-type are selected. The second mutation negates the effects of the first. Can find interacting proteins or alternative pathways. The second gene is a repressor. You must determine that it is not a mutation in the same gene.

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Test of allelism

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Test of complementation
Used to determine if independent mutant plants are mutated in the same gene. The two mutants are crossed. For dominant mutations, if the mutation is the same, F1 is mutant (A'A' x A'A' = A'A'), and if the mutation is different F1 is mutant (A'A'BB x AAB'B' = A'AB'B), and F2 analysis has a ratio of 15 mutant (A'_B'_ + A'BB + AAB'_):1 wild type (AABB). For recessive mutations, if the mutation is the same, F1 is mutant (aa x aa = aa), and if the mutation is different, F1 is wild type (AAbb x aaBB = AaBb). After identifying the gene, you can map it to a region of a chromosome and assess if other mutants have been reported in that area, then you can do an allelism test if you think your gene and another previously identified gene are the same.

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Yates correction

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A correction to the chi square test, used when there is one degree of freedom, or a small saple where the smallest expected class is between 5 and 10 in size.

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