Aquaculture Exam 2

exons

coding parts of the genome transcribed into RNA

Goals of domestication

more preditable performance of cultured populations

genetic improvement towards desirable phenotypes

will likely not respond to selection

if a trait has low repeatbility, how will it respond to selection

low

hertability level of surviivial and reproductive fitness traits

Strain testing exerpiment

exisitng strains are compared to determine WHICH strain to use and how to cross them for breeding

→ can be affected by maternal effects and interactions between strands

Diallel cross

mating scheme, type of strain test

where paretns and reciprocal crosses are invovled along the F1 generation

allows control of maternal and interaction effects

heterosis

breeders use a cross to start their founders if this trait is present

heterosis

hybrid vigor, where the hybrid is uperior to the average value of the two parents

improvement invovles crossing the two strains

Mosaic strain

occurs when multiple strains with similar value

uses founders from ALL strains

maximines the initial genetic variability and potential for genetic progress through selection

Quanitiative Traits

continous distribution and measured by some quanitiative variable

determined by a large number of genes

example: rsistance to diseases, growth, carcass yields, reproductive outputs

heritability

genetic variance/phenotypic variance

measure of the strength of genetic effects on the traits assesed

genetic variance

Vg = additive variance + epistatic variance +domiance variance

Vi

epistatic variance, interaction among loci

Hertability, with additive affects

in a more narrow sense,

H2 = additive genetic variance/phenotypic variance

predicts the degree of resembalnce among relatives and response to selection pressure

Va

additve variance, some aleles that have an additive or subsution effect

genetic effects contribute to the response of selection

response to selection

r = H2 X selection diifferential

selection differential

mean of the selected group - mean of the population

Degree of resemblance

comparsion amonst relatives to reflect the strength of additive effects

hertability of two full sublings

H2 = 2x variance among sibilings (R) / phenotypic variance

hertability among half siblings

h2 = 4x variance among half sibs (R) /phenotypic variance

Common Garden Design

controls for the effects of phenotypic plastiicity and genotype-by environment interactions by:

• growing idnividuals from DIFFERENT populations in the SAME environment

• After growth, the paramter is measure and genotyped

• pedigree anaylsis takes place to study genetic basis of trait

high hertaibility

H2 > .5

morphological tratins, coloration patterns may be present

H2 <.1

low hertability

typically surivival and reproductive fitness traits

H2 = .2-.5

intermediate hertaibility

traits: body size, growth rate, caracass yield traits

Pleiotropic effects

where the same gene effects multiple traits

Variance in phenotype

Vp = Ve + Vg + Vg X Ve

Gametic disequilibrium

occurs when genes affecting two traits are near each other (but on different loci), resulting in transmission during meisosis via corssing over

→ driven by recombation rates and gene distance from one another

→ ex: correlation between MP pelvic and pectoral rays in pink salmon

results in 2 haplotypes

Intra family selection

selection method where if H2 is low, the best individuals within a family is selected to improve efficiency

Peddigree based selection

selection method useful in animal models

extends family selection to complex multigenertional pedigrees

maximinizes knowledge of genetic relatedness

individual selection

type of selection method useful with high hertability traits

selection pressure

a trade off between the genetic gain and loss of diveristy, and increase cost of breeding

→ exctected genetic gain per generation

genetic gain per generation

→ increased if selection differential (mean value after selction) is higher

→ leads to reduced number of family contribution> increase cases of inbreeding and loss of genetic diveristy

→ ptoential to respond further to selection in future generations

Measure of resposne to selection, uncontrolled environment

• measured with a control line of unselected traits

• two lines should be bred

measure of selection response, controlled environment

- based on estimated genetic values of each generation accouting for pedigree relationship

• limitied in envionmental variable locations, where there is genetic and envriomental interaction

Marker assisted selection

genomic approach to selection wehre the major gene (single locus with quanitiative character) is marked

→detection o fmajor genes is either through the bimodial distirbution of phenotypes, or hetergenity varaicne within family and sgegregation in pedigreed populations

Molecular markers

type of marker assisted selection wehre tracking is absed on a DIRECT assessment of DNA sequence varaition using markers across the genome to find associations

→ genome scan: marked genome with small intervals inbetween

Quantiative trait loci

type of marker assisted selection wehre markers are proximal to major agenes affecting the trait

→ linkage measured by comapring the phentype in alternative genotypes at all markers

→f Frequency at which markers genotype results in a specific phenotype: informs distance between the marker and real ATL

→ bascially an indirect measurement of the location of the QTL

Association Mapping

type of marker

linkage between markers and trait identified with families or by genotyping alterative phenotypes within a population

→ genotyping alterative genotypes within a population

→ abased on high density gneotyping for the discvoery of association

→ statisically aossicated with a trait or disease

Marker asissted selection steps

1. once a QTL is found, individuals are genotyped. The marker and coalleles are seleccted if they carry favorable alelels

2. can be comvined with traditional pedigree based selection to efficency

3. measuring phenotype is needed, as selection is based solely on the genotype (allows for assessing genetiv values at the QTL at early life stages)

Limittions to Marker Asssitated Selection

breeding values need to estimaed based on phenotype

• limitation on the number of traits that can incororated

• low efficiecy for traits with low heritability

• restricted to tratis that can be measured cost effective on lots of animals

Genomic selection

type of selection that uses a reference populationa s a score at key production tratis and genotyped at thousands of SNPS

→ prediction equations are consturcted by combiing all the marker genotypes and theri effects to generate a GENOMIC ESTIMATE BREEDING VALUES

→ applied to a group of animals that have not been phenotyped, breeding values are estimated and the best animals are selected for breeding

→ genetic variance is tracked, as opposed to the subset of QTLS

→ involves heavy cost and effort to characterize individual breeding values

→ large base population needs to be assayed

Inbreeding Coefficient

the probability that two alelels at the locus are idnetnical by descenet

occurs in in small population (capative stock)

0-1

→ leads to increasing homozygosity

Effects of inbreeding depression

• reduced growth

• loss of genetic diveristy, leading to loss of capacity to respond to selection

Effective population size (Ne)

Size of an ideal population that experiences the same amount of genetic drift as the population under study

→ number of individuals who successfully transmit their genes to the next generation

Ne

standardized measure of the amount of genetic diversity that is maintained in the population and of the probability of inbreeding

→ any factor that increases the variane in reproductive success among brooders reduces this

→ effected by unequal sex ratio (large Vk (variance in reproductive success)) the smaller the Ne 3

Vk

variance in reproductive success among breeders

can be larger in some harchery spawns, especially among females

Management of inbreedng

• maintain two lines with a terminal corss for production

• introduce new genotypes to the line as (f)

• f stablzies as 1/1+4NeM

Effective Size

the harmonic mean of Ne X S in successive generations

infleunced mostly by generations with small Ne

→ important to keep Ne large to avoid bottleneck generations

Management of Ne

• Increase N3 and maintain stable over time to avoid bottle necks

• ensure mating of unrelated individuals by tracking individual pedigrees

• equalize family size

• maintain sub-cohorts and corss them according to a rotational scheme

Triploid

occurs when organisms have 3 sets of chromsomes instead of 2

→ females are typically sterile

→ sterlie individuals grow faster because they do not use energy and ntuirents to produce gametes

Triplodisation by shock

shock (temperature, pressure or chemical stimulus) induxues the 2nd polar body in an ooxyte to be reatined, resulting in a 3n state

Control of ploidy sex

obtain sterility in triploid (monosex female)

→ use of hormonal sex reversal to create a neomale to reproduce with a female

grow the faster growing sex if there is a sexual growth dimorphism

useful to avoid aggressive behavior or over reproduction in mixed sex populations

tetraplodization

prpduced direclty in inhbiting embyronic meiosis via shock treatmetns

produces a 4n individuals

tetraploidization in oysters

invovles two successive genreation where the first generation undergoes a triploid shock

second generation shcoks embryos to retain the first polar body (results in 3n and poalr body oocyte)

Production of triplodi by crossing tetraploid lines

→ tetrapplodi males produce 2n sperm> leads to fertilization of normal ooxytes

→ leads to 3n progeny

→ does not invovle shock on eggs> higher viability

→ low success rates in producting 4n genotypes though, leads to low diveristy in 4n stocks avalaible

Gene transfer

the direct injection of transgenes into somatic tissue to induce

IMMUNITY to disease

0> requires injecting DNA in every indvidiual

→ incoroprotated into germ line to that every fish in subsequent generation posesses the transgene

Gene modification

facilitiated by external fertilization

→ microinjections of gene construct in gertilized eggs

→ regulatory barriers for this method might be lifted in the US soon

Transgensis via microinjection

→ DNA is injected in the cytoplasm before the first embryonic mitosis (very short time frame)

→ 10^6-10^8 copies of the transgene injected in small volume

→ difficulties going throgh the chorion and localizing the chromosome in the egg

other methods of transgensis

electroporation, biolitsitcs, virus meidated transmission

Success of transgenesis in fish

→ low success rate, as a stable transgenic line must have intergated transgees in cells of germline

→ issues with expression control:

genes can be integrated into the geone but not expressed (disrupted by reciipent cell if it is non fish DNA)

Transitiory expression

fconsquecnes of transgensis

rom cytoplasmic fragments not integrated in the genome does not allow for stable integration

CRISPR-CAS9

gene editing tech that induces a ds break at a target location in the genome and repiar with modified

→ uses a DNA binding domain that recognizes a specific sequence and a DNA cleavage domain

→ DNA cutting activates a repair mechanism that can be used to rewrite DNA around cutting site

→ enhance or knock out the gene

→ uses in vivo/cell lines of major aquaculture species

GnRH

native analog produced by the brai hypothamlus

gonadotropin releasing hormone

small peptipe (10 amino acids)

Pituitary gland

stimulated by Gnrh to syntheize and secrete gonadotropins and lutenziing hormoens from the anterior

gondaotropins

heterdimer glycoproteins with 200 amino acids

produces follicle stimulating hormome, lutenzing hormomes

steroid and prostaglandins are produced in the ovaries or testis

11-Ketotersoterone

male gondald steorid that is unique to males

begins as progesterone and can transform into testeroine

Vitellogenin

proteins produced in the liver

→ stimualted by 17B estradio

→ integrated into the developing ooxyte within the ovary to provide egg with ntuureitn resources to compelte embryogensis

ovaries

female gonads that are tube shaped

Oogenesis

maturation of female gametes.

Oogonia undergoes meiosis

primary ooxyte is arrested in first prophse I stage, where it stays dormant until final maturation

Previtellogensis

characterixed by growth of the primary oocyte and ovarian lamellae

primary growth phase

characterized by the growth of primary oocyte and the formation of cortical alveouli, where the vitelline envelope becoems prominent

Vitellogensis

•  occurs during the beginning of prophase I 

  • process of production and accumulation of yolk in a developing oocyte 

  • Collects vitellin proteins and integrates them into developing oocyte within the ovary to provide egg with nutrient resources to complete embryogenesis