GENE222 Mod 5&6, Maori Inheritance and Genetic Mapping

Describe the order of Maori family hierarchies

Whanau - closely related family

Hapu - A group of closely related families, you can marry within your hapu

Iwi - Broad collections of many families, some are connected by common ancestors

Pan-Iwi - (Across many different tribes with varying relatedness)

What are some of the main constructs that are key to Maori concepts of inheritance? (5)

Constructs such as;

‘whakapapa’,

‘pepeha’

‘mokopuna’

‘momo’

‘kākano

Describe the concept of whakapapa

It means ‘to place in layers’ and it is an understanding of ones ancestors and history. One’s whakapapa is their family tree and a knowledge of your background is seen as a sign of intelligence and wisdom. Often used in a powhiri to welcome visitors on a marae.

Describe the concept of Pepeha and how it relates to quantitative genetics

Pepeha is a traditional introduction of ones heritage and identity. The first half explains ones environment that they come from, their mountain and river etc, and the second half explains their ancestors/heritage. This reflects the genetics relationship that Phenotype = Environment + Genotype.

Describe the concept of mokopuna

Moko means tattoo or marking, and Puna means spring (of water). This reflects that people are seen as the blueprint of their ancestors. This means grandchildren or descendants, grand nephews/nieces.

Describe the concept of Momo and its derivatives

Momo means ‘type, variety, race, breed, classification’ kind of thing.
He Momo means ‘true to form, it's a family trait, inherited quality, hereditary trait -this idiom highlights a person's character and inherited qualities or those of his/her ancestors. It can be applied to both good and bad traits.

Momo mate

– hereditary disease

• Mātauranga momo whakaeke

– genetics

Describe the concept of Kakano

Relates to inheritance and passing things on, can mean seed or to reproduce, or ova or sperm. It can also mean to descend, or stock or pedigree.

Give an example of Matauranga Maori being used in modern Genetics research.

Traditional Ancestral Knowledge of Whakapapa (Genealogy) Enables the He Kākano/Variome Project. They do this by surveying Hapu around New Zealand for their whakapapa information.

Whakapapa knowledge (waka/hapu/iwi/whanau) enables:

1. More accurate prediction of disease risk

2. Lower cost of prediction – whakapapa cheaper than DNA for similar

outcome

What are the limitation of Mendels 2nd law?

The Law of Independent Assortment. Linkage is the primary limitations of M2L, genes very close together on a chromosome do not recombine relative to each other very much.
In 1905, Bateson, Saunders and Punnett crossbred sweet peas, and did not find the expected 9:3:3:1 ratio, they found more “parental” phenotypes than recombinant phenotypes. This made them think the genes were ‘linked’

What is the difference between Dominant/Recessive vs Parental/Non-parental inheritance?

Dominant/Recessive – based on molecular action of allele Determined based on phenotype seen in F1 generation Dominant: purple flowers + long pollen Recessive: red flowers + round pollen
Parental/Non-Parental – based on coupling/linkage of loci Determined based on phenotype seen in P generation Parental: purple flowers + long pollen OR red flowers + round pollen Non-Parental: purple flowers + round pollen OR red flowers + long pollen

What can affect rate of crossing over of a point in a chromosome?

If the chromatin is open, so euchromatin, it is more likely to cross over and recombine.

• How do you calculate if two genes/traits are linked by their phenotype ratios.

Chi squared test, observed versus expected. If the variability is already captured in expected values (ie it has a confidence interval), you only have to use one degree of freedom.

What is the Difference between a genetic and physical map

A physical map occurs through sequencing of DNA, the human one is nearly done. Genetic maps are usually formed through linkage and frequency of recombination between genes. Physical map is much more accurate and specific.

How do we form a linkage/genetic map?

The further away two genes on a chromosome are the more likely a crossing over event will occur between them

• This can be used to map genes onto chromosomes

• Use frequency of recombinants to predict distance between genes

• Map units are centiMorgans (cM)

• Genes must have a visible/ detectable phenotype

What does the map unit centimorgan mean?

One genetic map unit (m.u.) or centiMorgan (cM), is defined as the distance between two genes for which 1 product of meiosis in 100 is recombinant. => one map unit is a recombinant frequency of 1%

What do we use to map genes or other genetic elements that don’t cause visible phenotypes.

Molecular Markers

• Single nucleotide polymorphisms (SNPs)

• Single base change in genetic sequence

• Range from really rare to really common

• “Variants” not “mutations”

• Millions in the human genome (5-6 million in individual genome)

• Most have two alleles (can have up to four)

• Usually 3 possible genotypes e.g. GG, AG, AA

• Some have functional consequences

In the FecX sheep gene example, how did the researchers perform step 1 of gene mapping and characterise the phenotype?

In sheep to find the FecX gene that causes common twinning and triplets during lambing in sheep.

Step 1: Characterising the phenotype

A flock of highly prolific Romney ewes: One particular ewe (A281) had 33 lambs over 11 lambings - her daughters also had consistently high progeny rates. Set up a series of progeny tests. Measured ovulation rates via laparoscopy. From the pedigree, determined an X-linked gene is responsible for increased ovulation. Named this gene FecX.

In the FecX sheep gene example, how did they map FecX chromosome position?

Step 2 and 3: What is already known and how do we map FecX position

• Had already created a partial gene map of sheep X chromosome.
A three-generation test cross for FecX was set up •

FecXI = allele causing increased fertility, FecX+ = wildtype allele Searched available X-chromosome markers for one with a very low recombination frequency = Must be close to FecX on genetic map

In the sheep FecX gene example, after finding the relative position of the gene, how did they identify the actual FecX gene?

Step 4: Finding the variant in the linked gene(s)

• TIMP1 and BMP15 are genes in the mapped region for FecX

• Searched for sequence differences between FecXI /FecXI and FecX+ / FecX+ sheep

• Found no differences within TIMP1 Later found a TIMP1 recombinant to further confirm this is not the gene of interest

• Found a T→A change in FecXI carriers at nucleotide position 92 (c.92T>A) of BMP15 • Results in a valine to aspartate substitution at amino acid 31 p.(V31D)

• Interrupts a conserved region of the protein. This allowed them to conclude BMP15 was the important gene, which was later found to be a transforming growth factor (TGFBeta) expressed in oocytes.

What are some kinds of genetic markers? (4)

DNA fingerprinting (think forsenics) Detects mini/microsatellites PCR around repeat region and visualise product length

• Restriction fragment length polymorphism (RFLP) Detects SNPs that change a restriction enzyme recognition site PCR around SNP, then cut with restriction enzyme, visualise fragment lengths

• TaqMan or gene-chipping Detects SNPs Small specific probe binds SNP, PCR around SNP – probe releases fluorescent molecule, different colour per allele, measure how much of each colour seen

• Genotyping by sequencing (GBS) Detects SNPs and indels (very short insertions/deletions) Use high-throughput short read sequencing for a fraction of the genome (DNA fragments chopped up by restriction enzymes) Line up sequence across individuals and call SNPs