BIOINFORMATICS

Dr. Aladdin Hamwieh Khalid Al-shamaaAbdulqader Jighly

2010-2011

Lecture 7Genome Mapping

Aleppo UniversityFaculty of technical engineeringDepartment of Biotechnology

INDEPENDENT ASSORTMENT AND PUNNETT SQUARE

A dihybrid cross produces F2 progeny in the ratio 9:3:3:1.

CROSSOVER

Independent assortment produces

a recombinant frequency of 50

percent.

LINKAGE Loci that are close enough together on the

same chromosome to deviate from independent assortment are said to display genetic linkage

BUT The linked loci that are far from each others

are in danger of

CROSSINGOVER

DEVIATIONS FROM INDEPENDENT ASSORTMENT

In the early 1900s, William Bateson and R. C. Punnettwere studying inheritance of two genes in the sweet pea.

In a standard self of a dihybrid F1, the F2 did not show the 9:3:3:1 ratio predicted by the principle of independent assortment.

In fact Bateson and Punnett noted that certain combinations of alleles showed up more often than expected, almost as though they were physically attached in some way. They had no explanation for this discovery.

Thomas Hunt Morgan found a similar deviation from Mendel’s second law while studying two autosomal genes in Drosophila. Morgan proposed a hypothesis to explain the phenomenon of apparent allele association.One of the genes affected eye color (pr, purple, and pr, red), and the other wing length (vg, vestigial, and vg, normal). The wild-type alleles of both genes are dominant.

DEVIATIONS FROM INDEPENDENT ASSORTMENT

When two genes are close together on the same chromosome pair (i.e., linked), they do not assort independently.

Chiasmata (the visible manifestations of crossing-over): a cross-shaped structure forming the points of contact between non-sister chromatides of homologous chromosomes.

Frequencies of recombinants arising from crossing-over. The frequencies of such recombinants are less than 50 percent.

LINKAGE MAPS (DISTANCE BETWEEN THE GENES.)

Recombinant frequencies are significantly lower than 50 percent and the recombinant frequency was 12.97 percent.

(146+157) * 100 / 2335 = 12.97 Morgan studied

linked genes, proportion of recombinant progeny varied considerably,

Morgan concluded actual distances separating genes on the chromosomes.

Alfred Sturtevant suggested that we can use this percentage of recombinants as a quantitative index of the linear distance between two genes on a genetic map, or linkage map.

Sturtevant postulated the greater the distance between the linked genes, the greater the chance of crossovers in the region between the genes.

Sturtevant defined one genetic map unit (m.u.) as that distance between genes for which one product of meiosis in 100 is recombinant. Put another way, a recombinant frequency (RF) of 0.01 (1 percent) is defined as 1 m.u. A map unit is sometimes referred to as a centimorgan (cM) in honor of Thomas Hunt Morgan.

LINKAGE MAPS (DISTANCE BETWEEN THE GENES.)

A chromosome region containing three linked genes. Calculation of AB and AC distances leaves us with the two possibilities shown for the BC distance.

Recombination between linked genes can be used to map their distance apart on the chromosome. The unit of mapping (1 m.u.) is defined as a recombinant frequency of 1 percent.

EXAMPLE

For the v and ct loci 89+94+3+5= 191For the ct and cv, loci 45+40+3+5 = 93For the v and cv, loci 45+40+89+94 = 268

MAPPING THE12 CHROMOSOMES OF TOMATOES.

MORPHOLOGICAL MARKERS1. Small Number2. Limited genomic coverage3. Could be influence by environment4. Most of them exhibit dominance nature

LINKAGE MAPPING Genes are points on the genome and

there are a flanking regions around them link to these genes.

The central idea of the linkage mapping is to put a lot of points on the genome in order to get points that linked to another interesting points (genes).

These points that we add are called as:

“MARKERS”

MOLECULAR MARKERS Dominant or Co-dominant nature in different types:1. Protein-based

Isozyme Allozyme

2. Hybridization-based RFLP DArT

3. PCR-based RAPD, AP-PCR AFLP STS (SSR, ISSR, SCAR, CAPS) RGA

4. Single Nucleotide Polymorphism (SNP)

Hamwieh et al. 2005

INTRODUCTION

Molecular markers:•RFLP•AFLP•RAPD•SSR•SNP•STS•ISSR

Genetic map of lentil

RAPDAFLPSSR

HOW TO GENOTYPE?

a bb b a a b b b a a a a b b b a b b H

P1 P2

CO-DOMINANT MARKERP1 P2

1 2 3 4 5 6 7 8 9 10 11 12 13 14

DOMINANT MARKERP1 P2

1 2 3 4 5 6 7 8 9 10 11 12 13 14

UNACCEPTED MARKERS (RIL POP.)

P1 P2 1 2 3 4 5 6 7 8 9 10 11 12 13 14

P1 P2 1 2 3 4 5 6 7 8 9 10 11 12 13 14

Could be determined by Chi-square test

Segregation distortion : Asegregation distortion marker/gene produces a distortion in normal expected segregation

CHI-SQUARE Obs.A=45 Exp.A=50 Obs.B=55 Exp.B=50

ExpExpObsx

22 )(

150

)5550(50

)4550( 222

x

CHI-SQUARE TABLE

DF 0,995 0,9500 0,100 0,050 0,025 0,010 0,005 1 0,000 0,004 2,706 3,842 5,024 6,635 7,879 2 0,010 0,103 4,605 5,992 7,378 9,210 10,597 3 0,072 0,352 6,251 7,815 9,348 11,345 12,838 4 0,207 0,711 7,779 9,488 11,143 13,277 14,860 5 0,412 1,146 9,236 11,071 12,833 15,086 16,750 6 0,676 1,635 10,645 12,592 14,449 16,812 18,548 7 0,989 2,167 12,017 14,067 16,013 18,475 20,278 8 1,344 2,733 13,362 15,507 17,535 20,090 21,955 9 1,735 3,325 14,684 16,919 19,023 21,666 23,589

10 2,156 3,940 15,987 18,307 20,483 23,209 25,188 11 2,603 4,575 17,275 19,675 21,920 24,725 26,757 12 3,074 5,226 18,549 21,026 23,337 26,217 28,300 13 3,565 5,892 19,812 22,362 24,736 27,688 29,819 14 4,075 6,571 21,064 23,685 26,119 29,141 31,319 15 4,601 7,261 22,307 24,996 27,488 30,578 32,801 16 5,142 7,962 23,542 26,296 28,845 32,000 34,267 17 5,697 8,672 24,769 27,587 30,191 33,409 35,718 18 6,265 9,390 25,989 28,869 31,526 34,805 37,156 19 6,844 10,117 27,204 30,144 32,852 36,191 38,582 20 7,434 10,851 28,412 31,410 34,170 37,566 39,997

RECOMBINANT FRACTION

P1 P2 1 2 3 4 5 6 7 8 9 10 11 12 13 14

M1

M2

CM3.14100142

LOD SCORE

)5.0()5.0(log_ 10

LLScoreLOD

n

nmm

LLratioLikelihood

5.0)1(

)5.0()5.0(_

•A statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefore likely to be inherited together.

ZMAX N=35 M=7

0 0.1 0.2 0.3 0.4 0.5

-1

0

1

2

3(0.20,2.9297

8)

Recombinant fraction

LOD

Sco

re

n

nmm

Z5.0)1(logmax 105.00max

M:RecombinantN: Total NumberM-N: Non Recombinant

A LOD score of three or more is generally taken to indicate that the two loci are close.

MAPPING FUNCTIONHaldane

Kosambi

0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50

50

100

150

200

qHaldaneKosambi

Recombinant fraction

Cent

imor

gan

Haldane's map function assumes that the probability of a crossover in one region is independent of the probability of a crossover in the second region.

rAC = rAB + rBC - 2CrABrBC

rAC = rAB + rBC - 2rABrBC

Kosambi's mapping function is based on empirical data regarding the proportion of double crossovers as the physical distance varies. Kosambi's function adjusts the map distance based on interference which changes the proportion of double crossovers.

C =coefficient of coincidence

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