Transcript Genetic map construction

Fall 2014
HORT6033
Molecular
Plant Breeding
INSTRUCTOR: AINONG SHI
HORT6033 web site: http://comp.uark.edu/~ashi/MB
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture 9 (09/22/2014)
I. Genetic map construction
II.Genetic mapping
III.Example
IV.Homework
V.Reading
In classic genetics, genes can be mapped to specific locations on chromosomes.
Genetic map: A graphic representation of the arrangement of genes or DNA
sequences on a chromosome. Also called gene map.
Locating and identifying genes in a genetic map is called genetic mapping.
A linkage map describes the linear order of markers (such as SSRs and SNPs)
within a linkage group. A linkage map = a genetic map.
Genetic mapping (linkage mapping) means to build genetic map(s) with a set
of markers (such as SSRs and/or SNPs). It can map only one genetic map or
whole genome maps of a species.
Usually, what we say ‘conduct linkage mapping’ means we map a major gene
of a trait to a genetic map (linkage group (LG) or chromosome).
What we say ‘conduct QTL mapping’ means we map a QTL (quantitative loci
trait) to one LG (chromosome) or several LGs (chromosomes)
M1
M2
0.1cM
0.2cM
M3
0.25cM
M4
M6
0.1cM
LG
0.1cM
0.2cM
0.1cM
0.15cM
0.1cM
M1
M2
M3
T1 (flower color)
M4
M5
Linkage map
0.1cM
0.2cM
M1
M2
M3
0.25cM
0.1cM
M4
M6
QTL mapping
Cowpea Whole Genome Genetic Maps
11 chromosome
928 EST-SNPs
Fig. S1. Graphical representation of the consensus cowpea genetic linkage map constructed
by using 928 EST-derived SNP markers segregating in six recombinant inbred populations.
Muchero et al. 2009. PNAS 106:18159–18164.
Cowpea Bacterial Blight
CoBB susceptible
CoBB resistance
QTL mapping for CoBB Resistance
• Three QTLs, CoBB1, CoBB2, and CoBB3,
were reported to be linked to CoBB
resistance on linkage group LG3, LG5 and
LG9 of cowpea (Agbicodo et al. 2010).
CP02_50192757
• Two SNP markers, CP08_5433936 and
CP02_50192757 were identified to be
associated with CoBB resistance located at
the same regions of CoBB1 and CoBB2,
respectively. The accuracy of selecting
resistance lines was 86.7% based on the
data of 201 cowpea lines from this study.
CP08_5433936
SNP
Soy
Pos
CP02_50192757
Gm02
50,192,757
CP08_5433936
Gm08
5,433,936
1_0037
Gm02
45,862,359
1_0853
Gm08
3,450,676
1_0183
Gm08
4,014,465
Agbicodo et al. 2010. Euphytica 175:215-225
Estimate the linkage of two alleles in
a segregating population
Recombination fraction
LOD score
Haldane and Kosambi mapping function
Recombination Frequency
Recombination fraction is a measure of the distance
between two loci.
Two loci that show 1% recombination are defined as being 1
centimorgan (cM) apart on a genetic map.
1 map unit = 1 cM (centimorgan)
Two genes that undergo independent assortment have
recombination frequency of 50 percent and are located on
nonhomologous chromosomes or far apart on the same
chromosome = unlinked
Genes with recombination frequencies less than 50 percent
are on the same chromosome = linked
Calculation of Recombination Frequency
The percentage of recombinant progeny produced in a
cross is called the recombination frequency, which is
calculated as follows:
Recombination Frequency
Recombination fraction
LOD SCORE
• The LOD score is calculated as follows:
• LOD = Z = Log10 probability of birth sequence with a given linkage
probability of birth sequence with no linkage
• By convention, a LOD score greater than 3.0 is considered
evidence for linkage.
• On the other hand, a LOD score less than -2.0 is considered
evidence to exclude linkage.
LOD Score Analysis
The likelihood ratio as defined by :-
L(pedigree| = x)
L(pedigree |  = 0.50)
where  represents the recombination fraction and where 0  x  0.49.
( (1   ) )
N
(  0.5)
R
L.R. =
NR
The LOD score (z) is the log10 (L.R.)
Method to evaluate the statistical significance
Maximum-likelihood analysis, which estimates the “most likely” value of the recombination
fraction Ø as well as the odds in favour of linkage versus nonlinkage.
Given by Conditional probability L(data 1 Ø), which is the likelihood of obtaining the data if the
genesare linked and have a recombination fraction of Ø.
Likelihood of obtaining one recombinant and seven nonrecombinants when the recombination
fraction is Ø is proportional to Ø1(1–Ø)7,
Where: Ø is, by definition, the probability of obtaining a recombinant ,
(I – Ø) is the probability of obtaining a nonrecombinant.
Mapping function
The genetic distance between locus A and locus B is
defined as the average number of crossovers occurring
in the interval AB.
Mapping function is use to translate recombination
fractions into genetic distances.
In 1919 the British geneticist J, B. S. Haldane proposed
such Mapping function
Haldane defined the genetic distance, x, between two
loci as the average number of crossovers per meiosis in
the interval between the two loci.
What is Haldane ’s mapping function ?
Assumptions: crossovers occurred at random along the
chromosome and that the probability of a crossover at one
position along the chromosome was independent of the
probability of a crossover at another position.
Using these assumptions, he derived the following relationship
between
Ø, the recombination fraction and
x ,the genetic distance (in morgans):
Ø=1/2(1-e-2x) or equivalently,
X=-1/2ln(1-2Ø)
Genetic distance between two loci increases, the
recombination fraction approaches a limiting value
of 0.5.
Cytological observations of meiosis indicate that the
average number of crossovers undergone by the
chromosome pairs of a germ-line cell during meiosis
is 33.
Therefore, the average genetic length of a human
chromosome is about 1.4 morgans, or about 140
centimorgans.
Integration of MAP
Suppose: A SNP marker M1 [A/C] is linked to the pea color gene ‘T1’ with the recombination
rate r. In the BC1F1(P2) population, the genotypes and phenotypes and their count are below.
M1
0.064 cM
T1
Haldane ’s mapping function
X=-1/2ln(1-2Ø) = -0.5*ln(1-2*0.06)
=0.064cM
M1
female
BC1F1(P2)
male
Ct1
100%
genotype
frequency
Phenotype
Obs.
r
AT1
(1-r)/2
Ct1
(1-r)/2
At1
r/2
CT1
r/2
ACT1t1
CCt1t1
ACt1t1
CCT1t1
(1-r)/2
(1-r)/2
r/2
r/2
purple
flower
48
white
flower
46
white
flower
2
purple
flower
4
recombination rate ( r) = 0.06
0.06 cM
T1
Kosambi function using the formula
CM1T1 = 1/4ln [(1+2r)/(1-2r)]
= 0.25 * ln[(1+2*0.06)/(1-2*0.06)]
= 0.06 cM
Construction of Genetic Map using JoinMap
 Download and install JoinMap 4.1 at
http://www.kyazma.nl/index.php/mc.JoinMap/sc.Evaluate/
 Please also download the manual at
http://www.kyazma.nl/index.php/mc.JoinMap/sc.Manual/
 The JionMap slideshow at http://www.kyazma.nl/docs/JM4slideshow.pdf
 Example data at http://comp.uark.edu/~ashi/MB/lecture/geneticMapExample1.loc
http://comp.uark.edu/~ashi/MB/lecture/geneticMap_rowDataExmaple.xlsb
;create genetic maps
name=GeneticMapExample1
popt=F2 ; population generation
nloc=720 ; number of markers
nind=184 ; population size
SNP
SNP
SNP
SNP
SNP
M042843
M018895
M029431
M050787
M054083
M029477
M065003
M038631
M031343
M053459
M904050
M047945
M054471
M057845
M049907
M052125
M016279
M028373
M062461
M047743
M061245
M044363
M039805
M042937
M064319
M050763
M062955
M050075
M027560
M050165
M032147
M045145
M051167
M042999
M048299
M054849
M046124
M015079
M041129
M055533
M060767
M064775
M014325
M050697
M038977
M015539
M044973
M035383
M030479
M059889
M042473
M021577
M056167
M059135
M064293
M020481
M028177
M020357
M058783
M025567
M051595
M059919
M063255
M039899
M057467
M032511
M021937
M051039
M055613
M050237
M048517
M025913
M028159
M044481
M015135
M021491
M053591
M027950
P1
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P1
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M042843
M018895
M029431
M050787
M054083
M029477
M065003
M038631
M031343
M053459
M904050
M047945
M054471
M057845
M049907
M052125
M016279
M028373
M062461
M047743
M061245
M044363
M039805
M042937
M064319
M050763
M062955
M050075
M027560
M050165
M032147
M045145
M051167
M042999
M048299
M054849
M046124
M015079
M041129
M055533
M060767
M064775
M014325
M050697
M038977
M015539
M044973
M035383
M030479
M059889
M042473
M021577
M056167
M059135
M064293
M020481
M028177
M020357
M058783
M025567
M051595
M059919
M063255
M039899
M057467
M032511
M021937
M051039
M055613
M050237
M048517
M025913
M028159
M044481
M015135
M021491
M053591
M027950
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60
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M042843
HHHHHHHBHBHBAAHHBAHHHBBHHHHHHBHABHAHBBHHAABHHABBAAHBHHHAHHBHHHBHBBHBHABAHHHHHHHBABBAHHHHBBAH
HBBAHHHBHHXABBAHHBBBHHAHBAXBABHAHHHABAHHHAABHBAHHBAHBBHAAHAAHBHABBAAHHBHAHHABBBAAAHBHHBBBHBH
……………………………………………….
M050787
HHHBHAHHAHBHAHBHAAHHHHHAABHHBHABHHBHBHHBAHAHHBHAHBHBBBBHAHHBHHBBHHAHHAHHBHHHHBAAHAHHBHBHABHB
HHBXHHHHBBHHBHHHBHHAHHHHAAXAHBHHHBHHHHBHBBBHHAHBHABAHBBHABABHHHBHHHHBHHHHAABHAHBBBAAHBHBHHAH
Example
Linkage mapping of wheat
powdery mildew resistance
(wheat-pm.pps)
Homework
1. Create 6 genetic maps of spinach using Zebu F2
SNP data
1a. Using a JoinMap format file:
spinach_ZebuF2_a.loc
1b. Using SNP data: Zebu_F2_SNP.xlsb
1c. Using GBS sequence data.
Request: 1a
1b and 1c are extra work for bonus.
Reading
 Muchero, M., N.N. Diop, P.R. Bhat, R.D. Fenton, S. Wanamaker, M. Pottorff, S. Hearne, N.
Cisse, C. Fatokun, J. D. Ehlers, P.A. Roberts, and T.J. Close. 2009. A consensus genetic map
of cowpea [Vigna unguiculata (L.) Walp.] and synteny based on EST-derived SNPs. PNAS
106:18159–18164 (http://www.pnas.org/content/106/43/18159.full.pdf)
 Agbicodo, E.M., C.A. Fatokun, R. Bandyopadhyay, K. Wydra, N.N. Diop, W. Mucher, J.D.
Ehlers, P.A. Roberts, T.J. Close, R.G.F. Visser, and C.G. van der Linden. 2010. Identification
of markers associated with bacterial blight resistance loci in cowpea. Euphytica 175:215226 (http://link.springer.com/article/10.1007/s10681-010-0164-5/fulltext.html)
 Genetic Mapping:
http://web.pdx.edu/~justc/courses/IntroGenetics/Ch4&5GeneLinkageRecombinationAna
lysis.ppt
 agrico.rakesh_linkage
 Genetic_mapping-100917050507-phpapp01