Fall 2014HORT6033

Molecular Plant BreedingINSTRUCTOR: AINONG SHI

HORT6033 web site: http://comp.uark.edu/~ashi/MB

Fall 2014 HORT6033Molecular Plant Breeding

Lecture 9 (09/22/2014)

I. Genetic map constructionII.Genetic mappingIII.ExampleIV.HomeworkV.Reading

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.

In classic genetics, genes can be mapped to specific locations on chromosomes.

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)

M1M2

M3

M4M6

0.2cM

0.1cM

0.25cM

0.1cM

M1M2

M3T1 (flower color)M4

M5

0.2cM

0.1cM

0.1cM0.15cM0.1cM

LG Linkage map

M1M2

M3

M4M6

0.2cM

0.1cM

0.25cM

0.1cM

QTL mapping

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 Whole Genome Genetic Maps

11 chromosome928 EST-SNPs

Cowpea Bacterial Blight

CoBB susceptible

CoBB resistance

QTL mapping for CoBB Resistance

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

CP08_5433936

CP02_50192757

• 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).

• 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.

Recombination fraction

LOD score

Haldane and Kosambi mapping function

Estimate the linkage of two alleles in a segregating population

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.

L.R. =

The LOD score (z) is the log10 (L.R.)

N

NRR

)5.0(

))1((

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.

BC1F1(P2)female

AT1 (1-r)/2

Ct1(1-r)/2

At1r/2

CT1r/2

male

Ct1100% ACT1t1 CCt1t1 ACt1t1 CCT1t1

genotype frequency (1-r)/2 (1-r)/2 r/2 r/2

Phenotype purple flower

white flower

white flower

purple flower

Obs. 48 46 2 4

r recombination rate ( r) = 0.06

M1

T1

Haldane ’s mapping function X=-1/2ln(1-2Ø) = -0.5*ln(1-2*0.06)=0.064cM

Kosambi function using the formulaCM1T1 = 1/4ln [(1+2r)/(1-2r)]

= 0.25 * ln[(1+2*0.06)/(1-2*0.06)]

= 0.06 cM

0.064 cM

M1

T1

0.06 cM

;create genetic maps

name=GeneticMapExample1popt=F2 ; population generationnloc=720 ; number of markersnind=184 ; population size

M042843HHHHHHHBHBHBAAHHBAHHHBBHHHHHHBHABHAHBBHHAABHHABBAAHBHHHAHHBHHHBHBBHBHABAHHHHHHHBABBAHHHHBBAHHBBAHHHBHHXABBAHHBBBHHAHBAXBABHAHHHABAHHHAABHBAHHBAHBBHAAHAAHBHABBAAHHBHAHHABBBAAAHBHHBBBHBH……………………………………………….M050787HHHBHAHHAHBHAHBHAAHHHHHAABHHBHABHHBHBHHBAHAHHBHAHBHBBBBHAHHBHHBBHHAHHAHHBHHHHBAAHAHHBHBHABHBHHBXHHHHBBHHBHHHBHHAHHHHAAXAHBHHHBHHHHBHBBBHHAHBHABAHBBHABABHHHBHHHHBHHHHAABHAHBBBAAHBHBHHAH

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

geneticMapExample1.loc

SNP P1 P2 SNP 7 8 10 12 16 19 30 33 35 37 41 42 43 44 48 50 58 59 60SNP P1 P2 SNP 7 8 10 12 16 19 30 33 35 37 41 42 43 44 48 50 58 59 60SNP P1 P2 SNP 7 8 10 12 16 19 30 33 35 37 41 42 43 44 48 50 58 59 60SNP P1 P2 SNP 7 8 10 12 16 19 30 33 35 37 41 42 43 44 48 50 58 59 60SNP P1 P2 SNP 7 8 10 12 16 19 30 33 35 37 41 42 43 44 48 50 58 59 60M042843 AA GG M042843 AG AG AG AG AG AG AG GG AG GG AG GG AA AA AG AG GG AA AGM018895 TT TT M018895 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TTM029431 GG AA M029431 GG AA AA AG AG AG AG AG AA AA AA AG AA AA AG AA AG AG AGM050787 CC AA M050787 AC AC AC AA AC CC AC AC CC AC AA AC CC AC AA AC CC CC ACM054083 CC GG M054083 CG CC CG GG CG GG CG CC CG CG CG CG CG CG CG CC GG CG GGM029477 TT TT M029477 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TTM065003 AA GG M065003 AG AA GG AA GG AG AA GG AG AA AG AG AA GG AG AA AG AA AAM038631 GG AA M038631 GG GG AG AA AA AG AG AA AA AG GG GG AG AG AA AG AG GG AGM031343 AA GG M031343 GG AG AG GG AG AG AG AA GG AG AA AG GG AG GG AG AG AG AGM053459 GG AA M053459 AG AG AA AA AG AG AG AG AG AG AG AG AA AA AA AG AG AG AGM904050 TT TT M904050 TT TT TT TT TT TT TT TT TT TT TT TT TT AT TT TT TT TT TTM047945 TT AA M047945 AT AT AT TT AA AT AA AT AT AT AT AA AA AT AA AA AT AT ATM054471 AA GG M054471 GG AG AG AG GG AG AA AG AG AG GG GG GG AA GG GG AA AG AGM057845 CC AA M057845 AC AC AC AC AA CC AC CC AA AA CC CC AC AA AA AC CC AC ACM049907 AA AA M049907 AT AA AA AA AA AA AA AA AA AA AT AT AT AA AA AA AT TT AAM052125 AA AA M052125 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM016279 TT TT M016279 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TTM028373 AA AA M028373 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM062461 AC AC M062461 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC ACM047743 GG AA M047743 AG AG AA GG AG AG GG AG GG AG AG GG AG AG GG AA AG AG GGM061245 GG AA M061245 AA AG AG AG AA AG GG AG AG AG AA AA AA - AA AA GG AG AGM044363 AA TT M044363 TT AT AT AT TT AA AT AA TT TT AA AA TT TT TT AT AA AT ATM039805 AA TT M039805 AT AT AT TT TT AT TT AA AT TT AA TT AT AT AA AT TT TT TTM042937 GG AA M042937 AA AA AA GG AA AA AG AG AG GG AG GG AG AA AG AG AG GG AGM064319 AA GG M064319 AG GG GG AG AG GG AA AA AG AG GG AA AA AA GG AA AG AA GGM050763 AA GG M050763 AG GG GG AG AG GG AG AA AG AG GG AA AA AA GG AA AG AA GGM062955 TT AA M062955 AA TT AT TT AA AT AT AT AA TT AA TT AA TT TT AT AT AT ATM050075 AA AA M050075 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM027560 GG AA M027560 GG AA AG AA GG AG AG AG AG AG GG AG GG AA AG AA AG AG AGM050165 AA GG M050165 AG GG GG AG AG GG AA AA AG AG GG AA AA AA GG AA AG AA GGM032147 AA AA M032147 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM045145 AA TT M045145 AT TT AT TT TT AT AA AA TT AT AT TT AT AA AA TT AA AT AAM051167 GG GG M051167 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM042999 AA GG M042999 AG GG AG AG GG AA AG AG GG GG AG AG AA AG AG AG GG AG AAM048299 AA GG M048299 AG AA AA AG AG GG GG AG AA GG AG GG AA GG GG AG AG AG AGM054849 AA AA M054849 AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AAM046124 AA AA M046124 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM015079 GG GG M015079 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM041129 GG CC M041129 CC CG GG CG CG GG CC CG CG CG CC CG CC GG CG CG GG CG CGM055533 AG AG M055533 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AGM060767 CC CC M060767 CC CC CC CC CC CC CC CC CC CC CC CC CC CG CG CC CC CC CCM064775 CC CC M064775 CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CCM014325 GG CC M014325 GG GG CG CC CC CG CG CG CG CG GG GG CG CC CC CG CG GG CGM050697 AA AA M050697 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM038977 GG GG M038977 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM015539 AA AA M015539 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM044973 TT TT M044973 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TTM035383 TT TT M035383 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TTM030479 AA AA M030479 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM059889 AA GG M059889 AG GG GG AA AG AG AA AG AA GG GG AG AG AA GG AG GG AG AGM042473 GG GG M042473 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM021577 GG GG M021577 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM056167 GG CC M056167 CC CG CC GG CC CG CG CC CG CG CG CG GG CC CG GG CG GG GGM059135 AA GG M059135 AA AA AG AG AA AG GG AG AA GG AG AG AG GG AG AG AG AG AAM064293 AA TT M064293 AT TT AA AT AT AT AA AA TT TT AT AA TT AT AT AT AT TT TTM020481 AA AA M020481 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM028177 AA GG M028177 GG AA GG AG GG AA AA AA GG AA GG GG AG AA AG GG AA AG AGM020357 AA CC M020357 CC AA AA CC AA AA AA AA AA AA AA AA CC AA AA AA AC AC CCM058783 AA AA M058783 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM025567 GG GG M025567 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM051595 AA AA M051595 AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AAM059919 CC GG M059919 CG CC CC CG CG GG CG CG CC GG CG GG CC CC GG CG CG CG CGM063255 AA CC M063255 AC AC CC AA CC AA AC CC AC AC AC AC AA CC AC AA AC AC ACM039899 TT AA M039899 TT TT TT AA AA AT AT TT AT AA TT AT AA AT AA TT AT TT AAM057467 AA GG M057467 GG AA AG AA AG GG AG AG AG AA GG GG AA AA AA AG AG AG AGM032511 AG AG M032511 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AGM021937 GG GG M021937 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM051039 AA AA M051039 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AAM055613 AA GG M055613 AA AG AA AG AG AA AG AG AG GG AA AG AG GG AG AA AG GG AGM050237 CC AA M050237 CC AA CC AA CC CC AC AC CC CC CC AC AA CC AC AC AC CC ACM048517 GG AA M048517 AG AG AA AG GG GG AA GG AA AA AG AG AG AG AA GG AA AA AGM025913 GG GG M025913 GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GGM028159 GG AA M028159 AG GG GG AG AG AA AG AG GG AA AG AA GG GG AA AG AG AG AGM044481 AA GG M044481 - AA AG GG AG GG AA AA AA AG AG GG GG GG GG AG AG GG AGM015135 AA GG M015135 AA AG AG AG AA AG AG AA GG GG AA AG AA AG AG AA AG GG AGM021491 AA AA M021491 AA AA AC AA AA AA AA AC AA AC AC - AC CC AA AA AC AC AAM053591 CC CC M053591 CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CCM027950 AA AA M027950 AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA

Linkage mapping of wheat powdery mildew resistance(wheat-pm.pps)

Example

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.

ReadingMuchero, 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 175:215-226 (http://link.springer.com/article/10.1007/s10681-010-0164-5/fulltext.html)

Genetic Mapping: http://web.pdx.edu/~justc/courses/IntroGenetics/Ch4&5GeneLinkageRecombinationAnalysis.ppt

agrico.rakesh_linkage

Genetic_mapping-100917050507-phpapp01