3 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.
4 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)M1M1M10.1cM0.1cM0.1cMM2M2M20.2cM0.2cM0.2cMM3M3M30.1cM0.25cMT1 (flower color)0.25cM0.15cMM4M4M40.1cM0.1cM0.1cMM6M5M6LGLinkage mapQTL mapping
5 Cowpea Whole Genome Genetic Maps 11 chromosome928 EST-SNPsFig. 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 PNAS 106:18159–18164.
7 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).Two SNP markers, CP08_ and CP02_ 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.CP02_CP08_SNPSoyPosCP02_Gm0250,192,757CP08_Gm085,433,9361_003745,862,3591_08533,450,6761_01834,014,465Agbicodo et al. 2010. Euphytica 175:
8 Estimate the linkage of two alleles in a segregating population Recombination fractionLOD scoreHaldane and Kosambi mapping function
9 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 = unlinkedGenes with recombination frequencies less than 50 percent are on the same chromosome = linked
10 Calculation of Recombination Frequency The percentage of recombinant progeny produced in a cross is called the recombination frequency, which is calculated as follows:
13 LOD SCORE The LOD score is calculated as follows: LOD = Z = Log10 probability of birth sequence with a given linkageprobability of birth sequence with no linkageBy 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.
14 LOD Score Analysis L(pedigree | = 0.50) 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.)
15 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.
17 Mapping functionThe 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 functionHaldane defined the genetic distance, x, between two loci as the average number of crossovers per meiosis in the interval between the two loci.
18 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 betweenØ, the recombination fraction andx ,the genetic distance (in morgans):Ø=1/2(1-e-2x) or equivalently,X=-1/2ln(1-2Ø)
19 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 centimorgans.
22 recombination rate ( r) = 0.06 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.M10.064 cMT1Haldane ’s mapping functionX=-1/2ln(1-2Ø) = -0.5*ln(1-2*0.06)=0.064cMM1BC1F1(P2)femaleAT1 (1-r)/2Ct1 (1-r)/2At1 r/2CT1 r/2maleCt1 100%ACT1t1CCt1t1ACt1t1CCT1t1genotype frequency(1-r)/2r/2Phenotypepurple flowerwhite flowerObs.484624rrecombination rate ( r) = 0.060.06 cMT1Kosambi function using the formulaCM1T1 = 1/4ln [(1+2r)/(1-2r)]= 0.25 * ln[(1+2*0.06)/(1-2*0.06)]= 0.06 cM
23 Construction of Genetic Map using JoinMap Download and install JoinMap 4.1 atPlease also download the manual atThe JionMap slideshow atExample data at;create genetic mapsname=GeneticMapExample1popt=F2 ; population generationnloc=720 ; number of markersnind=184 ; population sizeM042843HHHHHHHBHBHBAAHHBAHHHBBHHHHHHBHABHAHBBHHAABHHABBAAHBHHHAHHBHHHBHBBHBHABAHHHHHHHBABBAHHHHBBAHHBBAHHHBHHXABBAHHBBBHHAHBAXBABHAHHHABAHHHAABHBAHHBAHBBHAAHAAHBHABBAAHHBHAHHABBBAAAHBHHBBBHBH……………………………………………….M050787HHHBHAHHAHBHAHBHAAHHHHHAABHHBHABHHBHBHHBAHAHHBHAHBHBBBBHAHHBHHBBHHAHHAHHBHHHHBAAHAHHBHBHABHBHHBXHHHHBBHHBHHHBHHAHHHHAAXAHBHHHBHHHHBHBBBHHAHBHABAHBBHABABHHHBHHHHBHHHHAABHAHBBBAAHBHBHHAH
24 Linkage mapping of wheat powdery mildew resistance (wheat-pm.pps) Example
25 Homework 1. Create 6 genetic maps of spinach using Zebu F2 SNP data 1a. Using a JoinMap format file: spinach_ZebuF2_a.loc1b. Using SNP data: Zebu_F2_SNP.xlsb1c. Using GBS sequence data.Request: 1a1b and 1c are extra work for bonus.
26 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 A consensus genetic map of cowpea [Vigna unguiculata (L.) Walp.] and synteny based on EST-derived SNPs. PNAS 106:18159–18164 (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 Identification of markers associated with bacterial blight resistance loci in cowpea. Euphytica 175: (Genetic Mapping: lysis.pptagrico.rakesh_linkageGenetic_mapping phpapp01