1How many genes?How many genes?Mapping mouse traitsMapping mouse traitsLecture 1, Statistics 246January 20, 20042Aim of today’s and Thursday’s lecture To review basic Mendelian genetics, the basicsof recombination, and go on to see how genescontributing to qualitative and quantitative traitsare mapped using data from crosses of inbredstrains of mice.32.1 Genetic background 2.1 Loci and markers We need to know the following notions fromMeldelian genetics: autosomes, sexchromosomes, genotypes, phenotypes, loci,alleles, homozygous, heterozygous, dominant,recessive, (fully) inbred, markers.4Our markers are Microsatellites..AGTCCACACACACACACATGT....AGTCCACACACACACACATGT....AGTCCACACACACACACATGT....AGTCCACACACACACACACACACATGT....AGTCCACACACACACACACACACATGT....AGTCCACACACACACACACACACATGT..PCR andelectrophoresisABH Desirable: to call the genotypes (A, H, or B) automatically Problems: stutters and noise, variability of the patterns, etc.5Similarity Sortingunsorted correlation matrixsortedThis is a useful technique to enhance presentation of gel traces and assist manual examination.6Genotype CallingThis is a statistical pattern recognition problem:• Fit mixture models• Discriminant analysisA BH7JnoTyper: software implementation in Java82.2 Inbred strains and their crosses Our main players are the C57BL/6 (BL forblack, abbreviated B6), a robust strain that hasbeen around about 90 years, and the NOD(non-obese diabetic) mouse strain, a delicatediabetes-prone strain discovered in 1990. Coat colours: agouti is standard, B6 is black,NOD is albino (i.e. white).9Normal (wild-type) mouse coat: color = agoutia grizzled color of fur resulting from the barring of each hair in several alternate dark and light bands10Black mouse: C57/BL6 strain11Albino mouse: non-obese diabetic (NOD) strain12Coat color loci in miceFour main loci : A, B, C and D• Locus A – agouti• Locus B – black• Locus C (known as Tyr) – albinism• Locus D – dilution gene13Alleles at the Agouti (A) locus• Ay, Lethal dominant yellow• Avy, Viable yellow• Aw, White-bellied Agouti• A, Agouti or Wild type• At, Black and Tan• Am, mottled agouti• a, Non-agouti• ae., Extreme non-agoutiA and a are a dominant/recessive allele pair14Alleles at the Albino (C) Locus• C, full color gene• cch, chincilla• ch, himalayan• c, albino geneC and c are a dominant/recessive pair of alleles15Alleles at A and C interact(called epistasis in genetics))• If the mouse is aaCx it is not agouti andnot albino (in our case a black mouse)• If the mouse is AxCx it is agouti and notalbino• If the mouse is xxcc it is albino no matterwhat the alleles at the agouti locus arebecause they are irrelevant16Crosses We will denote the NOD mice by A, and the B6mice by B. This same notation will denote thetwo homozygotes at a polymorphic marker. Two main crosses interest us, following the firstfilial generation or F1 , which we denote byA×B → H. Here H denotes heterozygote, whichis the case for our F1s. The backcross BC is arrived at via H×B → BC,or a variant, while the F2 intercross is given byH×H → F2.17 2.3 Data• An F2 inter cross was performed starting withC57BL/6 and NOD parental lines.• We have 133 female mice at the F2generation, just females for the reason thatmales fight, and this influences other(quantitative blood) phenotypes of interest• They were genotyped at 153 microsatellitemarkers spanning all 19 autosomes and theX chromosome. We also have coat color anda few white blood cell phenotypes.18A small portion of the data (beginning)data type f2 intercross .133 153 7*D10M106 BBABBBBBHBBABBBBAABBBB-BABABABBABBBBBBBBBBBBB-BBBBBBABBAAABBBBBBBBB-HBABABB-ABBBBAB-BBBABABBB-BBBBBCBCBCBHBBBHCBBHBHHBCBBBBBBBHBHBHCH*D10M14 AHHBHHHAHHABAHBHHBABAA-BHHAHAAHAHHHHHBAHHHAHHBAHBHABBBHAAHHHHAHBHHH--HHHHAHAHAHBHHHAHHABAHHHAHHHAHBHBBHHHAAHAAHHBHHAHAH-HBABAHAHBHHAH*D10M163 AHBBHHB-HHAB-HBH-BAHBA-BHHAHAAHAAHHAHBAHHHHHHHAHBHABBBHAAHBBHAHBBHHBBHBHHHH-HBHHHHHAHHAHABH-AHHHAHBABBBBAAAHAAHHBHHAHHHBHBAHAHABHHHAH*D10M20 HCBHAHBAHHAHAHBABAHHBH-HHHABAAHAAABHHBH-HAHBHAAHBCABABHAAABBHAHBHHBBBHBHAHH-HBHHHABAHHHHAHHBAAHHABHABHBHAAHBHAAHBHAAHBHBHBHHHHABAHAAHdata type f2 intercross .133 153 7*D10M106 BBABBBBBHBBABBBBAABBBB-BABABABBABBBBBBBBBBBBB-BBBBBBABBAAABBBBBBBBB-HBABABB-ABBBBAB-BBBABABBB-BBBBBCBCBCBHBBBHCBBHBHHBCBBBBBBBHBHBHCH*D10M14 AHHBHHHAHHABAHBHHBABAA-BHHAHAAHAHHHHHBAHHHAHHBAHBHABBBHAAHHHHAHBHHH--HHHHAHAHAHBHHHAHHABAHHHAHHHAHBHBBHHHAAHAAHHBHHAHAH-HBABAHAHBHHAH*D10M163 AHBBHHB-HHAB-HBH-BAHBA-BHHAHAAHAAHHAHBAHHHHHHHAHBHABBBHAAHBBHAHBBHHBBHBHHHH-HBHHHHHAHHAHABH-AHHHAHBABBBBAAAHAAHHBHHAHHHBHBAHAHABHHHAH*D10M20 HCBHAHBAHHAHAHBABAHHBH-HHHABAAHAAABHHBH-HAHBHAAHBCABABHAAABBHAHBHHBBBHBHAHH-HBHHHABAHHHHAHHBAAHHABHABHBHAAHBHAAHBHAAHBHBHBHHHHABAHAAHD10M106 = a marker on chr 10 defined by MITIncompleteness code: C = B or H, D = A or H, - = missing#individuals #loci #traits marker next column = data from mouse119A small portion of the raw data (end)data type f2 intercross .133 153 7*D10M106 BBABBBBBHBBABBBBAABBBB-BABABABBABBBBBBBBBBBBB-BBBBBBABBAAABBBBBBBBB-HBABABB-ABBBBAB-BBBABABBB-BBBBBCBCBCBHBBBHCBBHBHHBCBBBBBBBHBHBHCH*D10M14 AHHBHHHAHHABAHBHHBABAA-BHHAHAAHAHHHHHBAHHHAHHBAHBHABBBHAAHHHHAHBHHH--HHHHAHAHAHBHHHAHHABAHHHAHHHAHBHBBHHHAAHAAHHBHHAHAH-HBABAHAHBHHAH*D10M163 AHBBHHB-HHAB-HBH-BAHBA-BHHAHAAHAAHHAHBAHHHHHHHAHBHABBBHAAHBBHAHBBHHBBHBHHHH-HBHHHHHAHHAHABH-AHHHAHBABBBBAAAHAAHHBHHAHHHBHBAHAHABHHHAH*D10M20 HCBHAHBAHHAHAHBABAHHBH-HHHABAAHAAABHHBH-HAHBHAAHBCABABHAAABBHAHBHHBBBHBHAHH-HBHHHABAHHHHAHHBAAHHABHABHBHAAHBHAAHBHAAHBHBHBHHHHABAHAAH*DXM210 --HAAAAHHHAHAAAAAHAH-HAHHAHAHHH-HHH-H-H-AHH-AAHAA-HHAAAAAHH-AHHAAHHHAHAAH-HAHA-HAAHAHAA-A-HH-AAHHHAHAAHAAAAAHHHHAAAHAAHHAHHHHHHAHAAHA*DXM222 HAAHHAA-HHAAHAAHHAAAHH-HAAHAAHHHHHAHHHH-AAHHAHHAAHHHHHHAAHHAHHHHAAH-AHHHAHHAAAHHHAAAHAHAAHHAAHA-HAA--HHAHHA-AAHAAAAA-HH-AHAAAH-HHAAHA*DXM39 HAAAHAA-HHAH-AAA-HAAHH-HAAAAHHHHHHAHHHHAAHHAAAHAAHHHHAAAAHHHHHHAAHH--HAAAHH-AAHHAAHAHAHAAHH-AAAHHAAHAHAHAAAAHH-AAAAAAAH-AHAAHHAAAAAHA*trait1 1 1 2 3 1 1 2 3 1 2 2 2 1 1 1 1 3 1 1 1 1 1 1 1 2 1 1 3 1 1 2 1 1 1 2 1 2 3 1 1 2 3 1 1 2 3 1 2 2 1 1 2 3 1 3 3 1 3 1 1 1 1 3 1 1 3 1 2 3 3 1 1 1 2 2 3 1 1 2 2 1 1 1 1 1 3 1 1 2 2 3 3 3 1 1 1 1 1 1 1 1 1 2 2 2 2 1 3 1 1 1 1 1 2 3 1 1 3 3 1 1 2 2 3*trait2 8.90472059883773 8.62455170973674 8.45460831622462 8.43453595773523 8.58360495693549 8.35936910622267 9.09754487783084 8.3999100308015 8.46379241468912 8.69506039786081 8.1840487448877 8.89745444516111 8.40886531453061
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