QTL Analysis

a) Quan­ti­ta­tive trait locus (QTL) map­ping requires parental strains (red and blue plots) that dif­fer genet­i­cal­ly for the trait, such as lines cre­at­ed by diver­gent arti­fi­cial selec­tion.

b) The parental lines are crossed to cre­ate F1 indi­vid­u­als (not shown), which are then crossed among them­selves to cre­ate an F2, or crossed to one of the par­ent lines to cre­ate back­cross prog­eny. Both of the­se cross­es pro­duce indi­vid­u­als or strains that con­tain dif­fer­ent frac­tions of the genome of each parental line. The phe­no­type for each of the­se recom­bi­nant indi­vid­u­als or lines is assessed, as is the geno­type of mark­ers that vary between the parental strains.

c) Sta­tis­ti­cal tech­niques such as com­pos­ite inter­val map­ping eval­u­ate the prob­a­bil­i­ty that a mark­er or an inter­val between two mark­ers is asso­ci­at­ed with a QTL affect­ing the trait, while simul­ta­ne­ous­ly con­trol­ling for the effects of oth­er mark­ers on the trait. The results of such an analy­sis are pre­sent­ed as a plot of the test sta­tis­tic again­st the chro­mo­so­mal map posi­tion, in recom­bi­na­tion units (cM). Posi­tions of the mark­ers are shown as tri­an­gles. The hor­i­zon­tal line marks the sig­nif­i­cance thresh­old. Like­li­hood ratios above this line are for­mal­ly sig­nif­i­cant, with the best esti­mate of QTL posi­tions given by the chro­mo­so­mal posi­tion cor­re­spond­ing to the high­est sig­nif­i­cant like­li­hood ratio. Thus, the fig­ure shows five pos­si­ble QTL, with the best-sup­port­ed QTL around 10 and 60 cM.




MIKAWA Satoshi (美川智博士)


2. phylogeny





plink –23file JPT-NA19001.snp JPT ID002 –out JPT-NA19001

plink –bfile JPT-NA19001 –exclude merge.missnp –make-bed –out new

plink –bfile source1 –bmerge source2_­tri­al –make-bed –out merged_­tri­al

plink –merge-list merge_list –make-bed –out merge