תפריט נגישות
ניגודיות עדינהניגודיות גבוהה
מונוכרום
הדגשת קישורים
חסימת אנימציה
פונט קריא
סגור
איפוס הגדרות נגישות
להורדת מודול נגישות חינם תפריט נגישותניגודיות עדינהניגודיות גבוההמונוכרוםהדגשת קישוריםחסימת אנימציהפונט קריאסגוראיפוס הגדרות נגישותלהורדת מודול נגישות חינם
Abstract:
In 2010 Illumina Inc., released the 3K bovine BeadChip, which included 3,000 markers for a price of $40, as compared to $95 for the 54K BeadChip, which includes 54,609 markers. In 2012 Illumina replaced the 3K BeadChip with the 9K BeadChip, which includes 8,762 markers, also for $40. The Israeli Herdbook committee decided as a first step to genotype 500 cows, including all elite cows, for the low density chip. The objective of this project was to develop and test an algorithm for imputation of genotypes for markers included in the 54K chip, but missing on the 9K chip. Several algorithms were developed for imputation of genotypes, and correct imputation rates of 95% under optimal conditions were reported. During the first year of the project we tested the “BEAGLE” program on simulated data. During the second year of the project we tested the “Findhap” program, which takes advantage of the unique population structure of commercial dairy cattle populations. This program is much faster that BEAGLE without a significant reduction in the accuracy of imputation. A total of 1,770 animals were genotyped for the 54K chip, including 374 elite cows.
In order to test the algorithm, the genotypes of the cows were deleted, except for each ninth marker, leaving 4,248 markers out of 38,629 valid markers on the 54K chip. For the remaining 1,394 animals (bulls and calves) with pedigree information, complete genotypes were retained. Accuracy of imputation was 93%, provided that the sire was genotyped for the 54K chip. Thus it is possible for $40 to compute genomic evaluations for calves or cows. This information can also be used to verify parentage or theft, and can be used by the farmer to improve decisions on selection, mating and embryo transplantation.
Abstract:
In 2010 Illumina Inc., released the 3K bovine BeadChip, which included 3,000 markers for a price of $40, as compared to $95 for the 54K BeadChip, which includes 54,609 markers. In 2012 Illumina replaced the 3K BeadChip with the 9K BeadChip, which includes 8,762 markers, also for $40. The Israeli Herdbook committee decided as a first step to genotype 500 cows, including all elite cows, for the low density chip. The objective of this project was to develop and test an algorithm for imputation of genotypes for markers included in the 54K chip, but missing on the 9K chip. Several algorithms were developed for imputation of genotypes, and correct imputation rates of 95% under optimal conditions were reported. During the first year of the project we tested the “BEAGLE” program on simulated data. During the second year of the project we tested the “Findhap” program, which takes advantage of the unique population structure of commercial dairy cattle populations. This program is much faster that BEAGLE without a significant reduction in the accuracy of imputation. A total of 1,770 animals were genotyped for the 54K chip, including 374 elite cows.
In order to test the algorithm, the genotypes of the cows were deleted, except for each ninth marker, leaving 4,248 markers out of 38,629 valid markers on the 54K chip. For the remaining 1,394 animals (bulls and calves) with pedigree information, complete genotypes were retained. Accuracy of imputation was 93%, provided that the sire was genotyped for the 54K chip. Thus it is possible for $40 to compute genomic evaluations for calves or cows. This information can also be used to verify parentage or theft, and can be used by the farmer to improve decisions on selection, mating and embryo transplantation.
