engleski

Estimation of genomic inbreeding using runs of homozygosity - cattle expirience

In plant, animal and human genetics the detrimental effect from parental relatedness (inbreeding depression) are well known. Inbreeding depression has traditionally been studied using pedigrees. Pedigree data are usually difficult to obtain, they are potentially unreliable, and do not count for inbreeding arising from distant common ancestors. Recently it is discovered that rates of inbreeding in large outbreed human populations are high enough to have detectable effects. This ancient inbreeding was recorded using “Runs of homozygosity” (ROH). To investigate rates of ancient inbreeding in cattle we used three breeds (Simmental n= 502, Tyrol Grey n = 217, Brown Swiss n = 499) with well known pedigrees (complete generation equivalents 6, 46- 8, 19). We calculated inbreeding from pedigree for whole pedigree (FpedT) and for five generation pedigree (Fped5). Obtained values were highest in Brown Swiss (FpedT = 4, 1%, Fped5 = 2, 1%), and lowest in Simmental (FpedT = 1, 4%, Fped5 = 0, 9%). In order to calculate genomic inbreeding, animals were genotyped with Illumina Bovine 50k SNP chip. From five ROH lengths (>1Mb, >2Mb, >4Mb, >8Mb and >16Mb) inbreeding coefficients (FROH1 , FROH2 , FROH4, FROH8, and FROH16 ) were calculated as sum of all ROHs of specific length divided by length of genome covered with SNPs. Small segments (>1Mb), which represent ancient inbreeding, indicated much higher inbreeding levels than pedigree. Highest was in Brown Swiss (FROH1 = 14, 2) and lowest in Tyrol Grey (FROH1 = 14, 2). Bigger segments (>8Mb and >16Mb), which represent recent inbreeding gave values similar to pedigree coefficients. To conclude we confirmed that pedigree inbreeding coefficients do not detect ancient inbreeding while ROH coefficients do. Insight in ancient inbreeding should help for better quantification of the risk, which is arising from recessive detrimental genetic variants in different populations.

Runs of homozygosity; genomic inbreeding; cattle

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