S. Yu. Bakoev, L. V. Getmantseva
Federal Scientific Center of Animal Husbandry – L. K. Ernst All-Russian Research Institute of Animal Husbandry, pos. Dubrovitsy, 60, Podol’skii r-n, Moskovskaya obl., 142132, Russian Federation
Abstract. The article analyzes approaches and software based on methods for ROH (runs of homozygosity) search and identification. These are continuous homozygous regions of genotypes that are present in the animal, since both parents transmit the same haplotypes to their offspring. The methods used in software opened up opportunities for searching for ROH regions and can be classified as observational, model-oriented and methods, allowing the search for short sequences. The paper presents the main characteristics of ROH analysis software: Plink, Germline, Beagle, detectRUNS, SVS, Garlic, LOD, VCFtools, BCFtools/ROH. The identification and characterization of ROH helped to identify genomic regions responsible for the characteristics which are of interest in terms of increasing the productivity of commercial herds of farm animals. Based on genomic information, the inbreeding coefficient can be calculated using four indices: F(UNI), F(HOM), F(GRM), F(ROH). The determination of ROH was effective in assessing inbreeding using the F(ROH) index, as well as for identifying selection signatures in farm animals. The studies based on the analysis of the ROH frequency were aimed at identifying their relationship with economically useful traits in various types of farm animals. The potential of ROH for traditional production methods is huge, and the exponential increase in available genomic data due to the emergence and development of new genotyping technologies provides all the prerequisites for the use of ROH in other fields.
Keywords: farm animals; inbreeding; ROH; selection signatures; software.
Author Details: S. Yu. Bakoev, Cand. Sc. (Biol.), senior research fellow (e-mail: Этот адрес электронной почты защищён от спам-ботов. У вас должен быть включен JavaScript для просмотра.); L. V. Getmantseva, Cand. Sc. (Agr.), leading research fellow.
For citation: Bakoev S. Yu., Getmantseva L. V. Methods for Assessing Inbreeding and Selection Signatures of Farm Animals Based on Runs of Homozygosity. Dostizheniya nauki i tekhniki APK. 2019. Vol. 33. No. 11. Pp. 63–68 (in Russ.). DOI: 10.24411/0235-2451-2019-11114.