جستجوی مقالات مرتبط با کلیدواژه « جزایر roh » در نشریات گروه « علوم دام »

In this study in order to estimate inbreeding coefficient and identify the ROH Islands associated with the genes under selection, the 50k BeadChip genotyped data of 206 sheep from 3 different Egyptian breeds were used. After quality control, 48361 SNPs in 204 sheep were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. One percent of SNP with the highest frequency in ROH were considered as ROH Islands. The lowest rate of inbreeding according to (FGRM, FHOM, and FUNI) was related to Wahati and the highest was related to Saidi breed. The highest amount of FROH (0.043) was observed in Saidi and the lowest amount (0.018) was observed in Barki breed. Average length of ROH ranged from 45.02 to 205.87 Mb, while the average number of ROH ranged from 8.14 to 14.07. The highest number ROH was observed on chromosome 2, while the lowest was on chromosome 26. Average inbreeding coefficient from FROH in Barki, Saidi and Wahati were estimated 0.018, 0.043 and 0.027 respectively. A total of 62 ROH Islands with length: 24.60 Kb to 13 Mb were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform and varied among breeds, but some common were identified. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with reported genes that directly or indirectly influenced traits for adaptation and immune system (SEMA3D, CSF2, ITPR1), development of the skeletal muscle (UGGT1, ITGA2), and reproduction (ABHD16B). The results of this study revealed that, the selection processes in different sheep breeds for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.

Run of homozygosity (ROH) was used to detecting the genomic inbreeding in sheep. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. As detecting the ROH Islands, the genomic regions containe economic traits could be detectable.

In this study in order to identify the ROH Islands associated with the genes under selection, the 50k BeadChip genotyped data of 2536 sheep from 68 different breeds from all over the world were used. After quality control, ROHs were identified using Plink v1.09 software. One percent of SNP with the highest frequency in ROH were considered as ROH Islands.

A total of 465 ROH Islands (length: 27.43 Kb to 17 Mb) were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform and varied among breeds, but some common were identified. The highest and largest ROH islands were observed in European breeds. In contrast, the lowest and shortest were detected in African and American breeds, respectively. In this study, 256 genes were identified in 111 ROH Islands from total of 465 ROH Islands. of A quarter of the total reference genes identified in the sheep genome, were detected within the ROH islands. Totally 103 QTLs associated with milk, carcass, body weight, and wool traits were identified in these regions.

The results of this study revealed that, the formation of sheep breeds and selection for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome can be an alternative strategy to identify genes and associated loci with economic traits.