نوع مقاله : مقاله پژوهشی
نویسندگان
1 گروه علوم دامی، دانشکده کشاورزی و محیط زیست، دانشگاه اراک، اراک، ایران
2 گروه علوم دامی، دانشکده کشاورزی، دانشگاه ایلام، ایلام، ایران
چکیده
کلیدواژهها
موضوعات
عنوان مقاله [English]
نویسندگان [English]
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.
کلیدواژهها [English]
Extended Abstract
Introduction
SNP genotyping technology is being used to study animal breed diversity and population structure. Understanding this diversity may lead to inferences about the interactions between different breeds that share geographic regions, including further information about the genetic evolution of animals and their historical origins in ancient parts of the world. Using genotyping technologies can help to identify animals with superior adaptive traits, such as the ability to withstand environmental stressors common in harsh environments, which will ensure the long-term viability of future breed improvement strategies. It can provide a genetic selection model for breeding programs to produce elite and well-adapted breeds. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. ROH one of the most methods was used to detecting the genomic inbreeding. 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. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable. Three local sheep breeds (Saidi, Wahati, and Barki) were studied. The animals were exercised under natural heat stress. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on their response to meteorological and physiological parameters.
Materials and methods
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. Genomic variation in these breeds was assessed using 64,756 single nucleotide polymorphic markers (SNPs). All the animals were non-lactating, non-pregnant females ranging in parity from 2 to 4. A) The Barki desert sheep, a native of the CZWD known for its adaptation to desert environments, is a fat-tailed sheep with open, coarse wool, a white body, and a colored head. For centuries, they have been subject to natural selection in desert areas known for high temperatures, intense sunlight, frequent drought, and extensive grazing. B) Wahati sheep have a narrow, medium-sized body and a medium-sized head with a straight profile. Most rams are unhorned and have white fleece and small ears. The fat tail has a broad base that ends in a cylindrical part. The animals have a white body with a brown head or an all-white and C) Saidi sheep, the native Upper Egyptian breed, are bred in small flocks; they are known for their tolerance to heat stress and the prevailing hot, dry environment. The Saidi sheep are considered the oldest Egyptian sheep breed and are characterized by good fertility but high mortality of the young animals
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.
Results and discussion
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).
Conclusion
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. Also, our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study sheep.
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