Mahdi Mokhber; Mohammad Moradi Shahre Babak; Mostafa Sadeghi; Hossein Moradi Shahrbabak; Javad Rahmani-Nia
Abstract
In order to detect signature of selection on buffalo genome, a set of 287 water buffalo samples from 260 Azari and 27 Mazandarani buffalo breeds were genotyped using the Axiom® Buffalo Genotyping 90K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, ...
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In order to detect signature of selection on buffalo genome, a set of 287 water buffalo samples from 260 Azari and 27 Mazandarani buffalo breeds were genotyped using the Axiom® Buffalo Genotyping 90K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 14 regions with outlier FST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected and 105 genes and 28 QTLs with selection signatures were detected. A high proportion of identified genes (N=27) in regions under selection were involved in olfactory receptor, also some of the detected genes were associated with growth and body development, metabolicand apoptosis possesses, immune system development, and mammary gland development. Some of the identified QTLs in regions under selection were associated with growth traits such as body weight at birth, weaning and mature, subcutaneous fat, meat yield and carcass weight. The detected QTL for milk traits were only associated with milk contents and somatic cell count. However, it is recommended to carry out association studies to show the actual function of these genes.
Zohre Yousefi; Mohammad Taghi Beige Nasiri; mohammad hosein moradi; Rostam Abdollahi Arpanahi; Masoud Shirali
Abstract
The detection of genomic regions under positive selection is one of the important topics in population genetics. The objective of the present study was to identify the genomic regions that have been under natural or artificial selection in Afshari and Moghani sheep breeds. Seventy-five samples from Afshari ...
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The detection of genomic regions under positive selection is one of the important topics in population genetics. The objective of the present study was to identify the genomic regions that have been under natural or artificial selection in Afshari and Moghani sheep breeds. Seventy-five samples from Afshari (N=41) and Moghani (N=34) breeds have been genotyped using the Illumina Ovine SNP50K BeadChip. Unbiased method of population differentiation index (Theta) was used to detect the positive selection signatures using Lokern R package. The results of this study revealed 16 genetic regions on chromosomes 2, 3, 4, 8, 9, 13, 15, 22 and 26 where have been under positive selection in these two Iranian sheep breeds. A majority of the genes were involved in signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures were identified spanning several genes that directly or indirectly influenced pigmentation (EDN3, BNC2), skeletal morphology and body size (ALX4, EXT2, BMP2), metabolic regulation (PPP1R3D) and immune response (IL2RB). The results of the present study and identified genomic regions suggest that the selection during the evolution and adaptation to the different environments and geographical conditions led to population differentiation in Afshari and Moghani breeds. In conclusion, finding of this study can play an important role in tracing the genomic regions associated with the distinctive traits of these two indigenous breeds.
Mahdi Mokhber; Mohammad Moradi Shahrbabak; Mostafa Sadeghi; Hossein Moradi Shahrbabak; John Williams
Abstract
Identification of selection targeted genomic regions is one of the most challenging areas of research in animal genetics, particularly in livestock. We carried out a genome-wide scan for signatures of positive selection to identify genomic regions that had been under selection in Iranian Khuzestani and ...
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Identification of selection targeted genomic regions is one of the most challenging areas of research in animal genetics, particularly in livestock. We carried out a genome-wide scan for signatures of positive selection to identify genomic regions that had been under selection in Iranian Khuzestani and Mazandrani buffalo breeds. A total of 148 water buffalo from Khuzestani (N=121) and Mazandrani (N=27) buffalo breeds were genotyped using Axiom® Buffalo Genotyping 90K Array. Unbiased method of population differentiation index (FST) was applied to detect signatures of selection. In total, 23 regions exceeding the 0.1 percent threshold of the empirical posterior distribution were identified as extremely differentiated. These selected genomic regions were surveyed to find encoding putative candidate genes and 64 genes and 27 QTL were extracted from the corresponding areas in UMD3.1 Bos Taurus Genome Assembly. Some of these genes have previously reported as signature of positive selection in the last studies. Some of these genes were also found to be involved in milk production traits and domestication-related changes include sensory perceptions, brain and neural system development, pigmentation, and geographic adaptation. Also, survey on extracted QTLs was shown that these QTLs involved in some economicl important traits in buffalo such as feed conversion ratio, subcutaneous fat, body weight, average daily gain, type, Meat tenderness, milk production conentent, udder attachment, calf size and calving ease traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.
