A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes.

BACKGROUND: In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K. RESULTS: CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database. CONCLUSIONS: This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo's natural adaptive history together to a recent selection for milk used as primary food source from this species.

Correction to: Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.

Following publication of the original article [1], the authors flagged that the article had published with the author 'Ali Jalil Sarghale' erroneously omitted from the author list.

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.

BACKGROUND: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. RESULTS: In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). CONCLUSION: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

Expression of genes related to liver fatty acid metabolism in fat-tailed and thin-tailed lambs during negative and positive energy balances.

Fat-tailed sheep breeds can tolerate periods of negative energy balance without suffering from elevated concentration of plasma non-esterified fatty acid (NEFA). This ability was attributed to unique metabolism of fat-tailed adipose depot, whereas role of liver as an influential organ in fatty acid metabolism was not evaluated yet. Hence, current study was conducted to evaluate the effects of negative and positive energy balances on liver expression of genes related to fatty acid metabolism in fat-tailed and thin-tailed lambs. Lambs experienced negative (21 days) and positive (21 days) energy balances and were slaughtered at the beginning and end of negative energy balance and at the end of positive energy balance. Real-time quantitative polymerase chain reaction (RT-Q-PCR) was conducted to evaluate changes in gene expression. Expression of diglyceride acyltransferase 1 (DGAT1), 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2) and apolipoprotein B (APOB) was not affected by genotype, energy balance and their interaction. Expression of carnitine palmitoyltransferase 1 (CPT1) was significantly higher in liver of fat-tailed comparing to thin-tailed lambs regardless of energy balance (p < 0.02). Catalase mRNA abundance was increased in response to negative energy balance (p < 0.02), and severity of this enhancement was higher in fat-tailed lambs (p < 0.06). Expression of CPT1 was positively correlated with expression of HMGCS2 in both fat-tailed (p < 0.05) and thin-tailed lambs (p < 0.002); however, the correlation was weaker in fat-tailed lambs (0.72 vs. 0.57, respectively, for thin-tailed and fat-tailed lambs). There was a positive correlation between DGAT1 and APOB genes expression in fat-tailed lambs (0.94; p < 0.001), whereas this correlation was not observed in thin-tailed lambs. Results demonstrate that liver of fat-tailed lambs has higher capacity for metabolism of mobilized NEFA exposed to liver during negative energy balance.

WITHDRAWN:Investigating population structure and genetic diversity of some Iranian native cattle breeds using SNP markers.

Ahead of Print article withdrawn by publisher.

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds.

BACKGROUND: Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals. RESULTS: A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 13 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 regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2. CONCLUSIONS: Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight.

Linkage disequilibrium and within-breed genetic diversity in Iranian Zandi sheep.

This research aimed to measure the extent of linkage disequilibrium (LD), effective population size ( N e ), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD ( r 2 ) for single-nucleotide polymorphism (SNP) pairs in short distances (10-20 kb) was 0.21 ± 0.25 but rapidly decreased to 0.10 ± 0.16 by increasing the distance between SNP pairs (40-60 kb). The N e of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long ( > 10  Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.