Genetic analysis of Lori-Bakhtiari lamb survival rate up to yearling age for autosomal and sex-linked

Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (F_ROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, F_ROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

Relative contribution of Imprinting, X chromosome and Litter effects to phenotypic variation in economic traits of sheep

Data on Zandi sheep were analysed to quantify maternal and paternal imprinting, X chromosome and litter effects' contribution to phenotypic variation in birth weight (BW), weaning weight (WW), growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR). To this end, a two-step approach was adopted. In the first step, each trait was analysed with a series of 16 animal models, which were identical for fixed and autosomal additive genetic effects but differed for combinations of maternal permanent environmental, maternal genetic, X chromosome and litter effects. For each trait, the best model was selected by the Akaike information criterion (AIC) and likelihood ratio tests (LRTs). In the second step, three additional models were fitted by adding maternal imprinting, paternal imprinting or both (models 17, 18 and 19) to the best model selected in the first step. Estimators of bias, dispersion and accuracy of breeding values estimated within 19 models with whole, and partial data were used to evaluate how well were the 19 models in estimating breeding values for the animals when their records were masked. For all traits studied, fitting the litter effect led to a better data fit. Also, it resulted in noticeable decreases in residual variance and other maternal variances. For growth traits, models containing the X-linked effects fitted the data substantially better than corresponding models without the X-linked effects. For BW, WW and GR, estimates of X-linked heritability ( h s 2 $$ {h}_s^2 $$ ) ranged between 0.09 (GR) and 0.14 (BW). Ignoring X-linked effects from the genetic evaluation model resulted in significant inflated autosomal additive genetic variance. For BW, WW, EF and RGR, models containing the imprinting effects provided a better fit of the data than otherwise identical models. Imprinting effects contributed significantly to the phenotypic variation of these traits in a range between 5% (RGR) and 8% (BW, WW). A sharp decline was observed in autosomal additive genetic variance following including imprinting effects in the model (27% to 40% depending on the trait). The least bias and dispersion, as well as greater accuracies for breeding values of focal animals, were for a model which included imprinting, X-linked and litter effects. It was concluded that imprinting, X-linked and litter effects need to be included in the genetic evaluation models for growth and efficiency-related traits of Zandi lambs.

Analysis of X chromosome and autosomal genetic effects on growth and efficiency-related traits in sheep

Abstract Context It is believed that the X chromosome plays an important role in influencing quantitative traits. Despite this, until recently, X-linked genetic effects have not been considered in models to estimate genetic parameters for economically important traits of livestock. Aims A large dataset was analysed to quantify autosomal additive genetic, X-linked additive genetic and maternal effects on growth and efficiency-related traits in Baluchi sheep. Methods Traits included bodyweight at birth, weaning (WW), 6 months (W6), 9 months and yearling age, pre- and post-weaning average daily gain, pre- and post-weaning Kleiber ratio, pre- and post-weaning efficiency of growth (EFb), and pre- and post-weaning relative growth rate. Each trait was analysed using the REML procedure fitting a series of eight univariate animal models. For each trait, the most appropriate model was selected by the Akaike information criterion and Bayesian information criterion. Key results The X-linked genetic effect was significant only in models fitted to EFb, where the estimate of X-linked heritability was 0.02 ± 0.01 from the best model. Other traits were not affected significantly by X-linked genetic effects. Estimates of autosomal heritability () for growth traits were between 0.06 ± 0.02 (post-weaning average daily gain, pre-weaning relative growth rate) and 0.22 ± 0.04 (bodyweight at yearling age), and ranged between 0.02 ± 0.01 (EFb) and 0.08 ± 0.02 (pre-weaning Kleiber ratio) for efficiency-related traits. Maternal effects significantly contributed to phenotypic variation of most traits, with larger effects on traits measured early in life. For EFb, the Spearman’s correlation between breeding values including and excluding X-linked effects was 0.95. It was 1.00 for traits that were not affected by X-linked genetic effects. Conclusions Although the proportion of phenotypic variance attributed to X-linked loci for most traits was zero, the importance of X-linked genetic effects should be at least tested in models when estimating variance components for growth and efficiency traits of Baluchi sheep. Implications As estimates of genetic parameters are breed-specific, we recommend for growth and efficiency traits of sheep that the importance of X-linked genetic effects should be evaluated to assess if these effects should be included in models used in genetic evaluation.

Variation in autosomal and sex-linked genetic effects for growth traits in Markhoz goat using multivariate animal models

The present study was conducted to estimate autosomal and sex-linked genetic parameters by restricted maximum likelihood method using four different multivariate models for growth traits in Markhoz goat. Data were collected over a period of 23 years (1992-2014) from the breeding station of Markhoz goat. The studied growth traits were birth weight (BW), weaning weight (WW), 6-month weight (6WT), 9-month weight (9WT), and 12-month weight (12WT). The best model was determined by Akaike's information criterion. Based on the best model, direct autosomal heritabilities of 0.18, 0.10, 0.12, 0.22, and 0.24 were obtained for BW, WW, 6WT, 9WT, and 12WT, respectively. On the other hand, estimates of direct sex-linked heritability for BW, WW, 6WT, 9WT, and 12WT were 0.02, 0.01, 0.002, 0.03, and 0.04, respectively. The maternal permanent environmental component was remarkable for growth traits. Direct autosomal additive genetic correlations among the traits were positive and varied from 0.11 between BW and 9WT to 0.95 between BW and WW. The positive correlations were also estimated for direct sex-linked additive genetic effect except between BW-6WT (- 0.07) and WW-6WT (-0.19). The result of this study indicated that sex-linked chromosome effect had more considerable influence at post-weaning traits.

Autosomal and sex-linked (co)variance components and genetic parameters for growth traits of Iranian Zandi sheep

Separation of autosomal and sex-linked direct additive genetic effects has significant role in sheep breeding programs. Hence, this study was conducted to determine the genetic parameters of autosomal and sex-linked effects for growth traits of Zandi sheep. The data set used in this study contained 7571 Zandi lambs, descendent of 220 sires and 1481 dams, which were collected from Zandi sheep breeding Station at Khojir, Tehran, Iran from 1992 to 2011. The fixed effects included of year (20 classes), season (winter and spring), sex (male or female), birth type (single or twin), and the age of dam (seven classes, 2-8 years old). The data were analyzed using REML methodology by WOMBAT software. In the most appropriate fitted model, based on Akaike's information criterion (AIC) and Bayesian information criterion (BIC), the values of direct autosomal heritabilities of birth weight (BW), kleiber ratio at weaning (KR), 6-month weight (6MW), and 9-month weight (9MW) were 0.12 ± 0.03, 0.29 ± 0.05, 0.14 ± 0.04, and 0.15 ± 0.04, respectively. Furthermore, weaning weight (WW), average daily gain from birth to weaning (ADG), and 12-month weight (12 MW) showed the values of 0.19 ± 0.03 and 0.22 ± 0.03, 0.13 ± 0.05 and 0.15 ± 0.03, and 0.15 ± 0.05 and 0.18 ± 0.05, respectively. Based on the best models through all traits, estimates of the direct sex-linked heritability ranged from 0.0 (WW, ADG, KR, and 6MW) to 0.02 ± 0.03 (12MW). The average of autosomal and sex-linked breeding values (BVs) of body growth traits except KR (for autosomal) and 9MW and 12MW (for sex-linked) were greater than zero. The Pearson's/Spearman's correlation coefficients varied between 0.344 and 0.599/0.30 and 0.61 for autosomal and sex-linked BVs. Direct autosomal and sex-linked additive correlations for growth traits were ranged from - 0.02 (BW-KR) to 0.98 (WW-ADG) and 0.04 (KR-9 MW) to 0.99 (WW-ADG), respectively. Our results revealed that the genetic parameters related to growth traits in Zandi sheep could be more useful in selection strategies.

Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds

Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.

The novel T755C mutation in <i>BMP15</i> is associated with the litter size of Iranian Afshari, Ghezel, and Shal breeds

Abstract. The present study was conducted to determine the molecular genetic variation in bone morphogenetic protein 15 (BMP15) of some selected Iranian sheep breeds and aims to provide relevant genetic information for twin-birth lambing. Therefore, a total of 44 rams and 213 ewes with single-, twin-, and triplet-birth lambing were used from Shal, Ghezel, Afshari and Lori-Bakhtiari sheep breeds. Three primer pairs were used for amplification of exons 1 and 2 of the BMP15 gene. The sequencing result of distinctive single-strand conformation polymorphism (SSCP) patterns showed segregation of the T755C mutation and the ensuing non-conservative substitution of L252P in the BMP15 propeptide. All three ewes with triplet-birth lambing and two sterile ewes were heterozygotic for this mutation. Association analysis revealed that this mutation was significantly related to the ewe's litter size, so that ewes with the CT genotype had 0.24 and 0.30 more lambs than those with the CC (p < 0.05) and TT (p < 0.01) genotypes, respectively. The mutation effect on the litter size was incomplete dominance in Afshari breed and over-dominance in Shal and Ghezel breeds. In conclusion, the findings in this experiment suggested synergistic effects of the T755C mutation and other unknown mutations in other effective genes which cause infertility and higher litter size in two different ways.