Phenotypic and genetic parameter estimates for reproductive traits in Zandi sheep

A study on the genetic and phenotypic factors affecting specific ewe productivity traits in Sangsari sheep

The study's objectives were to assess the genetic parameters of reproductive characteristics in Sangsari sheep. A data set of reproductive information with pedigree details from 1995 to 2016 was used. Studied traits were litter size at birth (LSB), litter size at weaning (LSW), litter mean weight per lamb born (LMWLB), litter mean weight per lamb weaned (LMWLW), total litter weight at birth (TLWB) and total litter weight at weaning (TLWW). Test significance of the environmental factors to be included in the model was conducted using the general linear model procedure of the SAS program. All traits were significantly affected by the year of lambing and ewe age at lambing (P < 0.01). The AI-REML procedure of the Wombat program was used to evaluate genetic parameters. A series of bivariate animal models were employed to calculate genetic (rg) and phenotypic (rp) correlations between traits. The total least square means ± standard error of LSB and LSW were 1.04 ± 0.05 and 0.96 ± 0.03, while LMWLB, LMWLW, TLWB, and TLWW were 3.12 ± 0.08, 15.40 ± 0.13, 3.28 ± 0.04, and 19.31 ± 0.16 kg, respectively. The estimates of h2 were relatively low (P < 0.01) and ranged from 0.063 ± 0.028 for LSW to 0.181 ± 0.063 for TLWW. Repeatability estimates varied from 0.101 for LSW to 0.241 for TLWW. The sire service effects for LMWLB, TLWB, and TLWW were 0.012 ± 0.004, 0.023 ± 0.006, and 0.039 ± 0.009, respectively. The traits studied showed a greater magnitude of genetic correlation than phenotypic correlation, with values ranging from - 0.59 (LSB-LMWLB) to 0.87 (LMWLB-TLWB). It appears that focusing on TLWW for selection could result in more significant improvements in the reproductive performance of Sangsari ewes.

Comparison of different animal models for estimating genetic parameters for early growth traits and reproductive traits in Tianmu Sainuo sheep

As the economic level of individuals rises, so too does the demand for mutton. Enhancing the breeds of mutton sheep not only boosts production efficiency and economic benefits but also fosters the sustainable growth of the mutton sheep breeding industry. Thus, this study examines the early growth and reproductive traits of Tianmu Sainuo sheep, analyzing the genetic interactions among these traits to furnish a theoretical foundation for refining breeding strategies and expediting the genetic advancement of this breed. The investigation compiled 29,966 data entries, involving 111 sires for birth weight (BWT) and 113 for other metrics. The data encompassed 10,415 BWT records from 1,633 dams, 12,753 weaning weight (WWT) records from 1,570 dams, 12,793 average daily gain (ADG) records from 1,597 dams, and 13,594 litter size (LS) records from 1,499 dams. Utilizing the GLM procedure in SAS 9.2 software, the study analyzed the non-genetic influences on lamb BWT, WWT, ADG, and LS. Concurrently, DMU software estimated the variance components across various animal models for each trait. Employing the Akaike Information Criterion (AIC) and likelihood ratio test (LRT), six models were tested, incorporating or excluding maternal inheritance and environmental impacts, to identify the optimal model for deriving genetic parameters. The findings reveal that birth year (BY), birth quarter (BQ), birth type (BT), age of mother (AM), and birth sex (BS) exerted significant impacts on BWT, WWT, and ADG (p < 0.01). Additionally, BQ and AM significantly influenced LS (p < 0.01). The most accurate genetic evaluation model determined the heritability of BWT, WWT, ADG, and LS to be 0.0695, 0.0849, 0.0777, and 0.1252, respectively.

Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis

Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.

Reproductive performance and milk production of Central Highland and Boer x Central Highland goats

This study was conducted to evaluate the reproductive performance and milk production potential of Central Highland and Boer x Central Highland goats under semi-intensive management. Data were collected from 2009 till 2018 in the Sirinka goat breeding station. A general linear model procedure of the Statistical Analysis System (SAS) was used to analyze the data. The overall least-squares mean litter size at birth (LSB), litter size at weaning (LSW), total litter weight at birth, total litter weight at weaning and gestation length (GL) were 1.6 ± 0.02 kids, 1.4 ± 0.02 kids, 3.9 ± 0.05 kg, 13.6 ± 0.35 kg and 148.0 ± 0.33 days, respectively. The LSB, LSW and GL did not differ between Central Highland and their F1 and F2 crossbred dams. However, F2 dams produce the lightest kid at birth and weaning. Besides, birth type, season, year and parity were important sources of variation for most of the reproductive traits. The least-squares mean for daily milk yield (DMY), lactation milk yield (LMY) and lactation length (LL) were 0.34 ± 0.02 kg, 39.16 ± 3.00 kg and 104.2 ± 4.45 days, respectively. The DMY and LMY of Boer x Central Highland goats were higher than pure Central Highland goats by 46.4% and 27.2%, respectively. However, the LL for both genotypes was found to be similar (P > 0.05). Dams kidding during the short rainy season produce more milk than kidding during dry and main rainy seasons. Boer x Central Highland goats produce more milk than pure Central Highland goats. However, using Boer crossbred dams did not reveal any advantage over the base Central Highland dams in terms of reproductive performance. Therefore, using Central Highland goat as a dam line, improving the management and integration of crossbreeding with selection could be an ideal option to improve the overall productivity of goats.

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 (Ne), 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 (r2) 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 Ne 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.

Genomic prediction of reproduction traits for Merino sheep

Economically important reproduction traits in sheep, such as number of lambs weaned and litter size, are expressed only in females and later in life after most selection decisions are made, which makes them ideal candidates for genomic selection. Accurate genomic predictions would lead to greater genetic gain for these traits by enabling accurate selection of young rams with high genetic merit. The aim of this study was to design and evaluate the accuracy of a genomic prediction method for female reproduction in sheep using daughter trait deviations (DTD) for sires and ewe phenotypes (when individual ewes were genotyped) for three reproduction traits: number of lambs born (NLB), litter size (LSIZE) and number of lambs weaned. Genomic best linear unbiased prediction (GBLUP), BayesR and pedigree BLUP analyses of the three reproduction traits measured on 5340 sheep (4503 ewes and 837 sires) with real and imputed genotypes for 510 174 SNPs were performed. The prediction of breeding values using both sire and ewe trait records was validated in Merino sheep. Prediction accuracy was evaluated by across sire family and random cross-validations. Accuracies of genomic estimated breeding values (GEBVs) were assessed as the mean Pearson correlation adjusted by the accuracy of the input phenotypes. The addition of sire DTD into the prediction analysis resulted in higher accuracies compared with using only ewe records in genomic predictions or pedigree BLUP. Using GBLUP, the average accuracy based on the combined records (ewes and sire DTD) was 0.43 across traits, but the accuracies varied by trait and type of cross-validations. The accuracies of GEBVs from random cross-validations (range 0.17-0.61) were higher than were those from sire family cross-validations (range 0.00-0.51). The GEBV accuracies of 0.41-0.54 for NLB and LSIZE based on the combined records were amongst the highest in the study. Although BayesR was not significantly different from GBLUP in prediction accuracy, it identified several candidate genes which are known to be associated with NLB and LSIZE. The approach provides a way to make use of all data available in genomic prediction for traits that have limited recording.