Journal Articles
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Item Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits(BioMed Central Ltd, 2023-07-11) Zhu M; Yang Y; Yang H; Zhao Z; Zhang H; Blair HT; Zheng W; Wang M; Fang C; Yu Q; Zhou H; Qi HBACKGROUND: Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS: We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS: Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.Item Genetic and phenotypic relationships between ewe reproductive performance and wool and growth traits in Uruguayan Ultrafine Merino sheep.(Oxford University Press on behalf of the American Society of Animal Science, 2023-03-07) Ramos Z; Garrick DJ; Blair HT; De Barbieri I; Ciappesoni G; Montossi F; Kenyon PRThis study reports genetic parameters for yearling and adult wool and growth traits, and ewe reproductive performance. Data were sourced from an Uruguayan Merino flock involved in a long-term selection program focused on reduced fiber diameter (FD), and increased clean fleece weight (CFW) and live weight (LW). Pedigree and performance data from approximately 5,700 mixed-sex yearling lambs and 2,000 mixed-age ewes born between 1999 and 2019 were analyzed. The number of records ranged from 1,267 to 5,738 for yearling traits, and from 1,931 to 7,079 for ewe productive and reproductive performance. Data on yearling and adult wool traits, LW and body condition score (BCS), yearling eye muscle area (Y_EMA), and fat thickness (Y_FAT), and several reproduction traits were analyzed. The genetic relationships between FD and reproduction traits were not different from zero. Moderate unfavorable genetic correlations were found between adult CFW and ewe lifetime reproduction traits (-0.34 ± 0.08 and -0.33 ± 0.09 for the total number of lambs weaned and total lamb LW at weaning, respectively). There were moderate to strong positive genetic correlations between yearling LW and all reproduction traits other than ewe-rearing ability (-0.08 ± 0.11) and pregnancy rate (0.18 ± 0.08). The genetic correlations between Y_EMA and reproduction traits were positive and ranged from 0.15 to 0.49. Moderate unfavorable genetic correlations were observed between yearling FD and Y_FAT and between adult FD and BCS at mating (0.31 ± 0.12 and 0.23 ± 0.07, respectively). The genetic correlations between adult fleece weight and ewe BCS at different stages of the cycle were negative, but generally not different from zero. This study shows that selection for reduced FD is unlikely to have any effect on reproduction traits. Selection for increased yearling LW and Y_EMA will improve ewe reproductive performance. On the other hand, selection for increased adult CFW will reduce ewe reproductive performance, whereas selection for reduced FD will negatively impact body fat levels. Although unfavorable genetic relationships between wool traits and both FAT and ewe reproductive performance existed, simultaneous improvements in the traits would occur using appropriately designed indexes.Item Genome-Wide Association Studies of Live Weight at First Breeding at Eight Months of Age and Pregnancy Status of Ewe Lambs(MDPI (Basel, Switzerland), 2023-03-27) Haslin E; Pettigrew EJ; Hickson RE; Kenyon PR; Gedye KR; Lopez-Villalobos N; Jayawardana JMDR; Morris ST; Blair HT; Ahmad SMThis study estimated genetic parameters and identified candidate genes associated with live weight, and the occurrence of pregnancy in 1327 Romney ewe lambs using genome-wide association studies. Phenotypic traits considered were the occurrence of pregnancy in ewe lambs and live weight at eight months of age. Genetic parameters were estimated, and genomic variation was assessed using 13,500 single-nucleotide polymorphic markers (SNPs). Ewe lamb live weight had medium genomic heritability and was positively genetically correlated with occurrence of pregnancy. This suggests that selection for heavier ewe lambs is possible and would likely improve the occurrence of pregnancy in ewe lambs. No SNPs were associated with the occurrence of pregnancy; however, three candidate genes were associated with ewe lamb live weight. Tenascin C (TNC), TNF superfamily member 8 (TNFSF8) and Collagen type XXVIII alpha 1 chain (COL28A1) are involved in extracellular matrix organization and regulation of cell fate in the immune system. TNC may be involved in ewe lamb growth, and therefore, could be of interest for selection of ewe lamb replacements. The association between ewe lamb live weight and TNFSF8 and COL28A1 is unclear. Further research is needed using a larger population to determine whether the genes identified can be used for genomic selection of replacement ewe lambs.Item Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep(MDPI (Basel, Switzerland), 2023-01-07) Ramos Z; Garrick DJ; Blair HT; Vera B; Ciappesoni G; Kenyon PRThe aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live weight (LW), body condition score (BCS), pregnancy rate (PR) and lambing potential (LP) of Uruguayan Merino sheep. Phenotypic records of approximately 2000 mixed-age ewes were obtained from a Merino nucleus flock. Genome-wide association studies were performed utilizing single-step Bayesian analysis. For wool traits, a total of 35 genomic windows surpassed the significance threshold (PVE ≥ 0.25%). The proportion of the total additive genetic variance explained by those windows was 4.85 and 9.06% for FD and CFW, respectively. There were 42 windows significantly associated with LWM, which collectively explained 43.2% of the additive genetic variance. For BCS, 22 relevant windows accounted for more than 40% of the additive genetic variance, whereas for the reproduction traits, 53 genomic windows (24 and 29 for PR and LP, respectively) reached the suggestive threshold of 0.25% of the PVE. Within the top 10 windows for each trait, we identified several genes showing potential associations with the wool (e.g., IGF-1, TGFB2R, PRKCA), live weight (e.g., CAST, LAP3, MED28, HERC6), body condition score (e.g., CDH10, TMC2, SIRPA, CPXM1) or reproduction traits (e.g., ADCY1, LEPR, GHR, LPAR2) of the mixed-age ewes.Item Functional development of the adult ovine mammary gland--insights from gene expression profiling.(5/10/2015) Paten AM; Duncan EJ; Pain SJ; Peterson SW; Kenyon PR; Blair HT; Dearden PKBACKGROUND: The mammary gland is a dynamic organ that undergoes dramatic physiological adaptations during the transition from late pregnancy to lactation. Investigation of the molecular basis of mammary development and function will provide fundamental insights into tissue remodelling as well as a better understanding of milk production and mammary disease. This is important to livestock production systems and human health. Here we use RNA-seq to identify differences in gene expression in the ovine mammary gland between late pregnancy and lactation. RESULTS: Between late pregnancy (135 days of gestation ± 2.4 SD) and lactation (15 days post partum ± 1.27 SD) 13 % of genes in the sheep genome were differentially expressed in the ovine mammary gland. In late pregnancy, cell proliferation, beta-oxidation of fatty acids and translation were identified as key biological processes. During lactation, high levels of milk fat synthesis were mirrored by enrichment of genes associated with fatty acid biosynthesis, transport and lipogenesis. Protein processing in the endoplasmic reticulum was enriched during lactation, likely in support of active milk protein synthesis. Hormone and growth factor signalling and activation of signal transduction pathways, including the JAK-STAT and PPAR pathways, were also differently regulated, indicating key roles for these pathways in functional development of the ovine mammary gland. Changes in the expression of epigenetic regulators, particularly chromatin remodellers, indicate a possible role in coordinating the large-scale transcriptional changes that appear to be required to switch mammary processes from growth and development during late pregnancy to synthesis and secretion of milk during lactation. CONCLUSIONS: Coordinated transcriptional regulation of large numbers of genes is required to switch between mammary tissue establishment during late pregnancy, and activation and maintenance of milk production during lactation. Our findings indicate the remarkable plasticity of the mammary gland, and the coordinated regulation of multiple genes and pathways to begin milk production. Genes and pathways identified by the present study may be important for managing milk production and mammary development, and may inform studies of diseases affecting the mammary gland.