Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep.

BACKGROUND: Tan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as "nine bends", which has high economic value. However, the "nine bends" characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively). RESULTS: In this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing. CONCLUSIONS: This study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.

Protein expression profiles in Meishan and Duroc sows during mid-gestation reveal differences affecting uterine capacity, endometrial receptivity, and the maternal-fetal Interface.

BACKGROUND: Embryonic mortality is a major concern in the commercial swine industry and primarily occurs early in gestation, but also during mid-gestation (~ days 50-70). Previous reports demonstrated that the embryonic loss rate was significant lower in Meishan than in commercial breeds (including Duroc). Most studies have focused on embryonic mortality in early gestation, but little is known about embryonic loss during mid-gestation. RESULTS: In this study, protein expression patterns in endometrial tissue from Meishan and Duroc sows were examined during mid-gestation. A total of 2170 proteins were identified in both breeds. After statistical analysis, 70 and 114 differentially expressed proteins (DEPs) were identified in Meishan and Duroc sows, respectively. Between Meishan and Duroc sows, 114 DEPs were detected at day 49, and 98 DEPs were detected at day 72. Functional enrichment analysis revealed differences in protein expression patterns in the two breeds. Around half of DEPs were more highly expressed in Duroc at day 49 (DUD49), relative to DUD72 and Meishan at day 49 (MSD49). Many DEPs appear to be involved in metabolic process such as arginine metabolism. Our results suggest that the differences in expression affect uterine capacity, endometrial matrix remodeling, and maternal-embryo cross-talk, and may be major factors influencing the differences in embryonic loss between Meishan and Duroc sows during mid-gestation. CONCLUSIONS: Our data showed differential protein expression pattern in endometrium between Meishan and Duroc sows and provides insight into the development process of endometrium. These findings could help us further uncover the molecular mechanism involved in prolificacy.

A post-GWAS confirming GPAT3 gene associated with pig growth and a significant SNP influencing its promoter activity.

Our previous genome-wide association study revealed that a SNP, ASGA0040372, located upstream of glycerol-3-phosphate acyltransferase 3 (GPAT3), is related to growth traits in Duroc pigs. In this study, we aimed to extensively investigate the genetic variation of GPAT3 and to further verify the contribution of ASGA0040372 to growth traits and its effect on promoter activity. Our data, obtained based on gene cloning and rapid amplification of cDNA ends experiments, showed that there are 14 exons and three alternative splicing variants. Five SNPs were detected, including ASGA0040372 and four novel SNPs. Furthermore, the five SNPs obtained were used to confirm their genetic effects on pig growth by an association study in a Duroc pig population. The results indicated that three SNPs (ASGA0040372, RS331766122 and RS346215414) are highly associated with average daily gain or days to 100 kg traits (P-value < 0.05). Subsequent analysis suggested that the promoter region of GPAT3 gene, from -950 to -500 bp, exhibited the highest activity. We also observed that ASGA0040372 (A/G) alleles have significantly different effects on promoter transcriptional activities, which leads to differential expression of GPAT3. Taken together, we conclude that the GPAT3 gene is associated with pig growth and that ASGA0040372 influences promoter activity of GPAT3 in pig.