Candidate circRNAs related to skeletal muscle development in Dazu black goats.

Circular RNA (CircRNA), as a classical noncoding RNA, has been proven to regulate skeletal muscle development (SMD). However, the molecular genetic basis of circRNA regulation in muscle cells remains unclear. In this study, the expression patterns of circRNAs in the longissimus dorsi muscle at embryonic day 75 and postnatal day 1 in DBGs were investigated to identify the key circRNAs that play an important role in SMD in goats. A total of 140 significantly and differentially expressed circRNAs (DEcircRNAs) were identified among the groups at different developmental stages. Among the 116 host genes (HGs) of DEcircRNAs, 76 were significantly and differentially expressed, which was confirmed by previous RNA_seq data. Furthermore, the expression pattern of 10 DEcircRNAs with RT-qPCR was verified, which showed 80% concordance rate with that of RNA_seq datasets. Moreover, the authenticity of seven randomly selected DEcircRNAs was verified by PCR Sanger sequencing. Based on the functional annotation results, among the 76 significantly and differentially expressed HGs, 74 were enriched in 845 GO terms, whereas 35 were annotated to 85 KEGG pathways. The results of this study could provide a comprehensive understanding of the genetic basis of circRNAs involved in SMD and muscle growth.

Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis.

This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding.

Whole-genome scanning for the heat-resistance-associated genes in the Droughtmaster breed (Bos taurus).

The Droughtmaster is a tropical breed of beef cattle developed in North Queensland that exhibits a combination of heat resistance and parasitic resistance from long-term artificial selection. Therefore, we used next-generation sequencing technology to screen the chromosomal regions and genes related to heat-resistance in cattle to provide data for improving cattle breeding. A total of 15,569,067 variants including 14,249,316 SNPs were obtained from two mixed pools by genome-wide resequencing. According to the results of the selective sweep analysis of the Droughtmaster pool compared to the nonheat resistant breeds pool, 81 candidate genes under selection in Droughtmaster were identified by combining Z HP and F ST analyses with a threshold standard of the top 1%, including SLC7A11, GYPC, and GYPC. In addition, 40 GO terms and 44 pathways were annotated from newly identified candidate genes. These signaling pathways were involved in environmental information processing, organismal systems, and metabolism. A majority of these genes have not been implicated in the previous studies of heat resistance. This study explored the genomic changes that result from long-term artificial selection, our findings help to explain the molecular mechanism of heat resistance in cattle.