Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.

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Objective: The purpose of the present study was to explore the transcriptome differences of sheep embryos. Embryos were at different developmental stages in order to assess the differences of the function, classification and metabolic pathway of differentially expressed genes and to provide a theoretical basis for revealing the regulatory mechanism of sheep early embryo development.Methods: 8-cell, 16-cell, morula and blastocysts were collected and the sequencing library was constructed by the Smart-Seq2 amplification technology. The transcriber was sequenced by Illumina HiSeqXten high-throughput sequencing technology and the effective sequences were analyzed by functional annotation and related bioinformatic analysis.Results: The results indicated that the Clean reads of 8-cell, 16-cell, morula and early blastocysts embryos were 441698590-48957974, of which 93.71-95.29% reads were compared with the reference genome sequence of sheep; 10 were compared with alternative splicing types of transcription terminal site (TTS) and with the transcription start site (TSS), which accounted for the largest proportion in sheep embryo transcripts. There were 171170-211487 sites of single nucleotide polymorphisms (SNPs) and 6435-8023 transcripts of novel transcripts in sheep embryos respectively. We used FDR < 0.05 and Fold Change > 2 as the criteria to screen for differential genes by comparing pairwise differences at four stage during embryo development. A total of 8281 differentially expressed mRNAs were identified, including 840 in E16vsE8, 6631 in E32vsE16, 810 in BlavsE32. Using the GO enrichment analysis, we explored the function of the DEGs. No significant difference was found at E16 vs E8.At E32 vs E16,Cellular components contained 127 significance terms (P < 0.05), 92 terms were significant enriched in molecular function, And biological processes involved 338 significance terms; At Bla vs E32,Cellular components contained 7 significance terms (P < 0.05). A total of 40 significance KEGG pathway terms were enriched in E32 vs E16.Conclusions: In this study, individual embryonic transcriptome sequencing of sheep was established for high-throughput sequencing and analysis of the transcriptomes of sheep 8-cell, 16-cell, morula, and early blastocysts. The number of differentially expressed genes was identified at different stages of sheep embryo development and the function, classification and metabolic pathway of differentially expressed genes were obtained. The current study offers substantial information on the identification of the sheep embryo transcriptome, revealing the molecular regulatory mechanism of sheep embryo development. and selects 30 key genes, and its function needs further exploration and research.