Summary
The Chinese Meishan pig breed is well known for its high prolificacy. Moreover, this breed can be divided into three types based on their body size: big Meishan, middle Meishan (MMS) and ...small Meishan (SMS) pigs. Few studies have reported on the genetic signatures of Meishan pigs, particularly on a genome‐wide scale. Exploring for genetic signatures could be quite valuable for revealing the genetic architecture of phenotypic variation. Thus, we performed research in two parts based on the genome reducing and sequencing data of 143 Meishan pigs (74 MMS pigs, 69 SMS pigs). First, we detected the selection signatures among all Meishan pigs studied using the relative extended haplotype homozygosity test. Second, we detected the selection signatures between MMS and SMS pigs using the cross‐population extended haplotype homozygosity and FST methods. A total of 111 398 SNPs were identified from the sequenced genomes. In the population analysis, the most significant genes were associated with the mental development (RGMA), reproduction (HDAC4, FOXL2) and lipid metabolism (ACACB). From the cross‐population analysis, we detected genes related to body weight (SPDEF, PACSIN1) in both methods. We suggest that rs341373351, located within the PACSIN1 gene, might be the causal variant. This study may have achieved consistency between selection signatures and characteristics within and between Meishan pig populations. These findings can provide insight into investigating the molecular background of high prolificacy and body size in pig.
The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing ...Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction.
In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA).
The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle.
Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.
Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, ...genome‐wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome‐wide scale. Surveying for selection footprints across porcine genomes can be quite valuable for revealing the genetic mechanisms of phenotypic diversity. Here, we employed a medium sequencing depth (5–20x/site per individual, on average) approach called genotyping by genome reducing and sequencing (GGRS) to detect genome‐wide selection signatures of two domestic pig breeds (Yorkshire and Landrace) that have been under intensive selection for traits of muscle development, growth and behavior. The relative extended haplotype homozygosity test, which identifies selection signatures by measuring the characteristics of haplotypes’ frequency distribution within a single population, was also applied to identify potential positively selected regions. As a result, signatures of positive selection were found in each breed. However, most selection signatures were population specific and related to genomic regions containing genes for biological categories including brain development, metabolism, growth and olfaction. Furthermore, the result of the gene set enrichment analysis indicated that selected regions of the two breeds presented a different over‐representation of genes in the Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathways. Our results revealed a genome‐wide map of selection footprints in pigs and may help us better understand the mechanisms of selection in pig breeding.
Coxiella burnetii est l’agent pathogène responsable de la fièvre Q. Dans le cadre de cette thèse nous nous sommes intéressés à l'étude de souches de C.burnetii responsables d'événements épidémiques. ...Nous avons séquencé une souche de génotype MST33 (Z3055), proche de la souche responsable de l'épidémie de fièvre Q aux Pays-Bas, et une souche de génotype MST17 (Cb175) clone provoquant l'une des formes les plus virulentes de fièvre Q aiguë jamais décrite auparavant et retrouvée à ce jour uniquement en Guyane Française. Les résultats de ces analyses montrent que le génome de la souche Z3055 était très similaire à celui de la souche de référence Nine Mile I. Les différences observées sont liées à la présence de mutations non synonymes dans le génome de Z3055. Le pourcentage élevé de protéines membranaires mutées pourrait expliquer l’ampleur de cette épidémie en Hollande. En effet, le changement de profil antigénique pourrait être à l’origine de la formation d’un nouveau sérotype capable d'échapper à la réponse immunitaire de l'hôte et de diffuser facilement dans une population au système immunitaire naïf. Nous avons d’ailleurs montré que la souche responsable de la fièvre Q en Guyane (Cb175) présente des différences chromosomiques importantes par rapport à NMI. Ces différences se manifestent principalement par la présence d’une délétion d’une région de 6105pb contenant l’opéron hlyCABD du système de sécrétion de type 1 (T1SS). Ce résultat est cohérent avec ce qui a été observé chez les bactéries épidémiques les plus dangereuses comparées à leurs espèces non-épidémiques plus proches qui ont un génome réduit et contiennent moins de protéines du système de sécrétion.
Coxiella burnetii is a human pathogen that causes the zoonotic disease Q fever. In this work, we focused on the study of strains responsible for epidemic events. Particularly, we sequenced the clone of the strain responsible for Netherlands outbreak having genotype MST33 (Z3055), and strain having MST17 (Cb175) responsible for one of the most severe form of acute Q fever never reported in literature and uniquely described in French Guiana. Our findings showed that the Netherlands outbreak responsible strain (clone Z3055) was highly similar to the reference strain Nine Mile I. Only slight differences were observed, which were related to non-synonymous mutations in Z3055 genome. The high proportion of mutated membrane proteins could explain this large-scale outbreak. Change of antigenic profile may have led to a new serotype, conferring to the novel clone the capacity to escape the host immune response and to disseminate easily in a immunologically naïve population. On the contrary, the type strain responsible for Q fever in Guiana (Cb175) showed an important difference in its chromosome sequence compared to the reference NMI because of the deletion of a sequence of 6105bp containing the Type 1 secretion systems (T1SS) hlyCABD operon. This result appear consistent with previous findings that showed the most dangerous epidemic bacteria compared with their closest non-epidemic species are characterized by reduced genomes accompanied by significant decrease in ORF content and contain less secretion system proteins.
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