Genome-Wide Population Structure and Selection Signatures of Yunling Goat Based on RAD-seq.

Animal diseases impose a huge burden on the countries where diseases are endemic. Conventional control strategies of vaccines and veterinary drugs are to control diseases from a pharmaceutical perspective. Another alternative approach is using pre-existing genetic disease resistance or tolerance. We know that the Yunling goat is an excellent local breed from Yunnan, southwestern China, which has characteristics of strong disease resistance and remarkable adaptability. However, genetic information about the selection signatures of Yunling goats is limited. We reasoned that the genes underlying the observed difference in disease resistance might be identified by investigating selection signatures between two different goat breeds. Herein, we selected the Nubian goat as the reference group to perform the population structure and selection signature analysis by using RAD-seq technology. The results showed that two goat breeds were divided into two clusters, but there also existed gene flow. We used Fst (F-statistics) and π (pi/θπ) methods to carry out selection signature analysis. Eight selected regions and 91 candidate genes were identified, in which some genes such as DOK2, TIMM17A, MAVS, and DOCK8 related to disease and immunity and some genes such as SPEFI, CDC25B, and MIR103 were associated with reproduction. Four GO (Gene Ontology) terms (GO:0010591, GO:001601, GO:0038023, and GO:0017166) were associated with cell migration, signal transduction, and immune responses. The KEGG (Kyoto Encyclopedia of Genes and Genomes) signaling pathways were mainly associated with immune responses, inflammatory responses, and stress reactions. This study preliminarily revealed the genetic basis of strong disease resistance and adaptability of Yunling goats. It provides a theoretical basis for the subsequent genetic breeding of disease resistance of goats.

Maternal origins, population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan.

Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well-recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481-bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 ± 0.079 to 0.982 ± 0.015 and from 0.028 ± 0.003 to 0.043 ± 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.

[Spatial Distribution of Perfluoroalkyl Acids and Transformation of Their Precursors in River Water Samples and Effluents of Wastewater Treatment Plans in a Typical Tourism City].

Perfluoroalkyl acids (PFAAs) are commonly detected in various environmental media and can cause potential risks to the ecological environment and human health. The levels and spatial distribution of 15 types of PFAAs and 3 types of PFAA precursors in the main river water and effluents of three sewage treatment plants (STPs) of Rizhao City were systematically investigated based on methods such as ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), solid phase extraction and enrichment, and hydroxyl radical (·OH) oxidation to explore the pollution characteristics of PFAAs and the contribution of their precursors to environmental pollution in different water bodies of typical tourist cities. The results of this study reveal that 15 types of PFAAs and only perfluorooctane sulfoneamide (FOSA) among the precursors are detectable in most of the water samples. The total concentration of PFAAs (∑PFAAs) in the river water and sewage effluents is 3.79-45.58 ng·L-1 and 54.04-105.64 ng·L-1, respectively. The predominant PFAAs are perfluorooctanesulfonic acid (PFOS), perfluorohexanesulfonic acid (PFHxS), perfluorooctanoic acid (PFOA), and perfluorononanoic acid (PFNA). The ∑PFAAs value of the river samples is notably lower than that of sewage treatment plant (STP) effluents. An increasing tendency was observed from the upstream to the downstream of the rivers. After hydroxyl radical oxidation treatment, the PFAA concentrations of rivers and STPs increase notably. The increased concentrations of perfluorinated carboxylic acids (PFCAs) with 4-12 perfluoroalkyl carbon chains (∑△PFCAC4~C12) in the STP effluents are much higher than those in the river, which might be induced by the degradation of precursors during the sewage treatment processes. The results of this research provide basic data and technical support for environmental pollution prevention of new emerging pollutants in tourist cities.