Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

Guo, Xing; Fang, Qi; Ma, Chendong; Zhou, B.; Wan, Yi; Jiang, Runshen

doi:10.1186/s12711-016-0239-4

Cited by 45 publications

(47 citation statements)

References 43 publications

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“…In addition, important mutations within these genes were also identified to enrich the pool of markers that can be used to further refine selection in these pigs in the future. Our research methods and findings should also be helpful in deciphering genomic footprints left by selection and domestication in other livestocks474849.…”

Section: Discussionmentioning

confidence: 99%

Genomic analysis reveals selection in Chinese native black pig

Tang

et al. 2016

Sci Rep

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Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production.

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Section: Discussionmentioning

confidence: 99%

Genomic analysis reveals selection in Chinese native black pig

Tang

et al. 2016

Sci Rep

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“…comparing FST values between distinct populations (Vitalis et al, 2001;Guo et al, 2016;Lillie et al, 2018).…”

Section: Genomic Regions With High Levels Of Genetic Differentiation mentioning

confidence: 99%

“…Among these studies, research subjects include chicken (Elferink et al, 2012;Guo et al, 2016;Zhang et al, 2017;Lillie et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Identifying Signatures of Selection Related to Comb Development

Liu

Zhang

et al. 2021

J. Poult. Sci.

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The aim of this study was to identify genes involved in comb development to provide insights into the molecular mechanism of chickens' comb formation. Fixation index (FST) and average number of base differences (π) of males with large and small combs were calculated based on whole-genome resequencing data. Chromosome regions with larger FST values and smaller π were considered candidate selection regions. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, FST and π were calculated using a 40 Kb sliding window strategy and eight regions were identified. Quantitative trait loci (QTL; FOX1 gene) related to comb length were found on chromosome 1. QTL (GLP1R, BTBD9, MIR6633, and MDGA1 genes) related to comb weight were found on chromosome 3. QTL (ALDH1A1, TMC1, and ANXA1 genes) associated with comb area were found on the Z chromosome. Nineteen genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and GO analysis. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC, and Wnt signaling pathways were related to immunity. MDGA1, BTBD9, MTSS1, SrGAPs, and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1α, and ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl, and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.

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“…Although smallholder production is outside the ambit of industrial production, it is practised by most rural households in China and developing countries and constitutes the majority of poultry and swine production. The farmers also raise other animals, and some households reported they sold Xishuangbanna fighting chickens, a chicken breed that has been subjected to strong (Guo et al 2016), as priced birds sell for between RMB 50 (US$7) and RMB 10,000 (US$1453), and collect geckos for an ingredient in alcoholic beverages believed to have medicinal qualities in folk medicine.…”

Section: Location and Participantsmentioning

confidence: 99%

Limited awareness of animal influenza prevention and control among Dai Lue smallholder farmers in Southwest China

Zhao

Davey

2017

Trop Anim Health Prod

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Awareness of animal influenza and its prevention and control is important for ensuring livestock health, production and welfare. In China, a country stereotyped as a major source of emerging zoonotic infectious diseases, research on the public understanding of animal influenza is limited to the Han, the main ethnic group. The present qualitative study in Southwest China investigated awareness of animal influenza among the Dai, an ethnic minority. The participants (15 men and 10 women, ages 18-83) were smallholder farmers of pigs and poultry in rural areas of Jinghong, Xishuangbanna, Yunnan Province. A mixture of interviews and group discussions took place in homes and villages. The participants were asked about their knowledge of avian influenza (H7N9), swine influenza (H1N1), precautions taken to protect against influenza, procedures when animals were sick and perceived risk of animal influenza. The data were analysed following coding and thematic analysis. The findings demonstrated a limited understanding of animal health and welfare among participants. Specifically, they were largely unaware of animal influenza (H7N9, H1N1) including its causes, symptoms, prevention and treatment. The farmers were also uninformed of the risks they faced and unknowingly engaged in behaviours which increased direct or indirect exposure to infected animals, a risk factor for human infection. They also reported poor usage of veterinary services. In order to guarantee the health, welfare and production of their livestock, immediate action is needed to enable Dai smallholder farmers to prevent and respond to animal influenza effectively and timely.

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Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection

Cited by 45 publications

References 43 publications

Genomic analysis reveals selection in Chinese native black pig

Genomic analysis reveals selection in Chinese native black pig

Identifying Signatures of Selection Related to Comb Development

Limited awareness of animal influenza prevention and control among Dai Lue smallholder farmers in Southwest China

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