Evidence map›Paper›PMID 30940068›Full record

ArticleBMC genomics2019

Population genomics identifies patterns of genetic diversity and selection in chicken.

Diyan Li, Yan Li, Miao Li, Tiandong Che, Shilin Tian, Binlong Chen, Xuming Zhou, Guolong Zhang, Uma Gaur, Majing Luo and 18 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.

0numbers the graph read from it
0cells of the map it votes in
36citing papers in PubMed
5.3field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

36 citing papers in PubMed, 73 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

28 authors at 6 institutions in 2 countries.

Diyan LiInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Yan LiInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Miao LiInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Tiandong CheInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Shilin TianInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Binlong ChenInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Xuming ZhouDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
Guolong ZhangDepartment of Animal Science, Oklahoma State University, Stillwater, OK, USA.
Uma GaurInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Majing LuoHubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, China.
Kai TianInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Mengnan HeInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Shen HeInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Zhongxian XuInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Long JinInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Qianzi TangInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Yifei DaiNovogene Bioinformatics Institute, Beijing, China.
Huailiang XuInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Yaodong HuInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Xiaoling ZhaoInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Huadong YinInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Yan WangInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
Rongjia ZhouHubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, China.
Chaowu YangSichuan Animal Science Academy, Chengdu, China.
Huarui DuSichuan Animal Science Academy, Chengdu, China.
Xiaosong JiangSichuan Animal Science Academy, Chengdu, China.
Qing ZhuInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China. zhuqingsicau@163.com.ORCID http://orcid.org/0000-0001-6423-8075
Mingzhou LiInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China. mingzhou.li@sicau.edu.cn.
Sichuan Agricultural University · CNSichuan Animal Science Academy · CNWuhan University · CNBrigham and Women's Hospital · USNovogene Bioinformatics Institute · CNOklahoma State University · US

Funding

the 13th Five-Year Plan for breeding programs in Sichuan - Selective breeding of new breeds and synthetic strains of broiler 2016NYZ0025 and 2016NYZ0043the China Agricultural Research System CARS-41the National Natural Science Foundation of China 31402063the National Natural Science Foundation of China 31522055the Sichuan Provincial Department of Science & Technology Program 2019JDTD0009
6 · The paper itself

Abstract

backgroundThere are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China.

resultsHere, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources.

conclusionsThe work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic traits.

Indexed as

Genetics, PopulationGenetic VariationSelection, GeneticAdaptation, PhysiologicalAnimalsBody WeightChickensGenomeHigh-Throughput Nucleotide SequencingLinkage DisequilibriumPhenotypePolymorphism, Single NucleotideSequence Analysis, DNATibetChickenGenetic diversityPopulation genomicsSelection

Identifiers

PMID30940068
PMCPMC6446315
OpenAlexW2942743882

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.