Evidence map›Paper›PMID 30092770›Full record

ArticleBMC genomics2018

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs.

Mengmeng Zhang, Wei Han, Hui Tang, Guohui Li, Minjie Zhang, Ran Xu, Yijun Liu, Tao Yang, Wenting Li, Jianmin Zou and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.

0numbers the graph read from it
0cells of the map it votes in
32citing papers in PubMed
–field-weighted citation impact
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

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3 · Its place in the literature

Who cites it

32 citing papers in PubMed.

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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

11 authors.

Mengmeng ZhangDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
Wei HanNational Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125, People's Republic of China.
Hui TangCollege of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
Guohui LiNational Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125, People's Republic of China.
Minjie ZhangDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
Ran XuDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
Yijun LiuDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
Tao YangDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
Wenting LiDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China. liwenting_5959@hotmail.com.
Jianmin ZouNational Chickens Genetic Resources, Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225125, People's Republic of China. jqszjm@163.com.
Keliang WuDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China. liangkwu@cau.edu.cn.ORCID http://orcid.org/0000-0003-0336-1912

Funding

the National Basic Research Program of China 973 Program, Grant 2014CB138501the Program for Changjiang Scholars and Innovation Research Teams in the University IRT_15R62
6 · The paper itself

Abstract

backgroundMaintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs.

resultsNinety DNA samples were collected from three generations for each breed. In the most recent generation, the highest genetic diversity was observed in LSC, followed by BEC and BYC. Inbreeding coefficients based on ROH for the three breeds declined slightly between the first and middle generations, and then rapidly increased. No inbreeding coefficients exceeded 0.1. Population structure assessments using neighbor-joining tree analysis, principal components analysis, and STRUCTURE analysis indicated that no genetic differentiation existed within breeds. LD decay and ROH at different cut-off lengths were used to identify traces left by recent or ancient inbreeding. Few long ROH were identified, indicating that inbreeding has been largely avoided with the current conservation strategy. The observed losses in genetic diversity and occurrences of inbreeding might be consequences of sub-optimal effective population sizes.

conclusionsThe conserved Chinese chicken populations have high genomic diversity under the current conservation program (R: F). Furthermore, this study highlights the need to monitor dynamic changes in genetic diversity in conserved breeds over successive generations. Our research provides new insights into genetic diversity dynamics in conserved populations, and lays a solid foundation for improving conservation schemes.

Indexed as

GenomePolymorphism, Single NucleotideAnimalsChickensHomozygoteInbreedingLinkage DisequilibriumPopulation DensityPopulation DynamicsSequence Analysis, DNAChinese indigenous chickenConservation schemeGenome-wide SNPsGenomic diversity

Identifiers

PMID30092770
PMCPMC6085637

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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.