Evidence map›Paper›PMID 35698044›Full record

ArticleBMC genomics2022

A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the depigmentation phenotype of non-classic Swiss markings in goats.

Jiazhong Guo, Xueliang Sun, Ayi Mao, Haifeng Liu, Siyuan Zhan, Li Li, Tao Zhong, Linjie Wang, Jiaxue Cao, George E Liu and 1 more

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

Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.8field-weighted citation impact, top 33% 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

7 citing papers in PubMed, 8 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

11 authors at 2 institutions in 2 countries.

Jiazhong Guo *College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Xueliang Sun *College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Ayi MaoCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Haifeng LiuCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Siyuan ZhanCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Li LiCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Tao ZhongCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Linjie WangCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Jiaxue CaoCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
George E LiuAnimal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA. george.liu@usda.gov.
Hongping ZhangCollege of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China. zhp@sicau.edu.cn.
Sichuan Agricultural University · CNAgricultural Research Service · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe pigmentation phenotype diversity is rich in domestic goats, and identification of the genetic loci affecting coat color in goats has long been of interest. Via the detections of selection signatures, a duplication upstream ASIP was previously reported to be a variant affecting the Swiss markings depigmentation phenotype in goats.

resultsWe conducted a genome-wide association study using whole-genome sequencing (WGS) data to identify the genetic loci and causal variants affecting the pigmentation phenotype in 65 Jintang black (JT) goats (i.e., 48 solid black vs. 17 non-classic Swiss markings). Although a single association peak harboring the ASIP gene at 52,619,845-72,176,538 bp on chromosome 13 was obtained using a linear mixed model approach, all the SNPs and indels in this region were excluded as causal variants for the pigmentation phenotype. We then found that all 17 individuals with non-classic Swiss markings carried a 13,420-bp duplication (CHI13:63,129,198-63,142,617 bp) nearly 101 kb upstream of ASIP, and this variant was strongly associated (P = 1.48 × 10

conclusionWe confirmed that a genomic region harboring the ASIP gene is a major locus affecting the coat color phenotype of Swiss markings in goats. Although the molecular genetic mechanisms remain unsolved, the 13,420-bp duplication upstream of ASIP is a necessary but not sufficient condition for this phenotype in goats. Moreover, the variations in the copy number of the duplication across different goat breeds do not lead to phenotypic heterogeneity.

Indexed as

Genome-Wide Association StudyGoatsAnimalsGenomePhenotypeASIPCoat colorCopy number variationsGenome-wide association studyGoatSwiss markingsWhole-genome sequencing

Identifiers

PMID35698044
PMCPMC9190080
OpenAlexW4282829638

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Registered trials

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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.