Evidence map›Paper›PMID 41023779›Full record

ArticleBMC genomics2025

Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats.

Jiazhong Guo, Qingsi Huang, Qiunan Xiang, Guo Wu, Peipei Bian, Xihong Wang, Li Li, George E Liu, Hongping Zhang

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Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed
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1 · What the graph read from it

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3 · Its place in the literature

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1 citing paper in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

9 authors.

Jiazhong Guo *Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Qingsi Huang *Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Qiunan XiangFarm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Guo WuFarm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Peipei BianCollege of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
Xihong WangCollege of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
Li LiFarm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, College 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.
Hongping ZhangFarm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China. zhp@sicau.edu.cn.

Funding

Science &Technology Department of Sichuan Province, China 2023NSFSC0232the USDA National Institute of Food and Agriculture 2019-67015-29321
6 · The paper itself

Abstract

backgroundCoat color is one of the most easily recognizable appearance traits used to discriminate livestock breeds and individuals. This study investigated the genetic loci and candidate genes affecting pigmented spots in Tianfu (TF) goats.

resultsThe pigmented spot scores in 96 TF goats ranged from 0.20 to 3.95. Whole-genome sequencing identified 15,132,291 bi-allelic autosomal SNPs in these animals. Linear mixed-model analyses identified a major locus near the EDNRA gene on chromosome 17 and a second strong association signal on chromosome 4. Annotation of short variants within the major locus revealed no apparent causal mutations. Further analysis of short-read data revealed a complex genomic rearrangement spanning ~ 1.1 Mb in TF goats, primarily comprising one inverted duplication, one direct duplication, and two deletion events. These structural variations (SVs) were validated using PacBio HiFi sequencing data from Boer goats, one of the parental breeds of TF goats. Among the SVs, an 83,630-bp inverted duplication approximately 80 kb upstream of EDNRA showed the strongest association with the phenotype, as demonstrated by a univariate model in which this duplication explained 30.99% of the phenotypic variation. In silico analysis revealed that this duplication contains putative binding sites for pigmentation-related transcription factors, including MITF and PAX3. Furthermore, this inverted duplication, combined with the lead SNP on chromosome 4, accounted for 55.79% of the phenotypic variation.

conclusionWe identified a genomic region with complex SVs near EDNRA on chromosome 17 as a major locus influencing pigmented spot sizes in TF goats. We further pinpointed the causal mutations to an approximately 80-kb inverted duplication. Additionally, we detected a strong secondary association signal on chromosome 4. Our findings deepen the understanding of genetic variations underlying pigmentation in goats and provide valuable insights for selective breeding and conservation efforts.

Indexed as

Genomic Structural VariationGoatsPigmentationWhole Genome SequencingAnimalsPhenotypePolymorphism, Single NucleotideComplex structural variationsEDNRAGenome-wide association studyPigmented spot sizesTianfu goats

Identifiers

PMID41023779
PMCPMC12482473

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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.