Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Lyu, Guangqi; Feng, Chunyu; Zhu, Shiyu; Ren, Shuang; Dang, Wanyi; Irwin, David M.; Wang, Zhe

doi:10.3389/fgene.2021.671686

Cited by 4 publications

(2 citation statements)

References 28 publications

(30 reference statements)

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“…The Mame Shiba Inu dogs were recently derived from the Shiba Inu dog breed and were recognized as a breed by the Kennel Club of Japan as well as a unique breed in both Japan and China [ 32 ]. It appears that the Shiba Inu dogs were bred, independently of other world-wide dog breeds, from the wolf in about 1000 BC [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice

Dang,

Gao,

Lyu

et al. 2024

Genes

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Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N+/+) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N+/−) and wild-type (S279N−/−) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.

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Section: Discussionmentioning

confidence: 99%

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice

Dang,

Gao,

Lyu

et al. 2024

Genes

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“…The cross-population composite likelihood ratio (XP-CLR) method is mainly based on the gene Site Frequency Spectrum (SFS) principle, which is based on the difference in multilocus allele frequency between two populations and is used in selection signal detection ( Maria Ines Fariello 2013 ; Chen et al 2010 ). These methods have been widely used to discover the loci and genes related to difference in traits, such as hair length in Tianzhu white yaks ( Bao et al, 2022 ), body size in dogs ( Lyu et al, 2021 ) and ponies ( Asadollahpour et al, 2020 ), and meat quality in Angus cattle ( Taye et al, 2018 ). We used XP-CLR (v1.1.2) ( Chen et al, 2010 ) statistical methods to detect genetic differentiation in Baicheng You chicken plumage colors ( Pavlidis et al, 2013 ).…”

Section: Methodsmentioning

confidence: 99%

Candidate pigmentation genes related to feather color variation in an indigenous chicken breed revealed by whole genome data

Wang

Wen

et al. 2022

Front. Genet.

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Chicken plumage color is an inheritable phenotype that was naturally and artificially selected for during domestication. The Baicheng You chicken is an indigenous Chinese chicken breed presenting three main feather colors, lavender, black, and yellow plumages. To explore the genetic mechanisms underlying the pigmentation in Baicheng You chickens, we re-sequenced the whole genome of Baicheng You chicken with the three plumage colors. By analyzing the divergent regions of the genome among the chickens with different feather colors, we identified some candidate genomic regions associated with the feather colors in Baicheng You chickens. We found that EGR1, MLPH, RAB17, SOX5, and GRM5 genes were the potential genes for black, lavender, and yellow feathers. MLPH, GRM5, and SOX5 genes have been found to be related to plumage colors in birds. Our results showed that EGR1 is a most plausible candidate gene for black plumage, RAB17, MLPH, and SOX5 for lavender plumage, and GRM5 for yellow plumage in Baicheng You chicken.

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PoolParty2: An integrated pipeline for analysing pooled or indexed low‐coverage whole‐genome sequencing data to discover the genetic basis of diversity

Willis,

Micheletti,

Andrews

et al. 2023

Molecular Ecology Resources

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Whole‐genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub‐sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low‐coverage whole‐genome sequencing of pooled or indexed‐individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non‐model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline called PoolParty2 that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite, angsd, and illustrate the compatibility and complementarity of these suites using angsd to generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided by PoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low‐coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility of PoolParty2 for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such as angsd.

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Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Cited by 4 publications

References 28 publications

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice

Candidate pigmentation genes related to feather color variation in an indigenous chicken breed revealed by whole genome data

PoolParty2: An integrated pipeline for analysing pooled or indexed low‐coverage whole‐genome sequencing data to discover the genetic basis of diversity

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