Dataset Information

Genomic regions and genes related to inter-population differences in body size in the ground beetle Carabus japonicus.

ABSTRACT: Body size is a key trait in diversification among animal species, and revealing the gene regions responsible for body size diversification among populations or related species is important in evolutionary biology. We explored the genomic regions associated with body size differences in Carabus japonicus ground beetle populations by quantitative trait locus (QTL) mapping of F2 hybrids from differently sized parents from two populations using restriction site-associated DNA sequencing and de novo assembly of the beetle whole genome. The assembled genome had a total length of 191?Mb with a scaffold N50 of 0.73?Mb; 14,929 protein-coding genes were predicted. Three QTLs on different linkage groups had major effects on the overall size, which is composed chiefly of elytral length. In addition, we found QTLs on autosomal and X chromosomal linkage groups that affected head length and width, thoracic width, and elytral width. We determined the gene loci potentially related to control of body size in scaffolds of the genome sequence, which contained the QTL regions. The genetic basis of body size variation based on a small number of major loci would promote differentiation in body size in response to selection pressures related to variations in environmental conditions and inter-specific interactions.

SUBMITTER: Komurai R

PROVIDER: S-EPMC5552851 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Genomic regions and genes related to inter-population differences in body size in the ground beetle Carabus japonicus.

Komurai Ryohei R Fujisawa Tomochika T Okuzaki Yutaka Y Sota Teiji T

Scientific reports 20170810 1

Body size is a key trait in diversification among animal species, and revealing the gene regions responsible for body size diversification among populations or related species is important in evolutionary biology. We explored the genomic regions associated with body size differences in Carabus japonicus ground beetle populations by quantitative trait locus (QTL) mapping of F<sub>2</sub> hybrids from differently sized parents from two populations using restriction site-associated DNA sequencing a ...[more]

PMID: 28798311

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Project description:Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens. In this study, 94 and 107 chickens from 4 Asian Game and 5 Asian Bantam type breeds, respectively, were genotyped using the chicken 580K single nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) and principal component analyses (PCA) were performed to identify genomic regions associated with body size related-traits such as wing length, shank length, shank thickness, keel length, and body weight. Hierarchical clustering of genotype data showed a clear genetic difference between the investigated Asian Game and Asian Bantam chicken types. GWAS identified 16 genomic regions associated with wing length (2, FDR ≤ 0.018), shank thickness (6, FDR ≤ 0.008), keel length (5, FDR ≤ 0.023), and body weight (3, FDR ≤ 0.041). PCA showed that the first principal component (PC1) separated the 2 chicken types and significantly correlated with the measured body size related-traits (P ≤ 2.24e-40). SNPs contributing significantly to PC1 were subjected to a more detailed investigation. This analysis identified 11 regions potentially associated with differences in body size related-traits. A region on chromosome 4 (GGA4) (17.3-21.3 Mb) was detected in both analyses GWAS and PCA. This region harbors 60 genes. Among them are myotubularin 1 (MTM1) and secreted frizzled-related protein 2 (SFPR2) which can be considered as potential candidate genes for body size related-traits. Our results clearly show that the investigated Asian Game type chicken breeds are genetically different from the Asian Bantam breeds. A region on GGA4 between 17.3 and 21.3 Mb was identified which contributes to the phenotypic difference, though further validation of candidate genes is necessary.

Dataset Information

Genomic regions and genes related to inter-population differences in body size in the ground beetle Carabus japonicus.

Publications

Genomic regions and genes related to inter-population differences in body size in the ground beetle Carabus japonicus.

Similar Datasets

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