Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology

WenHao, Wang; Zhang, Tao; Wang, Jinyu; Zhang, Genxi; Wang, Yongjuan; Zhang, Yinwen; Zhang, Jianhui; Li, Guohui; Xue, Qingwu; Han, Kai; Zhao, Xiuhua; Zheng, Hongkun

doi:10.3382/ps/pev266

Cited by 30 publications

(16 citation statements)

References 42 publications

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“…For CW, we further recognized two fibroblast growth factor-binding protein (FGFBP) genes, FGFBP1 and FGFBP2 , from QTL qCW1 that were tandemly located on LG1 and fibroblast growth factor receptor 1 ( FGFR1 ) gene from QTL qCW16 on LG16 which play important roles in embryogenesis, cellular differentiation, and proliferation. FGFBP1 and FGFBP2 genes had been reported that associated with carcass and meat quality traits in chickens 58 59 , and FGFR1 gene had been reported that correlated with fetal weight in ovine 60 . So these genes were considered that associated with CW in common carp as well.…”

Section: Resultsmentioning

confidence: 99%

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

Peng

Zhang

et al. 2016

Sci Rep

102

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High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.

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Section: Resultsmentioning

confidence: 99%

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

Peng

Zhang

et al. 2016

Sci Rep

102

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“…It is considered as a national cultivated meat breed characterized by its adaptability to poor quality feeds and environment (Zhao et al, 2012). According to previous studies, the Jinghai yellow chicken could be considered as a promising meat breed in terms of growth as many detected single nucleotide polymorphisms (SNPs) were associated with their growth and reproductive traits (Tang et al, 2014;Abdalhag et al, 2015;Zhang et al, 2015a;Wang et al, 2016). Insulin-like growth factors, IGF-I and IGF-II, are mitogenic polypeptides with a structure similar to insulin, and play an important role in the overall body and muscle growth in many species (Rotwein, 1991).…”

Section: Introductionmentioning

confidence: 99%

Association analysis of IGF-I gene expression with growth and reproductive traits in Jinghai yellow chickens

Abdalhag¹,

Li²,

Duan³

et al. 2016

Genet. Mol. Res.

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The insulin-like growth factor, IGF-I, plays an important role in the development of growth and reproductive traits. Single-strand conformation polymorphism analysis was used to detect and analyze polymorphisms and expression profiles of the IGF-I gene and its association with growth and reproductive traits of Jinghai yellow chickens. A point mutation g.295T>C was detected in the IGF-I gene with three genotypes CC, CT, and TT. The CT and TT genotypes were found to be significantly (P < 0.05) superior to the CC genotype in 8-, 10-, 12-, 14-, and 16-week-age weight of chickens (for growth traits) and in body weight at first egg-laying (for reproductive traits). Comparison of the expression level between males and females showed similarity in their expression curves, with females showing relatively higher IGF-I expression than males in all studied tissues. A similar IGF-I expression pattern was observed in the breast and leg muscles of both males and females, with the leg muscle showing relative higher IGF-I expression than the breast muscle. Our results indicate that, g.295T>C mutation in the IGF-I gene affects certain growth and reproductive traits, and it could be used to provide a theoretical basis as well as marker-assisted selection to upgrade the development of Jinghai yellow chickens in future.

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“…Additionally, four SNPs (GGaluGA225255, Gga_rs16-287013, Gga_rs14366866 and Gga_rs14366948) located near GJA1 are significantly associated with BrW and BrP. Another GWAS, using Jinghai yellow chickens, found that 15 SNPs are significantly associated with five carcass traits [57] . However, there has been no SNP identified by GWAS that is significantly associated with breast muscle weight or leg muscle weight, which are more representative of skeletal muscle development.…”

Section: Single Nucleotide Polymorphisms In the Myogenic Genes Relatementioning

confidence: 99%

The genetic regulation of skeletal muscle development: insights from chicken studies

Luo¹,

Abdalla²,

Nie³

et al. 2017

Front. Agr. Sci. Eng.

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Skeletal muscle development is a complex multi-process trait regulated by various genetic factors. The chicken embryo is an ideal model system for studying skeletal muscle development. However, only a small proportion of the genetic factors affecting skeletal muscle development have been identified in chicken. The aim of this review is to summarize recent knowledge about the genetic factors involved in the regulation of skeletal muscle development in the chicken, such as gene polymorphisms, epigenetic modification, noncoding RNAs and transcription factors, which can influence skeletal muscle development at the genome, epigenome, transcriptome and proteome levels. Research on the regulation of skeletal muscle development in chicken is not yet comprehensive and most of the candidate genes and single nucleotide polymorphisms related to chicken muscle growth remain to be verified in experimental studies. In addition, the data derived from transcriptome sequencing and genome-wide association studies still require further investigation and analysis and comprehensive studies on the regulation of chicken skeletal muscle development will continue as a major research focus.

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Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology

Cited by 30 publications

References 42 publications

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

Association analysis of IGF-I gene expression with growth and reproductive traits in Jinghai yellow chickens

The genetic regulation of skeletal muscle development: insights from chicken studies

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