Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology

Li, Fuwei; Han, Haitang; Lei, Qiuxia; Gao, Jinbo; Liu, Jie; Liu, Wei; Zhou, Yan; Li, Huimin; Cao, Deliang

doi:10.1007/s13353-018-0452-7

Cited by 18 publications

(15 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…GWAS based on SLAF-seq were successfully used to identify SNPs associated with important economic traits in chickens and pigs [ 18 , 19 ]. In this study, we performed SLAF-seq-based GWAS of six growth, two carcass and two meat quality traits using a General Linear Mixed (GLM) Model in meat rabbits.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

A Genome-Wide Association Study Identifying Genetic Variants Associated with Growth, Carcass and Meat Quality Traits in Rabbits

Yang

Deng

et al. 2020

Animals

View full text Add to dashboard Cite

Growth, carcass characteristics and meat quality are the most important traits used in the rabbit industry. Identification of the candidate markers and genes significantly associated with these traits will be beneficial in rabbit breeding. In this study, we enrolled 465 rabbits, including 16 male Californian rabbits and 17 female Kangda5 line rabbits as the parental generation, along with their offspring (232 male and 200 female), in a genome-wide association study (GWAS) based on SLAF-seq technology. Bodyweight at 35, 42, 49, 56, 63 and 70 d was recorded for growth traits; and slaughter liveweight (84 d) and dressing out percentage were measured as carcass traits; and cooking loss and drip loss were measured as meat quality traits. A total of 5,223,720 SLAF markers were obtained by digesting the rabbit genome using RsaI + EcoRV-HF® restriction enzymes. After quality control, a subset of 317,503 annotated single-nucleotide polymorphisms (SNPs) was retained for subsequent analysis. A total of 28, 81 and 10 SNPs for growth, carcass and meat quality traits, respectively, were identified based on genome-wide significance (p < 3.16 × 10−7). Additionally, 16, 71 and 9 candidate genes were identified within 100 kb upstream or downstream of these SNPs. Further analysis is required to determine the biological roles of these candidate genes in determining rabbit growth, carcass traits and meat quality.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Compared with high-density SNP arrays and whole-genome resequencing, SLAF-seq is an efficient method for de novo SNP discovery with such advantages as high genotyping accuracy, relatively low cost and a high capacity for large sample sizes. SLAF-seq has been successfully applied in chicken [ 17 , 18 ] and pig [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

A Genome-Wide Association Study Identifying Genetic Variants Associated with Growth, Carcass and Meat Quality Traits in Rabbits

Yang

Deng

et al. 2020

Animals

View full text Add to dashboard Cite

show abstract

“…Sewalem et al used an F 2 chicken population from a cross of a broiler sire-line and an egg laying (White Leghorn) line to identify QTLs on Chr1, -2, -4, -7, -8, and -13 that affected BW, and Chr4 had the largest single additive effect (Sewalem et al 2002). Researchers identified QTLs on Chr4 that affected growth performance in different varieties and populations (Brandt et al 2017;Jin et al 2015;Li et al 2018), such as a White Leghorn × Rhode Island Red cross (Sasaki et al 2004), a Silky Fowl × White Plymouth Rock cross (Gu et al 2011), Beijing-You chickens (Liu et al 2013), and a population of purebred white layers (WLA) with White Leghorn origin (Lyu et al 2018). In this study, 17 phenotypes, including BW8, BW12, SL12, CWe and the weight of several internal organs, were mapped on Chr4, indicating that genes on Chr4 may have large effects on BW.…”

Section: Figmentioning

confidence: 99%

Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Zhang

Wang

et al. 2020

Heredity

View full text Add to dashboard Cite

Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

show abstract

“…Pooled samples were separated by electrophoresis using a 2 % agarose gel; 300-500-bp fragments (including indices and adaptors) were excised and purified using the QIAquick Gel Extraction Kit (Qiagen). Gel-purified products were sequenced on the Illumina HiSeq 2500 system (Illumina, Inc., San Diego, CA, USA) per the manufacturer’s directions [ 31 ]. Reads with a single-base sequencing error rate over 1/100 were discarded.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks

Yang

Huang

et al. 2021

BMC Genomics

View full text Add to dashboard Cite

Background Birds have various plumage color patterns, and spot is a common phenotype. Herein, we conducted genome-wide association studies (GWAS) in a population of 225 ducks with different sized black spots to reveal the genetic basis of this phenomenon. Results First, we quantified the black spot phenotype within the duck population. The results showed that the uncolored area of the body surface first appeared on the ventral side. With increasing duck age, the area of the black spots was highly conserved across the whole body surface. The GWAS results identified a 198 kb (Chr4: 10,149,651 bp to 10,348,068 bp) genetic region that was significantly associated with the black spot phenotype. The conditional GWAS and linkage disequilibrium (LD) analysis further narrowed the ultimate candidate region to 167 kb (Chr4: 10,180,939 bp to 10,348,068 bp). A key gene regulating melanoblast migration and differentiation, EDNRB2 (Endothelin B receptor-like), was found in the candidate region and having significant mRNA expression level changes in embryonic duck skin tissue with different spot sizes. The significant SNPs (single nucleotide polymorphisms) associated with the EDNRB2 gene were annotated, and two mutations (Chr4: 10,180,939 T > C and Chr4: 10,190,671 A > T) were found to result in the loss of binding sites for two trans-factors, XBP1 and cMYB. The phenotypic effect of these two mutations suggested that they can regulate the size of black spots in a dose-dependent manner, and Chr4: 10,180,939 T > C was the major allele locus. Conclusions Our results revealed that EDNRB2 was the gene responsible for the variation in duck body surface spot size. Chr4: 10,180,939 T > C was the major allele that explained 49.5 % (dorsal side) and 32.9 % (ventral side) of the variation in duck body surface spot size, while 32.1 % (dorsal side) and 19.1 % (ventral side) of the variation could be explained by Chr4: 10,190,671 A > T. The trans-factor prediction also suggested that XBP1 and cMYB have the potential to interact with EDNRB2, providing new insights into the mechanism of action of these genes.

show abstract

Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology

Cited by 18 publications

References 39 publications

A Genome-Wide Association Study Identifying Genetic Variants Associated with Growth, Carcass and Meat Quality Traits in Rabbits

A Genome-Wide Association Study Identifying Genetic Variants Associated with Growth, Carcass and Meat Quality Traits in Rabbits

Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in ducks

Contact Info

Product

Resources

About