Genome‐wide association study of body size traits in Wenshang Barred chickens based on the specific‐locus amplified fragment sequencing technology

Abstract

Chicken body size (BS) is an economically important trait, which has been assessed in many studies for genetic selection. However, previous reports detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) of purebred Wenshang Barred chickens. A total of 250 one-day-old male chickens were assessed in this study. Body size in individual birds was measured at 56 days. SLAF-seq was used to genotype and GWAS analysis was carried out using the general linear model (GLM) of the TASSEL program. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, of which 175,211 were tested as candidate SNPs for genome-wide association analysis using the TASSEL general linear model. Three SNPs markers reached genome-

Fourth Report on Chicken Genes and Chromosomes 2022

“…Other low-cost methods such as reduced representation sequencing based on restriction enzyme cleavage have also been attempted for SNP discovery, validation, and characterization in chicken populations. Among them, restriction-site-associated DNA sequencing (RAD-seq) [Zhai et al, 2015;Yang Z et al, 2020], specific locus amplified fragment sequencing (SLAF-seq) [Jin et al, 2015;Wang W et al, 2016Wang W et al, , 2019Li F et al, 2018Li F et al, , 2021, genotyping by genome reducing and sequencing (GGRS) [Liao et al, 2015[Liao et al, , 2016Zhao QB et al, 2018], and genotyping by sequencing (GBS) [Pértille et al, 2016;Zhang M et al, 2018;Habimana et al, 2021] proved to be effective in identifying and genotyping some novel SNPs in chickens. However, these methods have not yet been widely applied.…”

Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population

“…In this study, we used SLAF-seq technology to obtain 227,921 highly consistent SNPs. Previous studies have proven the advantage of the SLAF-seq method in the GWAS, genetic diversities analysis, and construction of genetic map for animals and plants ( Qi et al, 2014 ; Li et al, 2017 ; Qin et al, 2020 ; Yang et al, 2020 ; Li et al, 2021 ; Mandozai et al, 2021 ). SLAF-seq technology can obtain more genomic variation sites than SNP chips, detect novel mutation sites and provide high SNP coverage at a low cost.…”

“…SLAF-seq technology has the following four significant advantages: the generation of millions of high-density SNP loci covering the whole genome, the ability to detect new SNP loci in unknown mutations, its applicability to any species whether there is a reference genome or not, and the use of representative libraries to reduce sequencing costs. As a consequence, SLAF-seq-based GWAS was successfully applied to detect SNP loci for important quantitative traits in rabbits ( Yang et al, 2020 ), chickens ( Wang et al, 2015 ; Wang et al, 2019 ; Li et al, 2021 ), ducks ( Xi et al, 2021 ), and geese ( Melak et al, 2021 ). SLAF-seq has also been successfully used for genotyping of pigs and detected abundant novel mutation sites ( Li et al, 2017 ; Qin et al, 2020 ).…”

Genome-wide association study identifying genetic variants associated with carcass backfat thickness, lean percentage and fat percentage in a four-way crossbred pig population using SLAF-seq technology

“…The number of chosen fragments can be used for individualized research purposes, so as to maintain the balance between tag density and population size [24]. GWAS based on SLAF-seq was successfully used to identify SNPs associated with important economic traits in chickens, ducks, geese, and rabbits [25][26][27][28][29][30]. Additionally, genotyping and genetic structure analysis were also successfully applied in pigs using the SLAF-seq genotyping method [31,32].…”