QTL analysis for early growth in an intercross between native Japanese Nagoya and White Plymouth Rock chicken breeds using RAD sequencing‐based SNP markers

Abstract

Summary An F2 population of 239 chickens was obtained by an intercross between Nagoya (NAG), a native Japanese breed with low growth, and White Plymouth Rock (WPR), a Western breed with high growth. Using SNP markers obtained by restriction site‐associated DNA sequencing, genome‐wide QTL analysis was performed and it revealed three QTL for early postnatal growth in the F2 population at genome‐wide 5% significance levels. The most highly significant QTL affecting body weights at 2–4 weeks of age and weight gains at 2–3 and 0–4 weeks was located on GGA4 between 34.0 and 65.6 Mb with LOD scores of 3.9–5.9 and it explained 4.9–9.9% of the total variance of the traits. The analysis provided evidence for significant QTL on GGA2 between 105.6 and 125.2 Mb (LOD = 4.6) and on GGA1 between 51.1 and 61.6 Mb (LOD = 4.0) which had effects on body weight at 3 weeks and body weight gain at 0–1 week respectively. These two genomic regions explained 6.6 and 6.9% of the phenotypic F2 variance of the corresponding traits respectively. The allele derived from WPR at all QTL increased the corresponding traits. Neither sex‐specific nor epistatic QTL was detected. The results showed that the GGA4 QTL affecting multiple traits is a key locus responsible for early growth in our chicken cross, suggesting that this QTL may make a great contribution to genetic improvement of growth performance of the NAG breed with a low growth rate.

Mapping QTLs for Breast Muscle Weight in an F2 Intercross between Native Japanese Nagoya and White Plymouth Rock Chicken Breeds

“…A linkage map of 313 SNP markers obtained by RAD-seq analysis was previously constructed using the Kosambi map function [ 16 ]. Briefly, the SNP markers were distributed in 27 linkage groups on 21 autosomes.…”

“…Before QTL analysis, the effects of five environmental factors (dams, sexes, rearing persons, dissection persons and hatching dates) on phenotypic traits were tested using a linear model of the JMP Pro software version 15.2.1 (SAS Institute Japan Ltd., Tokyo, Japan), as previously described [ 16 ]. After the environmental effects that were significant at nominal 5% levels were removed from the raw trait data, the residuals were tested for significant deviation from normality by the Shapiro-Wilk test of JMP Pro.…”

“…NAG and WPR are reported to be genetically distinct in breed origins [ 15 ], which can provide many informative markers between the two breeds to map quantitative trait loci (QTLs) affecting the trait differences. We previously succeeded to identify three QTLs for body weights and body weight gains at 1–4 weeks of age on chromosomes 1, 2 and 4 in an F 2 population of 239 chickens between the two breeds using 313 SNP markers obtained by restriction site-associated DNA sequencing (RAD-seq) analysis [ 16 ].…”

“…In the present study, using the same F 2 population as that of our previous study [ 16 ], we performed genome-wide QTL analysis to identify chromosomal positions associated with breast muscle weight, fat weight and serum and liver levels of biochemical parameters. To the best of our knowledge, no QTL study on those traits has so far been performed using the NAG breed.…”

“…The following are available online at , Figure S1: The linkage map of 313 SNP markers constructed by our previous study [ 16 ], Figure S2: Genome-wide LOD score plots obtained by single-QTL genome scans for three breast muscle weights, Figure S3: Genome-wide LOD score plots obtained by single-QTL genome scans for percentages of three breast muscle weights to body weight at 4 weeks of age, Figure S4: Genotype effect plots of the SNP101 marker nearest to the QTL for the percentage of the pectoralis minor weight to body weight at 4 weeks of age, Figure S5: Genome-wide LOD score plots obtained by single-QTL genome scans for fat weights, Figure S6: Genome-wide LOD score plots obtained by single-QTL genome scans for percentages of fat weights to body weight at 4 weeks of age, Figure S7: Genome-wide LOD score plots obtained by single-QTL genome scans for serum and liver levels of biochemical parameters, Table S1: Genome-wide significance threshold levels used for single-QTL genome scans.…”