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QTL analysis for early growth in an intercross between native Japanese Nagoya and White Plymouth Rock chicken breeds using RAD sequencing‐based SNP markers
Author(s) -
Essa B. H.,
Suzuki S.,
Nagano A. J.,
Elkholya S. Z.,
Ishikawa A.
Publication year - 2021
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.13039
Subject(s) - quantitative trait locus , biology , genetics , breed , epistasis , allele , population , locus (genetics) , snp , single nucleotide polymorphism , gene , genotype , demography , sociology
Summary An F 2 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 F 2 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 F 2 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.