Open Access Highly Accessed Research article

Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate

Kouji Setoguchi1, Masako Furuta2, Takashi Hirano3, Tomoko Nagao2, Toshio Watanabe3, Yoshikazu Sugimoto3 and Akiko Takasuga3*

Author Affiliations

1 Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima 899-8212, Japan

2 Kumamoto Prefectural Agricultural Research Center, Sakae, Koushi, Kumamoto 861-1113, Japan

3 Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima 961-8061, Japan

For all author emails, please log on.

BMC Genetics 2009, 10:43  doi:10.1186/1471-2156-10-43

Published: 4 August 2009



Growth-related traits have been mapped on bovine chromosome 6 (BTA 6) in various bovine breed populations. We previously mapped a significant quantitative trait locus (QTL) for carcass and body weight (CW-2) between 38 and 55 cM on BTA 6 using a Japanese Black half-sib family. Additional QTL mapping studies detected four QTL for body or carcass weight that overlapped with CW-2 in Japanese Black and Japanese Brown half-sib families. To map the region in greater detail, we applied cross-breed comparisons of haplotypes that have been shown to be powerful in canine.


We used 38 microsatellite markers to search for a shared Q (increasing carcass and/or body weight) haplotype within the 17-cM CW-2 region among five sires. Linkage disequilibrium mapping using maternal alleles of the offspring showed that an 815-kb shared Q haplotype was associated with body or carcass weight in both breeds. The addition of 43 single nucleotide polymorphism (SNP) markers narrowed the region to 591 kb containing 4 genes. The SNP changing Ile-442 to Met in NCAPG (chromosome condensation protein G) was significantly associated with carcass weight (p < 1.2 × 10-11) in a large Japanese Black population as well as in the five families. The Q allele of the SNP was also associated with a larger longissimus muscle area and thinner subcutaneous fat thickness in steers of all five families, indicating that the CW-2 locus is pleiotropic and favorable for marker-assisted selection of beef cattle.


A 591-kb critical region for CW-2 was identified. The SNP changing Ile-442 to Met in NCAPG (chromosome condensation protein G) can be used as a positional candidate of CW-2 for marker-assisted selection.