### INTRODUCTION

*Sus scrofa domesticus*) was found 300 years ago in the Berkshire county of United Kingdom. The king of England preferred Berkshire pork for his own personal meat supply, because of excellent meat quality (American Berkshire Association, 2013). They have a dark skin, which protects them from sunburn. Some parts of body such as legs, face and tail, are white pointed. Berkshire pigs are characterized with pink skin color and a strong body type with short neck. Legs of the breed are short and blocky and feet are strong. An adult pig of the breed has an average weight of 272 kg (600 pounds). Individuals of the breed are usually friendly and curious and exhibit excellent disposition (Kawaida, 1993).

### MATERIALS AND METHODS

### Animals and phenotypes

*longissimus dorsi*, LD) on the left side of the cold carcasses were used to determine meat quality parameters. As soon as all samples were placed in vacuum bags, the samples were transported to the laboratory and then frozen at −50°C until they were analyzed. The middle portions of each loin were used for experiment. For analysis of moisture content, fat content, drip loss, and heat loss, the only subcutaneous fat of meat samples was removed. For the others, all visible fat was trimmed off.

*g*for 10 min. WHC was calculated as the remaining moisture in the meat sample on the basis of the moisture content of the original meat sample. The drip loss was measured as the percentage weight loss of a standardized (3×3×3 cm) meat sample placed in a sealed petri-dish at 4°C during the storage of 2 d. The heat (cooking) loss was determined as the percentage weight loss of a standardized (3×3×3 cm) meat sample after cooking in an electric grill with double pans (Nova EMG-533, 1,400 W, Evergreen enterprise, Seoul, Korea) for 90 s, until the internal temperature of the meat sample reached 72°C.

### Molecular data

### Statistical analysis

*y*is the vector of phenotypic record of the animal,

*b*is the vector of overall mean, fixed and covariate effects,

*g*is the vector of breeding values,

*X*is the design matrix for the fixed and covariate effects,

*Z*is the design matrix allocating records to breeding values and

*e*is the vector of the residual of the phenotype. To construct genome relationship matrix (

*G*), the subroutine in R was used (version 2.15.0), which was then incorporated into the Animal model using ASREML (average sparsity residual maximum likelihood) 3.0 (Gilmour et al., 1995). The mixed model equation was then

*α*=

*σ*

_{e}

^{2}*/σ*

_{g}*= (1–*

^{2}*h*

*)/*

^{2}*h*

*,*

^{2}*σ*

_{e}*is the residual variance,*

^{2}*σ*

_{g}*the genetic variance, and*

^{2}*h*

*heritability.*

^{2}*G*matrix was calculated based on the observed allele frequencies of the markers. The equation used to calculate

*G*matrix was:

*M*, had order of

*n*×

*m*, in which

*n*is the number of individuals and

*m*is the number of markers. In the

*M*, alleles were coded as

*AA*(homozygous for the first allele) = −1,

*AB*(heterozygous) = 0,

*BB*(homozygous for the second allele) = 1. The elements of

*P*matrix were calculated using the formula

*P*

*= 2(*

_{j}*P*

*–0.5), where*

_{j}*P*

*was the minor allele frequency of the marker locus*

_{j}*j*. (

*M*-

*P*) is called the incidence matrix (

*Z*) for markers. The

*P*matrix was subtracted from the

*M*matrix to set the mean values of the allele effects to 0, and to give more credit to rare alleles than to common alleles. Genomic inbreeding coefficient would be greater if the individual is homozygous for rare alleles than if homozygous for common alleles.

*i*

*individual was calculated using standard errors of GEBV as*

^{th}*y*= the vector of phenotypesμ = overall mean.

*X*= the incidence matrix of the fixed and covariate effects.*b*= the vector of fixed and covariate effects.*z*= a vector of genotypes of a fitted marker_{i}*i*, that is coded as −10, 0, or 10.*a*= a random substitution effect of the fitted marker_{i}*i*with its variance,*σ*_{ai}.^{2}*e*= the vector of random residuals that was assumed to be normally distributed.

*σ*

_{ai}*>0 (Habier et al., 2011).*

^{2}### RESULTS AND DISCUSSION

*Sus scrofa*chromosome (SSC) 1, while SSC18 had the smallest number of SNPs (886). The SSCs 2, 4, 6, 7, 8, 9, 13, and 14 had more than 2,000 SNPs. The physical map with all of the available SNPs spanned about 2,195 Mb with an average distance of 67.9±106.7 Kb between adjacent SNPs. However, the average distances were various between chromosomes, ranging between 51.9 Kb in SSC14 and 92.4 in SSC15.