Genomic Pig Breeding for Growth and Meat Quality

Ming-Che Wu1, Yu-Chia Huang1 and Hsiu-Luan Chang2
1Livestock Research Institute, Council of Agriculture
2Department of Animal Science,
National Ping Tung University of Science and Technology
Taiwan ROC, 2005-12-01

Key words: Genetic marker, genomic resources, hog production, DNA test

Introduction

Pigs are often fed in confinement on small land holdings with small exercise yards, next to the owner's household. After World War II, Taiwan's successful small-scale farm development played various critical roles and laid the foundation for an economic miracle. Feed mills began producing formulated livestock feeds using mostly imported ingredients on a large scale at the end of the 1960s. Large swine farms, with thousands of sows, used modern feed, formulated on farms with modern management and housing systems. During 1986 and 1996, Taiwan became a major exporter of pork to Japan. The main island of Taiwan is mountainous and afforested, with fertile, cultivated, well-watered and heavily populated lowlands to the west of the central mountain range with a total land area of 36,179 km2. The human population is 23.1 million. The climate is subtropical, with hot humid summers, mild winters, and heavy rainfall. There is a continuous growing season for crops, hence, agriculture continues to prosper, in spite of typhoons, violent summer thunderstorms, and flooding, as well as prolonged winter droughts. About a quarter of the land is arable. Five percent of the land is meadow and pasture.

Due to high land prices and rising environmental awareness, most local farmers operate on a small scale in rural areas of central and southern Taiwan. Coupled with import-dependent feeds and expensive laborers, the local livestock industry operates at a rather high production cost. Fortunately, local livestock farmers are highly diligent, and have advanced feeding and breeding skills. There are 12 breeds of pig for genomic resources of hog production in Taiwan (Fig. 1). In 2003, the number of pig farms totaled 13,154, raising a total of 6,778,799 pigs or 515 pigs per farm and accounting for 16.06% of the total agricultural production value.

Molecular genomic analysis has revolutionized how geneticists and breeders evaluate the production differences that exist among domesticated animals. In this case the DNA tested gene is known as a marker, because it marks a section of chromosome affecting the performance. The gene whose presence it detects is known as a quantitative trait loci (QTL), with linkage between the marker and the QTL. The pig industry is actively using some genome information to improve swine production by marker-assisted selection. Over the past decade, tremendous progress has been made in mapping and characterizing the swine genome. Currently, moderate to high-resolution genetic linkage maps containing highly polymorphic loci have been produced using independent mapping populations. To date, >5,000 mapped loci are cataloged for the pig genome (http://www.thearkdb.org). Large scale sequencing of expressed sequences (ESTs) in conjunction with genomic sequencing has permitted the identification of single nucleotide polymorphisms (SNPs) that can be used to finely map economic traits, such as meat quality, growth rate and feed efficiency. Thus, the tools and information have been developed to permit application of genomics in improving the health and performance of pigs. Clearly, low cost diagnostics based on this information will be the next wave of development for livestock and poultry farming.

Growth Performance Test

The exotic Duroc, Landrace, and Yorkshire are the most popular breeds for three-way cross hog production in Taiwan. Young Duroc, Yorkshire and Landrace boars with registered parent(s) were performance tested at the Taiwan Livestock Research Institute, COA starting from the first test group of September 1989. There were 75 contemporary groups that finished the growth performance tests at the station by August 2004. There were 7,296 boars in attendance, with 89.8% completing the tests. The starting weight was set around 30 kg during 1989 to 1995, and was then increased to 40 kg in accordance with the national hog cholera free project requirements. The end weight was set at 110 kg during all test periods. The average daily gain, feed efficiency and back fat thickness of boars in 1989 ranged 0.837-0.873 kg, 2.47-2.57 and 1.65-1.97 cm, respectively. The above three traits were recorded and evaluated as a contemporary group deviation form for selection index calculation purposes. Selection index of boars at growth performance test station was set at SI=100 + 60 (ADG-MADG) _ 40 (FE-MFE) _ 45 (BF-MBF) in 1981 for improvement of lean production and had been used in Duroc breed from 1981 to 2004 and for Landrace and Yorkshire from 1981 to 1990. In consideration of reproductive performance after growth, selection index for Landrace and Yorkshire boars was reset to SI=100 + 130 (ADG-MADG) _ 40 (FE-MFE) _ 40 (BF-MBF) and was used from 1990 to 2004. Feed efficiency is the key factor for production cost, hence, selection index of 2005 version for Duroc was reset to SI=100 + 120 (ADG-MADG) _ 55 (FE-MFE) _ 50 (BF-MBF), and for Landrace and Yorkshire is SI=100 + 140 (ADG-MADG) _ 60 (FE-MFE) _ 30 (BF-MBF).

The minimum ages of the tested boars at 110 kg body weight were 120, 126 and 123 days of age in Landrace (200101 tested group), Yorkshire (200103 tested group) and Duroc (200101 tested group), respectively. The highest feed efficiency in terms of feed conversion ratios (Feed/Gain) from 40 to 110 kg body weight were 1.73, 1.95 and 1.90 in Landrace (200307 tested group), Yorkshire (200007 tested group) and Duroc (200311 tested group), respectively. Duroc, Landrace and Yorkshire boars born in 2004 had average daily gain of 1.056, 1.128 and 1.065 kg per day from 40 to 110 kg of body weight, respectively (Table 1). Feed efficiency in the ratio of feed uptake to weight gain from 40 to 110 kg was 2.038, 2.037 and 2.055 in Duroc, Landrace and Yorkshire boars. At 110 kg of body weight, Duroc, Landrace and Yorkshire boars had 1.216, 1.227 and 1.271 cm of back fat thickness. From 1989 to present, average daily gain, feed efficiency and back fat thickness of boars has been improved to 1.002-1.104kg, 1.99-2.07 and 1.17-1.27cm, respectively. All original data and evaluated results were stored in an internet-based database. The performance tested data and related information can be easily accessed from the web site (http://www.angrin.tlri.gov.tw).

Pig Genomics and Industry Applications

Present and future genetic improvements for the economically important traits in pigs will result from the more detailed genetic maps and our growing understanding of the function and structure of the individual genes. In pig, the DNA is distributed over 19 pairs of chromosomes and organized into some 100,000 functional genes (Visscher and Haley 1998). It has been known for 10 years that pale soft and exudative (PSE) pork and PSS (Porcine Stress Syndrome) pigs are associated with variation in the Halothane gene (RYR1 or CRC1) on chromosome 6. The halothane RYR1 appears to be functional gene or QTL responsible for all the effects on lean growth and stress susceptibility. The estrogen receptor ESR on chromosome 1 is associated with litter size (Rothschild et al. 1996). H-FABP (Heart fatty acid binding protein) gene on chromosome 6 was discovered to affect intramuscular fat in Duroc pig (Gerbens et al. 1998).

The economically important traits such as PSS genotype, lineage information such as registration information, and tested parental performance can be accessed recursively through the web of http://www.angrin.tlri.gov.tw/. Removal of the Halothane stress gene from breeding lines using the halothane test in 1988 and the MS-PCR DNA marker test in 1996 reduced mortalities of hogs and improved meat quality in fresh pork. In 1996, halothane gene free boars reached 74.2%, 90.0%, and 60.2% in Landrace, Yorkshire, and Duroc breed, respectively. To date, almost 100% of Landrace and Yorkshire sows in nucleus herds are PSS-gene free, but over 55% free in Duroc sows (Table 2).

Currently, methods for pig breeding in Taiwan are the combination of methods between index selection and genetic marker assisted selection. PSS, ESR, and H-FABP genetic markers have been applied at the growth performance test station for boars. For boars born after 2003, the frequency of ESR B allele (desirable allele) in 282 Duroc, 190 Landrace and 48 Yorkshire boars were 0.9, 6.1 and 50.0%, respectively. There were 5.74, 21.34 and 74.36% of Duroc, Landrace and Yorkshire boars from pig breed farms which had more piglets with the ESR B allele in 2004 (Table 3). Rothschild et al. (1996) estimated that the B allelic effect varied from 1.15 piglet per litter in Meishan pig to 0.42 piglets per litter in Yorkshire. Therefore, the relevance of results found in LY crosses involving the Landrace and Yorkshire breeds will have to be evaluated in commercial lines. There has been an increase in the rate of genetic response by incorporating the ESR genotype in selection indices for sow lines in nucleus herds. Furthermore, the increase in average litter size is observed in crossbred products derived from these lines. Litter performances of Duroc, Landrace, and Yorkshire sows in lineage populations with registration certificate are presented in Table 4. Number of piglets born alive in Landrace and Duroc sows significantly increased in 1999. Such results might be due to the application of Hal-1843 nucleotide mutation test to free PSS of each registered sow.

Meat Quality

Genetic makeup of pigs can have a significant influence on meat quality. Two of the main genes that can affect ultimate meat quality, are the halothane (stress) gene and the Napole (RN-) gene. Fresh meat color has a subtle but important impact on consumer purchase decisions. Most consumers prefer a bright reddish-pink color in fresh pork. Intramuscular fat or marbling has been related to meat eating quality which is defined as flavor, juiciness and/or tenderness of meat. Pork with a higher amount of intramuscular fat would be expected to produce meat with more desirable and less variable eating quality than the meat with less intramuscular fat. However, some consumers prefer pork containing little or no marbling, in order to avoid the associated calories.

H-FABP gene with three nucleotide mutations (defined as H, a, and d alleles) maps to chromosome 6 and wa found to be associated with variation in intramuscular fat in the Duroc breed (Gerbens et al. 1998) and not to the QTL regions on chromosomes 4 and 7 identified by De Koning et al. (1998). Three desirable alleles of H, a, and d in H-FABP gene were detected by genotyping and produced possible 27 combinations of their genotypes in Table 5. According to the amount of desirable alleles, we redefined various combinations into seven groups HH6 (Hhaadd, with 6 desirable alleles in total), HL5, HL4, HL3, LL2, LL1 and LL0 (hhAADD, with zero desirable allele). Frequency of HH6 in the Duroc registered boars born after 2003 in the performance test station was 61.7% (174/282), but zero percentage in Landrace and Yorkshire breeds (Table 6). More than half of Duroc boars (57.36%) or gilts (54.56%) sampled at five month of age had HH6 from pig breeding farms in 2004 (Table 7), but less than 2% of Landrace pigs had and zero in Yorkshire pig. Most of H-FABP genotype codes were HL4 (62.1%) in Landrace and LL1 (35.4%) in Yorkshire boars. Breeding for heart fatty acid binding protein gene for improvement of pork quality by using haplotype of H-a-d loci would be beneficial to breeding farms and hog producers (Fig. 2).

The pig industry will continue to compete based on low cost per kilo of lean meat. Today, the pig industry does not realize some 20-30% of genetic potential in small-scale farms due to poor herd health, poor husbandry, and incomplete application of nutritional needs of the modern improved genotype. Future developments in genomics research and quantitative genetics will likely accelerate the discovery process of additional genes and their use of gene sequencing in marker assisted selection for economic traits of food animal. The breeding companies will be integrators of a range of advanced technologies, providing a package of genetic services to the food chain.

Exportation of Pig Stocks

Taiwan pigs preserved a high percentage of exotic blood through a long-term agriculture trade relationship. New stocks of pigs have been imported to Taiwan from the USA and Canada since 1980. However, animals in Taiwan with the imported blood had survived after decades of tropical hot weather culling, which might have special genes for hot and high humidity weather adjustment. Lines of these excellent farm animals have high economic value in terms of production performance (Fig. 3). Taiwan was the No. 21 country in pig production in the 2003 world listings, and Canada was No. 12. Pig stocks of Taiwan, with USA/Canadian blood, have 2.19 of feed efficiency (Feed/Gain ratio) as compared to 2.67 for USA/Canadian pigs. Exchange of genes between two populations have developed an excellent pig breed which can be exported to other hot weather countries in Brazil (No. 3 in pig production) and Mexico (No. 9 in pig production) of South America, Spain (No. 5 in pig production) of Europe, or Vietnam (No. 6 in pig production), India (No. 8 in pig production) and Philippines (No. 14 in pig production) of Asia. Therefore, elite breeding stocks of Duroc, Landrace and Yorkshire pig raised in Taiwan with exotic blood origin based upon their genomic would be the excellent genetic resources for hog production in other areas.

References

• De Koning, D.J., L.L.J. Janss, J.A.M. Van Arendonk, P.A.M. Van Oers and M.A.M. Groenen. 1998. Mapping major genes affecting meat quality in meishan cross breeds using standard linkage software. Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, Armidale, Australia, January 11-16, 1998, Volume 26, p. 410.
• Gerbens, F., F. L. Harders, M. A. M. Groenen, J. H. Veerkamp and M. F. W. Te Pas. 1998. A dimorphic microsatellite in the porcine H-FABP gene at chromosome 6. Animal Genetics 29:408.
• Gerbens, F., G. Rettenberger, J. A. Lenstra, J. H. Veerkamp and M. F. W. Te Pas. 1997. Characterization, chromosomal localization, and genetic variation of the porcine heart fatty acid-binding protein gene. Mammalian Genome 8:328-332.
• Rothschild, M. F., C. Jacobson, D. A. Vaske, C. K. Tuggle, L. Wang, T. Short, G. Erchardt, S. Sasaki, A. Vincent, D. G. McLaren, O. Southwood, H. van der Steen, A. Mileham and G. Plastow. 1996. The Estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proceedings of the National Academy of Sciences of the United States of America. 93:201-205.
• Visscher, P. M. and C. S. Haley. 1998. Strategies for marker-assisted selection in pig breeding programmes. Proceedings of 6th World Congress on Genetics Applied to Livestock Production. Armidale, Australia, 23:503-510.

Index of Images

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  Figure 1 Breed Resources for the Hog Industry in Taiwan.

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  Figure 2 Breeding on Heart Fatty Acid Binding Protein Gene for Improvement of Pork Quality.

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  Figure 3 Taiwan Elite Boar and Meat Quality.

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  Table 1 Growth Performance of Halothane Gene Free Boars of Duroc, Landrace and

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  Table 2 Genotype Frequency of Hal-1843 Stress Gene in Duroc, Landrace and Yorkshire Boars Born in 2004 from Pig Breeding Farms

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  Table 3 Genotype Frequency of Estrogen Receptor Gene in Duroc, Landrace and Yorkshire Boars Born in 2004 from Pig Breeding Farms

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  Table 4 Number of Live Piglets at Birth Per Litter in Duroc, Landrace, and Yorkshire Breed

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  Table 5 Seven Codes Defined for 27 Combinations of Three Allelic Mutation Genotypes of Heart Fatty Acid Binding Protein Gene in Pigs

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  Table 6 Genotype Frequency of Seven Codes of H-Fabp Gene in Duroc, Landrace and Yorkshire Boars Born in 2004 at Growth Performance Test Station

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  Table 7 Genotype Frequency of Seven Codes of H-Fabp Gene in Duroc, Landrace and Yorkshire Boars Born in 2004 from Pig Breeding Farms

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