Hirohide Uenishi^1,2, Takeya Morozumi³, Tomoko Eguchi-Ogawa¹, Hiroyuki Kanamori⁴, Daisuke Toki3

¹Animal Genome Research Unit, ²Animal Immune and Cell Biology Research Unit, ³JATAFF Institute, ⁴Advanced Genomics Laboratory

［Abstract］

The Swine Genome Sequencing Consortium (SGSC), consisting of research institutes and universities from 12 countries and regions including NIAS, has completed the highquality sequencing of 90% of the pig genome. We have also participated in this effort by sequencing approximately 15,000 pig genes, which eventually contributed to the clarification of the structure of approximately 25,000 genes on the pig genome.

［Keywords］

genome sequence, gene, pig, international consortium, breeding, model animal

［Background］

Genome sequencing and isolation of responsible genes are important for effective breeding of pigs for valuable economic traits such as disease resistance, productivity, growth rate, and meat quality. On the other hand, genome sequence and precise information of genes is valuable for utilization of pig as a model animal for biomedical research. In collaboration with the international Swine Genome Sequencing Consortium (SGSC), we contributed to the sequencing of the entire pig genome. We also precisely sequenced and characterized the genes on the pig genome using full-length cDNA libraries that eventually led to an accurate estimation of the number and structure of genes in the entire genome

［Results and Discussion］

1. We took charge of sequencing of genomic DNA clones located in chromosomes 6 and 7 derived from the Duroc pig (Sus scrofa), an important breed for meat production worldwide (Fig. 1). The SGSC high-quality genome sequence corresponds to 90% (2.52 Gb) of the pig genome (approximately 2.8 Gb) (Table 1).
2. We also collected pig full-length cDNAs generated from various organs and cell populations, and completed the sequencing of 31,079 pig cDNA clones.
3. Comparison of the cDNA clone sequences and the pig genome sequence clarified the locations of the full-length cDNAs on the pig genome. The sequenced cDNAs were estimated to correspond to approximately 15,000 genes, and greatly contributed in characterizing the structure of approximately 25,000 genes on the pig genome.

1. The SGSC reference pig genome sequence will be used for comparative analysis of genome sequences derived from pigs of various breeds to elucidate the locations of genes related to valuable traits in pig production. This will accelerate many breeding strategies by shortening the period for selection of pigs with desirable traits such as outstanding meat quality, fertility and disease resistance.
2. Detailed information of the pig genome and the associated genes will facilitate preclinical studies of pharmaceutical agents, enhance applications of pig as biomedical model animal for transplantation therapies, and accelerate efficient utilization of pig as mid-size experimental animal in medical research.

Fig.1. Pigs cloned from a female pig (Duroc2-14) used for genome sequencing in SGSC. The cloned pigs were used in part for cDNA sequencing by NIAS. The photo is provided by Don Hamerman.

Fig.2. Mapping of cDNA clones sequenced by NIAS on the latest pig genome sequence (Sscrofa10.2). Numbers of locations (gene loci) where the cDNAs were mapped on autosomes, sex chromosomes and sequence fragments unplaced in any chromosomes are shown. Black and white bars indicate the mapping directions from pter to qter and from qter to pter, respectively.

Table 1. Summary of the latest pig genome sequence (Sscrofa10.2)

 

[Reference]

1. Groenen M, Archibald A, Uenishi H and SGSC collaborators (2012) Analyses of pig genomes provide insight into porcine demography and evolution Nature 491(7424): 393-398
2. Uenishi H, Morozumi T, Toki D, Eguchi-Ogawa T, Rund L, Schook L (2012) Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence BMC Genomics 13: 581