Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

Edea, Z.,Bhuiyan, M. S. A.,Dessie, T.,Rothschild, M. F.,Dadi, H.,Kim, K. S. Cambridge University Press 2015 Animal Vol.9 No.2

<P>Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.</P>

Analyses of pig genomes provide insight into porcine demography and evolution

Groenen, Martien A. M.,Archibald, Alan L.,Uenishi, Hirohide,Tuggle, Christopher K.,Takeuchi, Yasuhiro,Rothschild, Max F.,Rogel-Gaillard, Claire,Park, Chankyu,Milan, Denis,Megens, Hendrik-Jan,Li, Sheng Nature Publishing Group, a division of Macmillan P 2012 Nature Vol.491 No.7424

For 10,000??years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ?? million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

자가농가 자료에 의한 Yorkshire 돈의 몇개 형질에 대한 유전력 및 유전상관

서영석(Young Syek Sye),(M . F . Rothschild),(M . Healey) 한국축산학회 1989 한국축산학회지 Vol.31 No.9

This study was initiated to estimate genetic and phenotypic parameters from data of Yorkshire swine from a large breeding farm. These parameters were to be used in the future to estimate individual pig breeding values and to estimate progress due to selection. Although estimates of the parameters were generally within range of previous literature values, some fell outside the parameter space. These results may have been the result of sampling, previous selection of pigs to participate in the performance test or lack of large numbers of data to estimate the parameters. Despite these problems, consideration should be given to using estimates of genetic parameters from on-the-farm data because these estimates may be more representative of the underlying population in which breeding values are to be estimated. Acknowledgements This paper is Journal Paper No. J-13500 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa, Project .1901. Dr. Sye thanks Yeungnam University for their support during his leave and to express his appreciation to Iowa State University for the partial financial support that he received during his stay. The assistance of Drs. L. Christian and K. Boldman is greatly appreciated.

Development and Application of High-density SNP Arrays in Genomic Studies of Domestic Animals

Fan, Bin,Du, Zhi-Qiang,Gorbach, Danielle M.,Rothschild, Max F. Asian Australasian Association of Animal Productio 2010 Animal Bioscience Vol.23 No.7

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.

모돈의 자돈 생산성에 영향을 미치는 요인 분석

정흥우,( H . W . Chung,L . Wang,M . F . Rothschild ) 한국축산학회 1998 한국축산학회지 Vol.40 No.1

Records from 16,351 litters born between 1991 and 1996 from Duroc, Landrace and Yorkshire sows and Landrace × Yorkshire crossbred sows were used to estimate the effects of year, parity and breed on eight sow productive traits at birth. The model used in this study included effects of year, parity, breed, sow nested within breed, and the interactions of year by parity and parity by breed. The results obtained were as follows: Year had highly significant effects (P$lt;0.01) on the numbers of stillbirths, pigs mummified, small pigs, and pigs suckled and litter weight. The breeds of sow significantly affected (P$lt;0.01) the total number of pigs born, the number of stillbirths, small pigs, pigs culled, and pigs suckled and litter weight. The total number of pigs born, the number of pigs suckled and litter weight were the highest in the 4th parity. The number of stillbirths, pigs mummified and small pigs tended to inaease with the inaease of parity. Parity effects were significant on most of the traits. The total number of pigs born and the number of pigs suckled were greater in the crossbred sows than in the purebreds (P$lt;0.01) and litter weight was heavier in the crossbred sows than in the purebreds (P$lt;0.05). In purebreds, Landrace and Yorkshire sows were superior to Duroc sows in the total number of pigs born and the number of pigs suckled (P$lt;0.01). Landrace Yorkshire crossbred sows were similar to Yorkshire Landrace crossbreed in the sow productive traits. Heterosis were 9.3% for the total number of pigs, 11.6% for the number of pigs suckled, 4.3% for litter weight, 25.0% for the number of stillbirth, 23.1% for the number of pigs mummified and 20.0% for the number of pigs culled.

Investigation of Single Nucleotide Polymorphisms in Porcine Chromosome 2 Quantitative Trait Loci for Meat Quality Traits

Do, K.T.,Ha, Y.,Mote, B.E.,Rothschild, M.F.,Choi, B.H.,Lee, S.S.,Kim, T.H.,Cho, B.W.,Kim, K.S. Asian Australasian Association of Animal Productio 2008 Animal Bioscience Vol.21 No.2

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

랜드레이스 계통조성돈의 유전적 및 표현형가적 변화추세

정영철(Y . C . Jung),김광주(G . J . Jeon),김성훈(S . H . Kim),박홍양(H . Y . Park),박영일(Y . I . Park),(M . F . Rothschild) 한국축산학회 1992 한국축산학회지 Vol.34 No.1

An animal model with the best linear unbiased prediction properties was used to evaluate the genetic trend of a Landrace herd. The Landrace base population was imported from Sweden and has been closed and linebred for 7 generations. The average number of parental animals per generation were 45 gilts and 15 boars and a total of 1,402 pigs were tested for performance. An average inbreeding coefficient of the 7th generation was 6.19%. The animal model used in the study included a complete additive genetic relationship matrix among all the pigs. The phenotypic trends for days to 90 ㎏ (DAYS 90), average daily gain (ADG), feed conversion rate (FCR). and selection index (INDEX) showed a favorable increase except backfat thickness (BF), but the increase was statistically insignificant. However, the genetic trends for the 5 traits were statistically highly significant (P$lt;0.01). The annual genetic gains with corresponding S.E. were .95±.14 days (.62%) for DAYS90, 9.97±1.73g (1.16%) for ADG, .008±.002㎝ (.56%) for BF, .003±.001% (.11%) for FCR, and 1.65±.14 (.95%) for INDEX, respectively. The values in the parentheses are the corresponding ratio of annual genetic change to phenotypic means.