The evolution of the bulldog cranium
BBC documentary that explains the issues with inbreeding dogs and the medical/health impact of selective breeding
Techniques used in modern selective breeding: DNA Extraction, pcr & gel electrophoresis.
Have a go at PCR! |
The PCR song :-)Marker assisted selection (MAS) used in artificial selection in plants (DNA extraction, PCR & gel electrophoresis). |
Case study: Use of snp in detecting genetic disorder in chicken (http://www.dnalandmarks.ca/case-studies/chicken-ascites/)
Challenge
Pulmonary hypertension syndrome (ascites), which causes cardiac failure and early death, is observed in fast-growing broiler chickens at high altitudes. Our client was interested in the development of markers to screen for this genetic disorder.
Solution
We developed a 14K SNP panel that was specific to our client’s population and used this to conduct whole genome association analyses on birds affected and unaffected by ascites. This allowed us to identify multiple chromosomal regions showing small or medium genetic effects associated with ascites. In order to fine map the loci identified and to find new loci associated with ascites, we employed trait-specific whole genome sequencing to generate over 35 Gigabases each of sequence data from pooled genomic DNA samples from resistant and susceptible chickens. The sequence data generated was then aligned to a reference genome and sequence variants, such as SNPs, within and across resistant and susceptible pools were identified and compared between pools.
Result
The results from both the marker-based and sequence-based whole genome analysis were compared and significant markers are to be validated to establish a marker panel for selection of ascites resistance in broiler chickens.
Case study: SNP (single nucleotide polymorphism) used in improving sheep production in NZ.
Release of a High Density SNP Genotyping Chip for the Sheep Genome (http://www.farmiq.co.nz/News/Release-of-a-High-Density-SNP-Genotyping-Chip-for-the-Sheep-Genome.asp)
An international team has developed a powerful new tool that can be used to test a sheep's genetics and predict its productivity and meat quality.
FarmIQ in conjunction with Illumina and the International Sheep Genomics Consortium (ISGC) are today announcing completion of the "Ovine Infinium® HD SNP BeadChip".
This new chip is capable of identifying up to 600,000 points across the sheep genome (otherwise known as single nucleotide polymorphisms or SNPs). It is one of the first high-density chips developed for sheep and follows the release in January 2009 of the OvineSNP50 BeadChip, which can identify over 50,000 points.
FarmIQ commissioned the HD Chip as part of its mission to add value to red meat by improving linkages between animals' meat yield and quality, and what happens on the farm and in the processing plant.
During testing since May, the HD Chip has been used to test 5000 animals from a range of breeds and has proved "very accurate and robust," says John McEwan of AgResearch, who led the chip design work with Rudi Brauning.
Development of the HD Chip started with sequencing of the whole genome (gene map) for 75 individual sheep by Kim Worley and Richard Gibbs's team at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). DNA samples and measurements were also taken from 12,000 New Zealand lamb carcasses. The sheep tested represent a broad range of breeds.
Teams at AgResearch, BCM-HGSC, the Department of Primary Industries Victoria, USDA and CSIRO then collaborated to finalise the identification of more than 20 million sheep gene sequence variants.
John McEwan says the new HD chip is more than an expanded version of the OvineSNP50 chip and it will dramatically increase the power to identify key genes. "The HD chip includes 53,000 of the DNA variants that are known to affect proteins and therefore determine the animal's measurable traits.
"We have also intentionally included some of the more rare genetic variations distributed across the genome to give a better sense of the layout. It's the equivalent of giving a street map to someone who only knew the location of the city before."
The HD chip is designed to enable researchers to customise it or to update it with new SNP discoveries.
The HD chip provides the basis for the next generation of genomic selection when used in combination with other genotyping tools, says James Kijas of CSIRO. "For speed and cost-effectiveness, we expect researchers will probably use the high-density chip for key animals and a combination of the SNP50 BeadChip, whole genome sequencing and the low-density 7000 array for others."
The HD chip development used technology, including the sheep genome, created by ISGC. The work was underwritten by FarmIQ (www.farmiq.co.nz) a joint New Zealand government and industry Primary Growth Partnership programme. Illumina was selected as the genotyping platform provider after evaluation of the various technologies available.
The chief executive of FarmIQ, Collier Isaacs, says the SNP chip will provide the next step for genetic improvement in sheep. "FarmIQ is primarily interested in its application to improve sheep meat yield and quality, but the HD Chip will also be used to improve on-farm production and disease resistance traits. For instance it is already being used as part of investigations into how genetics could be used to reduce sheep greenhouse gas emissions."
An international team has developed a powerful new tool that can be used to test a sheep's genetics and predict its productivity and meat quality.
FarmIQ in conjunction with Illumina and the International Sheep Genomics Consortium (ISGC) are today announcing completion of the "Ovine Infinium® HD SNP BeadChip".
This new chip is capable of identifying up to 600,000 points across the sheep genome (otherwise known as single nucleotide polymorphisms or SNPs). It is one of the first high-density chips developed for sheep and follows the release in January 2009 of the OvineSNP50 BeadChip, which can identify over 50,000 points.
FarmIQ commissioned the HD Chip as part of its mission to add value to red meat by improving linkages between animals' meat yield and quality, and what happens on the farm and in the processing plant.
During testing since May, the HD Chip has been used to test 5000 animals from a range of breeds and has proved "very accurate and robust," says John McEwan of AgResearch, who led the chip design work with Rudi Brauning.
Development of the HD Chip started with sequencing of the whole genome (gene map) for 75 individual sheep by Kim Worley and Richard Gibbs's team at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). DNA samples and measurements were also taken from 12,000 New Zealand lamb carcasses. The sheep tested represent a broad range of breeds.
Teams at AgResearch, BCM-HGSC, the Department of Primary Industries Victoria, USDA and CSIRO then collaborated to finalise the identification of more than 20 million sheep gene sequence variants.
John McEwan says the new HD chip is more than an expanded version of the OvineSNP50 chip and it will dramatically increase the power to identify key genes. "The HD chip includes 53,000 of the DNA variants that are known to affect proteins and therefore determine the animal's measurable traits.
"We have also intentionally included some of the more rare genetic variations distributed across the genome to give a better sense of the layout. It's the equivalent of giving a street map to someone who only knew the location of the city before."
The HD chip is designed to enable researchers to customise it or to update it with new SNP discoveries.
The HD chip provides the basis for the next generation of genomic selection when used in combination with other genotyping tools, says James Kijas of CSIRO. "For speed and cost-effectiveness, we expect researchers will probably use the high-density chip for key animals and a combination of the SNP50 BeadChip, whole genome sequencing and the low-density 7000 array for others."
The HD chip development used technology, including the sheep genome, created by ISGC. The work was underwritten by FarmIQ (www.farmiq.co.nz) a joint New Zealand government and industry Primary Growth Partnership programme. Illumina was selected as the genotyping platform provider after evaluation of the various technologies available.
The chief executive of FarmIQ, Collier Isaacs, says the SNP chip will provide the next step for genetic improvement in sheep. "FarmIQ is primarily interested in its application to improve sheep meat yield and quality, but the HD Chip will also be used to improve on-farm production and disease resistance traits. For instance it is already being used as part of investigations into how genetics could be used to reduce sheep greenhouse gas emissions."
What are snips? |
Snp chip & Sheep |