Genetic Analysis News You Can Use
Sequenom at the Plant and Animal Genome XVIII Conference
Join our workshop at PAG 2010 and learn how agricultural genomic researchers use the Sequenom MassARRAY® platform in their genetic marker validation and large-scale sample screening process. Speakers from University of Illinois, Southern Cross University, and Pfizer Animal Genetics will share their experiences using the flexible and cost-effective genotyping assays in livestock and polyploid crop testing.
Casein haplotypes and their association with milk production traits in Norwegian Red cattle.
Nilsen, H et al. (2009) Genetics Selection Evolution. 41:24.
A high resolution SNP map, containing 73 SNPs in and around the bovine casein region on BTA6A, was constructed to identify haplotype structures and study associations with milk traits in Norwegian Red Cattle. The map covers approximately a 750 kb region. Both single SNPs and haplotypes within the SCN1S1-CSN2-CSN1S2 haplotype block were found to be significantly associated with both protein and milk yield. Among them, the SNP CSN2_67 with the C allele consistently associated with the milk traits. Four halpotypes that associated with reduced milk and protein production all contain the A-allele of CSN2_67 and G_allele of CSN2-BMC_9215. The SNP map facilitates accurate haplotype construction and can be used for comprehensive association studies in Norwegian Red cattle.
Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploidy plant species using 454 sequencing.
Bundock et al. (2009) Plant Biotechnology Journal. 7: 347-354
Discovering SNPs in a heterozygous and highly polyploidy species, such as sugarcane, is challenging because a given gene may be represented by a number of different alleles. In this study, a new generation sequencing technology, 454 sequencing, was used for the discovery of SNPs for marker development in a large number of sugarcane genes. Sequenom iPlex® Gold genotyping assays were used as a gold standard to validate the candidate SNP sites discovered by the sequencing technology. 106 of 209 validated SNPs fit a 1:1 segregation pattern in the test panel, indicating the utility of the 454 sequencing approach for the detection of single-dose SNP markers in sugarcane.
BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon.
Lorenz, S et al. (2009) Animal Genomics.
To increase the density of a linkage map for Atlantic salmon and to integrate genetic and physical maps, 284 BAC-end sequences of 14 Atlantic salmon were re-sequenced by PCR, yielding 180 putative SNPs. After successful validation of 152 sequence variations, 8 full-sib salmon mapping families comprising 376 individuals were genotyped using Sequenom iPLEX genotyping technology. 110 SNPs were heterozygous in at least one mapping parent, and were mapped onto a SNP map previously constructed for salmon. Tracing the 110 SNP markers back to the BACs enabled the integration of the genetic and physical maps by assigning 73 BAC contigs to Atlantic salmon linkage groups.
High-throughput genetic mapping of mutants via quantitative SNP-typing.
Liu, S et al. (2009) Genetics. ePub 11/2/2009
Liu et al. follow up on next-gen sequencing results, developing iPLEX Gold assays for rapid validation and fine mapping of maize mutants. The authors map mutants via quantitative bulked segregant analysis (BSA) and could rapidly map the loci associated with several recessive mutants. They started out with 1359 SNPs, of which 75% gave working assays in 48 different multiplexes (3% were false-positive SNPs found with 454, 13% of the assays failed and 13% of the markers were dominant only in one line). The resultant SNPs were used to construct a genetic map. A subset of 124 SNPs in 8 multiplexes can now be used with BSA to map phenotypic mutants in a highly cost-effective and high-throughput manner.