NEW YORK (GenomeWeb) – A research team at the University of Alberta has designed a 9,000-SNP Illumina Infinium BeadChip for studying polar bears.
Using the new genomic research tool, the researchers aim to investigate the fine-scale population structure among Canadian polar bears and to study the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation of bears, according to a new paper in the journal Molecular Ecology Resources.
Lead author René Malenfant told BioArray News this week that the team designed the array as part of a greater effort to conduct an updated analysis of the genetic population structure of Canadian polar bears.
According to Malenfant, a PhD candidate at the university, it has been 15 years since the last major analysis of the population, which relied on microsatellite markers that were unable to detect adaptive genetic differentiation across Canada.
In the paper, Malenfant and his fellow authors also noted that Canadian polar bears are currently threatened because of anticipated climate-change-induced habitat loss, and that phenotypic data collected by Environment Canada, the government ministry focused on environmental conservation, has shown an ongoing decline in body size since the 1960s.
"We wanted to explore the possibility that polar bears had adapted genetically to local environments," said Malenfant of the decision to design a SNP chip. "To do this, we needed to use a genomics approach, and it is much easier to genotype SNPs at a large scale than microsatellites."
Here, data provided by Environment Canada came again into play. Malenfant noted that the ministry maintains extensive pedigree data and phenotypic measurements of polar bear family groups in the Western Hudson Bay area, which he described as "the world's best studied subpopulation of polar bears." He noted that bears from this specific population have been shrinking for a number of decades — presumably because of reduced access to food caused by loss of sea ice — and that he and fellow researchers would like to examine the possibility of a genetic changes.
To obtain the content to inform the creation of a SNP chip, Malenfant and colleagues used restriction-site associated DNA sequencing from 38 bears across their circumpolar range, as well as blood and fat transcriptome sequencing of 10 individuals from Western Hudson Bay. About 6,000 RAD SNPs and 3,000 transcriptomic SNPs were then selected for the chip.
As reported in the paper, of the 9,000 SNPs ordered from Illumina, 8,042 were successfully printed, and, after genotyping 1,450 samples supplied by Environment Canada, 5,441 of the SNPs were found to be well clustered and polymorphic.
While such SNP arrays are widely used in human and livestock studies, they were not previously available for genotyping polar bears as well as many other non-model species, the authors noted in the paper, in part because of the cost of designing them. But the availability of affordable next-generation sequencing enables the researchers in this case to proceed with their array design.
"SNP arrays such as ours are expensive, but they provide much more reliable genotypes than next-generation sequencing, which we used to discover SNPs to create our array," said Malenfant. "With thousands of polymorphic SNPs in our array, we can achieve much more precise results than [were] possible using previous methods," he said.
Corey Davis, a co-author on the paper and an assistant professor in the department of biological sciences at the university, told BioArray News that when the team conceived of the project several years ago, sequencing technologies were still relatively expensive, and methods for genotyping large numbers of SNPs in large numbers of individuals by sequencing were not common at that time.
"We therefore chose to discover SNPs by sequencing a small panel of individuals and printing these discovered SNPs on a bead array for genotyping large numbers of individuals," said Davis. "Although this restricted the number of markers we could genotype, we believe in the end it gave us higher quality data than would be obtained with GBS approaches."
As part of the study, the researchers compared a subset of the genotyped bears with microsatellites genotyped for the same individuals. According to the authors, they were able to show rapid linkage disequilibrium decay among polar bears, and demonstrate that their SNP array detected known genetic structures more clearly than microsatellites genotyped for the same individuals.
In contrast to the SNP array results, the microsatellites also did not provide data sufficient to distinguish several sub-clusters of polar bears. "SNP results were concordant with each other with respect to the population of origin of all individuals, but not with those of microsatellites, which suggested that some individuals sampled in the Archipelago [cluster] had strong ancestry from the Hudson–Labrador cluster," the authors wrote.
"Because our goal is to characterize fine-scale genetic structure, particularly around Hudson Bay, the ability to identify genetically differentiated groups from a small sample size is an asset," they noted.
Ultimately, the researchers hope the new chip could be used to inform management decisions in regards to Canadian polar bear populations. Malenfant noted that the International Union for Conservation of Nature's Polar Bear Specialist Group recognizes 19 management units of polar bears worldwide, 13 of which are partially or wholly under Canadian jurisdiction.
These groups have been based primarily on following radio-collared bears, the vast majority of which are female, he said, though genetics can inform researchers "how non-collared bears are mixing on the ice during the breeding season."
Malenfant added that, under Canadian law, adaptive genetic differentiation can be used to establish "designatable units" for a species, groups that warrant separate protection efforts. "If a major genetic cluster of polar bears were found to be very low in adaptive genetic variation, we might want to consider a genetic rescue to ensure that the population remains genetically healthy and able to adapt to future challenges over time," he said.