Characterisation of genes impacting reproduction in the North Atlantic right whale

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The proposal focuses on identifying and analyzing sequences of genes, in the highly endangered North Atlantic right whale (Eubalaena glacialis), which are potentially associated with its reproductive dysfunction. Understanding the basis of fertility problems in endangered species has broad conservation implications, especially to captive breeding programs.This species is not recovering despite protection since 1935, partially because of a reproductive rate that is only 25-33% of its potential or its close relative the southern right whale, E. australis. Both right whale genomes were recently sequenced and this has allowed identification of DNA sequences of candidate genes potentially involved with fertility, based on whole genome scans in cattle and other intensely studied mammals. Holstein dairy cattle have similar fertility problems and low genetic diversity as North Atlantic right whales, because of selection for milk production. I have selected 50 candidate genes that impact male and female fertility in a number of mammals but primarily cattle. This gene identification was possible because of the availability of the wealth of reproductive and genetic data on semen and embryos. I propose to sequence these candidate gene regions in high and low reproducing males and females using sequence capture and Next Generation Sequencing. This has been shown to be a cost effective approach for examining multiple loci in multiple individuals both in human disease research and natural populations. It has advantages over SNP genotyping as it provides more phase information and also provides sequences of surrounding regions, which have been shown to be important for quantitative traits in livestock species. It also has advantages over direct Sanger sequencing of amplicons from heterozygotes for multiple loci from multiple individuals. The resultant genotypes and allele sequences will be examined for association the high and low reproductive performances. The nature of the variants identified will be compared with those found in the southern right whale as well as in cattle and other livestock.  My laboratory holds the North Atlantic right whale DNA and tissue bank with over 1130 samples for 609 individuals representing over 75% of the current species.We have DNA from many females that have had over 6 calves (one has had 9) and many older females that have never had a calf (nulliparous). The genetic data-base contains DNA profiles at 35 microsatellite loci, MHC loci and mitochondrial control region sequences and this has allowed the assignment of 165 paternities. The mating system appears promiscuous involving sperm competition. One male has 10 assignments, while many others have none. This preliminary analysis of candidate genes involved in fertility will form the molecular foundation for this highly endangered species species as it faces oceanographic changes resulting from climate change.