Characterisation of genes impacting reproduction in the North Atlantic right whale

该提案的重点是识别和分析高度濒危的北大西洋露脊鲸（Eubalaena glacialis）的基因序列，这些基因可能与其生殖功能障碍有关。了解濒危物种繁殖问题的基础具有广泛的保护意义，特别是对圈养繁殖计划。尽管自1935年以来一直受到保护，但该物种并没有恢复，部分原因是繁殖率仅为其潜力的25-33%，或者是其近亲南露脊鲸，E。澳大利亚。最近对两条露脊鲸的基因组进行了测序，这使得可以根据牛和其他深入研究的哺乳动物的全基因组扫描，确定可能与生育有关的候选基因的DNA序列。荷斯坦奶牛与北大西洋露脊鲸有着相似的生育问题和低遗传多样性，这是因为选择产奶。我已经选择了50个候选基因，这些基因影响了许多哺乳动物（主要是牛）的雄性和雌性生育能力。这种基因鉴定是可能的，因为可以获得关于精液和胚胎的大量生殖和遗传数据。我建议使用序列捕获和下一代测序技术对高繁殖和低繁殖的男性和女性中的这些候选基因区域进行测序。这已被证明是一种成本有效的方法，用于检查多个人在人类疾病研究和自然群体中的多个基因座。与SNP基因分型相比，它具有优势，因为它提供了更多的相位信息，并且还提供了周围区域的序列，这些序列已被证明对家畜物种的数量性状很重要。它还具有优于来自多个个体的多个基因座的杂合子的扩增子的直接桑格测序的优点。将检查所得基因型和等位基因序列与高和低繁殖性能的关联。这些变异的性质将与在南露脊鲸以及牛和其他牲畜中发现的变异进行比较。 我的实验室拥有北大西洋露脊鲸DNA和组织库，其中有609个个体的1130多个样本，代表了目前物种的75%以上。我们有来自许多雌性的DNA，这些雌性有超过6个小牛（其中一个有9个）和许多从未有过小牛的年长雌性（未经产）。遗传数据库包含35个微卫星基因座、MHC基因座和线粒体控制区序列的DNA图谱，因此可以确定165个父子关系。交配系统似乎混杂涉及精子竞争。一名男子有10项任务，而其他许多人则没有任务。对与生育力有关的候选基因的初步分析将为这种高度濒危物种的分子基础，因为它面临气候变化引起的海洋变化。

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.