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Genomic diversity and population structure of the Leonberger dog breed
Genetics Selection Evolution ( IF 4.1 ) Pub Date : 2020-10-14 , DOI: 10.1186/s12711-020-00581-3
Anna Letko , Katie M. Minor , Vidhya Jagannathan , Franz R. Seefried , James R. Mickelson , Pieter Oliehoek , Cord Drögemüller

Leonberger is a giant dog breed formed in the 1850s in Germany. Its post-World War II popularity has resulted in a current global population of ~ 30,000 dogs. The breed has predispositions to neurodegenerative disorders and cancer, which is likely due in large part to limited genetic diversity. However, to date there is no scientific literature on the overall demography and genomic architecture of this breed. We assessed extensive pedigree records, SNP array genotype data, and whole-genome sequences (WGS) on 142,072, 1203 and 39 Leonberger dogs, respectively. Pedigree analyses identified 22 founder animals and revealed an apparent popular sire effect. The average pedigree-based inbreeding coefficient of 0.29 and average kinship of 0.31 show a dramatic loss of genetic diversity. The observed average life span decreased over time from 9.4 years in 1989 to 7.7 years in 2004. A global health survey confirmed a high prevalence of cancer and neurological disorders. Analysis of SNP-based runs of homozygosity (ROH) identified 125,653 ROH with an average length of 5.88 Mb, and confirmed an average inbreeding coefficient of 0.28. Genome-wide filtering of the WGS data revealed 28 non-protein-changing variants that were present in all Leonberger individuals and a list of 22 potentially pathogenic variants for neurological disorders of which 50% occurred only in Leonbergers and 50% occurred rarely in other breeds. Furthermore, one of the two mtDNA haplogroups detected was present in one dog only. The increasing size of the Leonberger population has been accompanied by a considerable loss of genetic diversity after the bottleneck that occurred in the 1940s due to the intensive use of popular sires resulting in high levels of inbreeding. This might explain the high prevalence of certain disorders; however, genomic data provide no evidence for fixed coding variants that explain these predispositions. The list of candidate causative variants for polyneuropathy needs to be further evaluated. Preserving the current genetic diversity is possible by increasing the number of individuals for breeding while restricting the number of litters per sire/dam. In addition, outcrossing would help optimize long-term genetic diversity and contribute to the sustainability and health of the population.

中文翻译:

Leonberger犬种的基因组多样性和种群结构

Leonberger是1850年代在德国形成的巨型犬种。第二次世界大战后的受欢迎程度导致目前全球约有30,000只狗。该品种易患神经退行性疾病和癌症,这在很大程度上可能是由于有限的遗传多样性。但是,到目前为止,还没有关于该种群总体人口学和基因组结构的科学文献。我们分别评估了142,072、1203和39条Leonberger狗的广泛血统记录,SNP阵列基因型数据和全基因组序列(WGS)。家谱分析确定了22种始祖动物,并显示出明显的流行父亲效应。基于谱系的平均近交系数为0.29,平均亲缘关系为0.31,表明遗传多样性急剧下降。随着时间的推移,观察到的平均寿命从9下降。从1989年的4年到2004年的7.7年。一项全球健康调查证实,癌症和神经系统疾病的患病率很高。对基于SNP的纯合性(ROH)运行进行的分析确定了125,653个ROH,平均长度为5.88 Mb,并确认平均近交系数为0.28。对WGS数据进行全基因组过滤后,发现所有Leonberger个体中均存在28种非蛋白质变化变体,以及22种神经系统疾病的潜在致病变体列表,其中50%仅在Leonbergers中发生,而50%在其他品种中很少发生。此外,检测到的两个mtDNA单倍型之一仅存在于一只狗中。莱昂伯格人口的增加伴随着1940年代出现瓶颈之后的遗传多样性的大量丧失,这是由于广泛使用流行的公母导致近交水平高。这可能解释了某些疾病的高患病率;然而,基因组数据没有提供解释这些倾向的固定编码变体的证据。多发性神经病的候选致病变体列表需要进一步评估。可以通过增加繁殖个体的数量,同时限制每个父/母的窝数来保护当前的遗传多样性。此外,异源杂交将有助于优化长期遗传多样性,并有助于人口的可持续性和健康。这可能解释了某些疾病的高发病率;然而,基因组数据没有提供解释这些倾向的固定编码变体的证据。多发性神经病的候选致病变体列表需要进一步评估。可以通过增加繁殖个体的数量,同时限制每个父/母的窝数来保持当前的遗传多样性。此外,异化将有助于优化长期遗传多样性,并有助于人口的可持续性和健康。这可能解释了某些疾病的高发病率;然而,基因组数据没有提供解释这些倾向的固定编码变体的证据。多发性神经病的候选致病变体列表需要进一步评估。可以通过增加繁殖个体的数量,同时限制每个父/母的窝数来保护当前的遗传多样性。此外,异源杂交将有助于优化长期遗传多样性,并有助于人口的可持续性和健康。可以通过增加繁殖个体的数量,同时限制每个父/母的窝数来保护当前的遗传多样性。此外,异源杂交将有助于优化长期遗传多样性,并有助于人口的可持续性和健康。可以通过增加繁殖个体的数量,同时限制每个父/母的窝数来保护当前的遗传多样性。此外,异源杂交将有助于优化长期遗传多样性,并有助于人口的可持续性和健康。
更新日期:2020-10-15
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