Palaiokostas Christos, Anjum Anam, Jeuthe Henrik, Kurta Khrystyna, Lopes Pinto Fernando, de Koning Dirk Jan
Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden.
Aquaculture Center North Kälarne Sweden.
Evol Appl. 2021 Jul 2;15(4):565-577. doi: 10.1111/eva.13261. eCollection 2022 Apr.
Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost-effective solution for obtaining genome-wide information in species with a limited availability of genomic resources. In the current study, we implemented double-digest restriction site-associated DNA sequencing (ddRAD-seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013-2017 were genotyped using ddRAD-seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity-related metrics were estimated, and genome-wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise values and principal component analysis (PCA). The existence of associations was investigated between the mean genome-wide heterozygosity of each full-sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (-0.33) was estimated between the mean observed heterozygosity of each full-sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome-wide information in a cost-effective manner.
在大多数水产养殖物种中，常规利用基因组信息来指导选育决策尚不普遍。简化基因组测序方法为在基因组资源有限的物种中获取全基因组信息提供了一种经济高效的解决方案。在本研究中，我们对一个具有已知最长选育历史（约40年）的北极红点鲑品系实施了双酶切简化基因组测序（ddRAD-seq），旨在改进选育决策。总共对瑞典四个不同养殖场饲养的、涵盖2013 - 2017年不同年份的1730只动物进行了ddRAD-seq基因分型。鉴定出了约5000个单核苷酸多态性（SNP），估计了与遗传多样性相关的指标，并针对不同时间点的体长和性成熟年龄进行了全基因组关联研究（GWAS）。基于成对FST值和主成分分析（PCA）的结果，观察到不同养殖场的动物之间遗传分化较低。研究了每个全同胞家系（2017年份）的平均全基因组杂合度与相应的近交系数或眼点期存活率之间的关联。估计每个全同胞家系的平均观察杂合度与相应的近交系数之间存在中等相关性（-0.33），而与眼点期存活率未获得线性关联。GWAS未检测到对任何研究性状有主要影响的位点。然而，在14条不同染色体上发现了对任一研究性状解释超过1%加性遗传方差的基因组区域。总体而言，已获得了对北极红点鲑未来选育决策有价值的关键见解，表明ddRAD是一种以经济高效方式获取全基因组信息的有吸引力的基因分型平台。
