Parentage and relatedness reconstruction in Pinus sylvestris using genotyping by sequencing

Estimating kinship is fundamental for studies of evolution, conservation and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared to theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotypin...

亲缘关系鉴定是进化、保护与育种研究的核心基石。基于测序的基因分型（Genotyping-by-Sequencing, GBS）及其他基于限制性酶切的基因分型技术，已在非模式生物的相关研究中得到广泛应用。然而，测序错误、测序深度以及文库制备间的重现性问题，可能会对准确的遗传推断造成阻碍。本研究以欧洲赤松（Pinus sylvestris L.）为研究对象，通过测试多组数据过滤参数、不同参考群体以及八种亲缘关系估算方法，旨在构建一套稳健的亲缘关系鉴定流程。本研究采用种子园作为研究系统，其候选亲本信息已知，可将系谱重建结果与理论预期进行比对。研究发现，当共享单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点比例较低时，所有类别的亲缘关系估算值均低于预期。然而，若移除杂合子过剩的位点并开展基因分型（原文后续内容未完整）