Data from: Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups

Accurate estimates of heritability (h²) are necessary to assess adaptive responses of populations and evolution of fitness-related traits in changing environments. For plants, h² estimates generally rely on maternal progeny designs, assuming that offspring are either half-sibs or unrelated. However, plant mating systems often depart from half-sib assumptions, this can bias h² estimates. Here, we investigate how to accurately estimate h² in non-model species through the analysis of sibling designs with a moderate genotyping effort. We performed simulations to investigate how microsatellite marker information available for only a subset of offspring can improve h² estimates based on maternal progeny designs in presence of non-random mating, inbreeding in the parental population or maternal effects. We compared the basic family method, considering or not adjustments based on average relatedness coefficients, and methods based on the animal model. The animal model was used with average relatedness information, or with hybrid relatedness information: associating one-generation pedigree and family assumptions, or associating one-generation pedigree and average relatedness coefficients. Our results highlighted that methods using marker-based relatedness coefficients performed as well as pedigree-based methods in presence of non-random mating (i.e. unequal male reproductive contributions, selfing), offering promising prospects to investigate in situ heritabilities in natural populations. In presence of maternal effects, only the use of pairwise relatednesses through pedigree information improved the accuracy of h² estimates. In that case the amount of father-related offspring in the sibling design is the most critical. Overall, we showed that the method using both one-generation pedigree and average relatedness coefficients was the most robust to various ecological scenarios.

精准估算遗传力（heritability，h²）是评估种群适应性响应以及变化环境中与适合度相关性状演化的必要前提。对于植物而言，h²的估算通常依赖母本子代设计，其前提假设为子代均为半同胞或无亲缘关系。然而，植物的交配系统往往不符合半同胞前提假设，这会对h²的估算结果造成偏差。本研究旨在通过开展适度基因分型工作量的同胞设计分析，实现非模式物种h²的精准估算。我们通过模拟实验，探究在存在非随机交配、亲本种群近交或母本效应的场景下，仅部分子代可获得的微卫星标记（microsatellite marker）信息，如何提升基于母本子代设计的h²估算精度。我们对比了两类方法：一类是基础家系法，考量是否基于平均亲缘关系系数进行校正；另一类是基于动物模型（animal model）的方法。该动物模型可结合两类亲缘关系信息：一类为平均亲缘关系信息，另一类为混合亲缘关系信息——即结合单代系谱与家系假设，或结合单代系谱与平均亲缘关系系数。研究结果显示，在存在非随机交配（即雄性繁殖贡献不均、自交）的情况下，基于标记的亲缘关系系数法的表现与基于系谱的方法相当，为自然种群的原位遗传力估算提供了颇具前景的研究路径。当存在母本效应时，仅通过系谱信息计算成对亲缘关系的方法，方能提升h²的估算精度。在此类场景下，同胞设计中与父本存在亲缘关系的子代数量是最为关键的影响因素。总体而言，本研究证实，同时结合单代系谱与平均亲缘关系系数的方法，对各类生态场景均具备最强的鲁棒性。