Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway.
Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Caritasstraat 39, 9090, Melle, Belgium.
BMC Genomics. 2024 Sep 30;25(1):901. doi: 10.1186/s12864-024-10793-2.
Kelps are not only ecologically important, being primary producers and habitat forming species, they also hold substantial economic potential. Expansion of the kelp cultivation industry raises the interest for genetic improvement of kelp for cultivation, as well as concerns about genetic introgression from cultivated to wild populations. Thus, increased understanding of population genetics in natural kelp populations is crucial. Genotyping-by-sequencing (GBS) is a powerful tool for studying population genetics. Here, using Saccharina latissima (sugar kelp) as our study species, we characterize the population genetics at a fine geographic scale, while also investigating the influence of marker type (biallelic SNPs versus multi-allelic short read-backed haplotypes) and minor allele count (MAC) thresholds on estimated population genetic metrics.
We examined 150 sporophytes from 10 locations within a small area in Mid-Norway. Employing GBS, we detected 20,710 bi-allelic SNPs and 42,264 haplotype alleles at 20,297 high quality GBS loci. We used both marker types as well as two MAC filtering thresholds (3 and 15) in the analyses. Overall, higher genetic diversity, more outbreeding and stronger substructure was estimated using haplotypes compared to SNPs, and with MAC 15 compared to MAC 3. The population displayed high genetic diversity (H ranging from 0.18-0.37) and significant outbreeding (F ≤ - 0.076). Construction of a genomic relationship matrix, however, revealed a few close relatives within sampling locations. The connectivity between sampling locations was high (F ≤ 0.09), but subtle, yet significant, genetic substructure was detected, even between sampling locations separated by less than 2 km. Isolation-by-distance was significant and explained 15% of the genetic variation, while incorporation of predicted currents in an "isolation-by-oceanography" model explained a larger proportion (~ 27%).
The studied population is diverse, significantly outbred and exhibits high connectivity, partly due to local currents. The use of genome-wide markers combined with permutation testing provides high statistical power to detect subtle population substructure and inbreeding or outbreeding. Short haplotypes extracted from GBS data and removal of rare alleles enhances the resolution. Careful consideration of marker type and filtering thresholds is crucial when comparing independent studies, as they profoundly influence numerical estimates of population genetic metrics.
海带不仅是生态系统的重要组成部分，作为初级生产者和栖息地形成物种，它们还具有巨大的经济潜力。海带养殖产业的扩张引起了人们对海带养殖遗传改良的兴趣，同时也对养殖种群向野生种群遗传渗透的问题表示关注。因此，增加对自然海带种群群体遗传学的了解至关重要。基因分型测序（GBS）是研究群体遗传学的有力工具。在这里，我们以紫菜（糖海带）为研究对象，在小尺度的地理范围内描述种群遗传学特征，同时研究标记类型（双等位基因 SNP 与多等位基因短读回补单倍型）和次要等位基因计数（MAC）阈值对估计种群遗传指标的影响。
我们从挪威中部一个小区域的 10 个地点检查了 150 个孢子体。利用 GBS，我们在 20,297 个高质量 GBS 位点上检测到了 20,710 个双等位基因 SNP 和 42,264 个单倍型等位基因。我们在分析中同时使用了这两种标记类型以及两个 MAC 过滤阈值（3 和 15）。总体而言，与 SNP 相比，使用单倍型估计的遗传多样性更高、更多的异交和更强的亚结构，与 MAC 15 相比，MAC 3 的遗传多样性更高。该种群表现出较高的遗传多样性（H 范围为 0.18-0.37）和显著的异交（F≤-0.076）。然而，在构建基因组关系矩阵时，在采样地点内发现了一些近亲。采样地点之间的连通性很高（F≤0.09），但即使在相隔不到 2 公里的采样地点之间，也检测到了微妙但显著的遗传亚结构。距离隔离是显著的，解释了 15%的遗传变异，而将预测的海流纳入“海洋隔离”模型解释了更大的比例（约 27%）。
研究种群具有多样性，显著的异交，并表现出高连通性，部分原因是当地海流的影响。使用全基因组标记物结合置换检验提供了高统计能力，以检测微妙的种群亚结构和近交或杂交。从 GBS 数据中提取的短单倍型和去除稀有等位基因提高了分辨率。在比较独立研究时，需要仔细考虑标记类型和过滤阈值，因为它们会深刻影响种群遗传指标的数值估计。
