Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia.
Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia.
Int J Mol Sci. 2024 Nov 1;25(21):11767. doi: 10.3390/ijms252111767.
A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine ( Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms-SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [ Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype-dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine ( Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant's genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change.
对树木年代学和基因组数据进行联合分析，以确定适应的遗传机制，并评估西伯利亚石松（Du Tour）种群的适应遗传潜力。获得的数据对于预测气候变化的影响和减轻其负面影响是必要的。本文介绍了通过双酶切限制相关 DNA 测序（ddRADseq）获得的 84853 个遗传标记（单核苷酸多态性-SNPs）的变异与 110 个个体表型特征（包括基于 234 棵个体树木树轮宽度（TRW）动态的树木表型）之间的关联分析结果，这些特征来自西伯利亚石松的六个自然种群，这些种群经历了极端气候压力（例如干旱）和食叶害虫（例如松叶蜂[Geoff.])爆发。研究种群的遗传结构相对较弱；样本区分度差，属于遗传上相似的种群。使用三种不同的方法和相应的模型（一般线性模型[GLM]、贝叶斯稀疏线性混合模型[BSLMM]和贝叶斯信息和连锁不平衡迭代嵌套关键法[BLINK]）分析了基因型-树木表型的关联。通过至少两种不同的方法检测到 30 个 SNP，通过所有三种方法检测到 2 个 SNP。此外，通过所有三种方法还发现了三个与在多次气候胁迫下平均恢复树木表型（Rc）值相关的 SNP。使用非常近缘物种白皮松（Engelm.）的基因组注释对包含这些 SNP 的序列进行了注释。我们发现，具有适应性变异的大多数 SNP 都位于基因间区域。三个树木表型相关 SNP 位于 10 Kbp 区域内，一个 SNP 位于编码在环境胁迫条件下，特别是在能诱导 DNA 损伤的情况下，对确保植物遗传信息完整性起关键作用的蛋白质的基因的内含子内。此外，我们发现个体杂合性与某些树木表型之间存在相关性。在大多数这些具有统计学意义的情况下观察到杂种优势；也检测到了自稳态的迹象。尽管大多数鉴定的 SNP 未分配到特定基因，但它们的高多态性和与适应性特征的关联表明，它们具有很高的适应潜力，这有助于西伯利亚石松种群适应气候压力和气候变化。
