Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis
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结合 GWAS 和群体基因组分析来表征豆科植物与根瘤菌共生的共同进化
DOI：
10.1111/mec.16602
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发表时间：
2022
影响因子：
4.9
通讯作者：
Tiffin, Peter
中科院分区：
文献类型：
--
作者：
Epstein, Brendan;Burghardt, Liana T.;Heath, Katy D.;Grillo, Michael A.;Kostanecki, Adam;Hämälä, Tuomas;Young, Nevin D.;Tiffin, Peter
豆科植物和根瘤菌之间的互惠共生显然是过去共同进化的产物。然而，这些伙伴之间正在进行的演变的性质不太清楚。为了表征豆科植物和根瘤菌之间最近协同进化的性质，我们使用群体基因组分析来表征对功能注释的共生基因以及通过两种关联分析确定的共生基因候选者的选择。为了进行关联分析，我们将202份豆科寄主蒺藜苜蓿（Medicago truncatula）与88株苜蓿中华根瘤菌（Sinorhizobia（Ensifer）melilotistrains）共同接种。多菌株接种比单菌株接种更好地反映了自然界根瘤菌选择的生态现实，使菌株能够竞争结瘤机会和宿主资源，并使宿主优先形成根瘤并为某些菌株提供资源。我们发现共生体的广泛宿主，即基因型对根瘤菌适合度的影响，一些注释的根瘤菌基因具有最近正选择的特征。然而，无论是负责这种变化的基因，也没有注释的宿主共生基因富集阳性或平衡选择的签名。这一结果表明，稳定化选择支配着作用于共生性状的选择，这些性状的变异处于突变-选择平衡之下。与缺乏对宿主基因的正选择相一致，我们发现，无论植物是用根瘤菌还是氮肥生长，宿主之间的生长变化都是相似的，这表明共生可能不是多菌株环境中植物生长变化的主要驱动因素。
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two‐species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume hostMedicago truncatulawith a community of 88Sinorhizobia (Ensifer) melilotistrains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single‐strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype‐by‐genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation‐selection balance. Consistent with the lack of positive selection acting on host genes, we found that among‐host variation in growth was similar whether plants were grown with rhizobia or N‐fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.