The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula. Medicago truncatula

As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex plant phenotype and we know little about the pathways utilized by naturally tolerant plants. Legumes are important species in agricultural and natural ecosystems, since they engage in symbiotic nitrogen-fixation, but are especially vulnerable to salinity stress. Our studies of the model legume Medicago truncatula in field and greenhouse settings demonstrate that Tunisian populations are locally adapted to saline soils at the metapopulation level and that saline origin genotypes are less impacted by salt than non-saline origin genotypes; these populations thus likely contain adaptively diverged alleles. Whole genome resequencing of 39 wild accessions reveals ongoing migration and candidate genomic regions that assort non-randomly with soil salinity. Consistent with natural selection acting at these sites, saline alleles are typically rare in the range-wide species' gene pool and are also typically derived relative to the sister species M. littoralis. Candidate regions for adaptation contain genes that regulate physiological acclimation to salt stress, such as abscisic acid and jasmonic acid signaling, including a novel salt-tolerance candidate orthologous to the uncharacterized gene AtCIPK21. Unexpectedly, these regions also contain biotic stress genes and flowering time pathway genes. We show that flowering time is differentiated between saline and non-saline populations and may allow salt stress escape. This work nominates multiple potential pathways of adaptation to naturally stressful environments in a model legume. These candidates point to the importance of both tolerance and avoidance in natural legume populations. We have uncovered several promising targets that could be used to breed for enhanced salt tolerance in crop legumes to enhance food security in an era of increasing soil salinization.

随着全球气候变暖，农业生产日益受到土壤盐渍化加剧的冲击。解析植物对盐胁迫的适应机制，可为高效作物育种提供理论支撑。盐耐受性是一类复杂的植物表型，目前学界对天然耐盐植物所利用的适应性通路仍所知甚少。豆科植物（Legumes）在农业与自然生态系统中占据重要地位，因其可与根瘤菌形成共生固氮体系，但该类植物对盐胁迫尤为敏感。本研究以模式豆科植物蒺藜苜蓿（Medicago truncatula）为对象，开展田间与温室实验，结果显示：突尼斯居群在集合种群（metapopulation）尺度下已局部适应盐渍化土壤，且源自盐渍生境的基因型受盐胁迫的影响程度显著低于非盐渍生境来源的基因型；因此这些居群大概率携带适应性分化的等位基因。对39份野生种质资源（wild accessions）开展全基因组重测序分析，我们发现了持续存在的基因流，以及与土壤盐度呈非随机关联的候选基因组区域。与这些位点受到自然选择的推论相符，盐适应性等位基因在该物种的全球分布范围内的基因库中通常较为稀有，且相较于近缘种滨海苜蓿（M. littoralis），这些等位基因多为衍生型。候选适应性区域包含调控盐胁迫生理适应的基因，如脱落酸（abscisic acid）与茉莉酸（jasmonic acid）信号通路相关基因，还包括一个与未表征基因AtCIPK21同源的新型耐盐候选基因。出乎意料的是，这些区域同时涵盖生物胁迫相关基因与开花通路基因。研究证实，盐生与非盐生居群的开花时间存在分化，这种分化或可帮助植物逃避盐胁迫环境。本研究在模式豆科植物中鉴定出多条适应自然胁迫环境的潜在通路。这些候选位点凸显了耐受性与逃避策略在天然豆科居群中的重要性。我们发掘出多个极具应用前景的靶标，可用于培育耐盐性提升的作物豆科品种，以在土壤盐渍化日益加剧的时代保障粮食安全。