Ahmadi Nourollah, Barry Mamadou Billo, Frouin Julien, de Navascués Miguel, Toure Mamadou Aminata
UMR AGAP, CIRAD, TA-A 108/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France.
AGAP, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
Rice (N Y). 2023 Mar 22;16(1):15. doi: 10.1186/s12284-023-00633-4.
Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.
利用基因组扫描方法对植物适应气候变化的遗传基础进行分析，通常是在异交繁殖模式的假设下，对自然种群进行的。我们在此报告一项基于对西非热带森林和苏丹稀树草原上的自花授粉作物物种水稻（Oryza sativa）和光稃稻（Oryza glaberrima）进行历时采样（1980年和2011年）的研究。首先，利用历史气象数据，我们证实了目标地区温度（平均升高1°C）和降雨模式（可预测性降低且降雨量减少）的变化。其次，对种群的物候进行表型分析，我们观察到2010年样本中的抽穗时间显著提前。第三，通过对两个种群的测序基因型数据进行基因分型，实施两种基因组扫描方法（其中一种是专门为自交物种开发的），我们检测到31个独立的选择足迹。基因本体分析检测到这些选择足迹在参与生殖过程的基因中显著富集。其中一些带有已知的抽穗时间QTL和基因，包括OsGI、Hd1和OsphyB。这种快速的适应性进化源于调控抽穗时间的遗传网络中现有变异的细微变化，并没有像自花授粉植物中常见的那样转化为多位点基因型的优势，也没有转化为明显的选择性清除。观察到的高适应潜力源于水稻地方品种的多系遗传结构，以及农场、村庄和区域层面水稻复合种群相当大且相互交织的遗传多样性，在环境选择压力出现之前，这些层面在多个遗传背景中承载了适应性变异。我们的结果说明了通过人类和自然选择过程实现原地多样性的进化，并为旨在适应气候变化的水稻育种和品种部署策略提供了一个模型。它还呼吁进一步开发植物种群适应环境变化的种群遗传模型。据我们所知，这是第一项研究作物中气候变化选择性足迹的研究。
