局部适应通常涉及大效应的等位基因,当处于正连锁不平衡(LD)时,它们会体验到健身优势。由于分离倒置抑制了重组并促进了局部适应基因座之间LD的维持,它们也通常被发现与适应性发散有关。然而,尚不清楚适应性反应的哪一部分可以归因于倒位和大效应的等位基因,以及在没有重组抑制作用的情况下,反转中的基因座是否仍然可以驱动适应。这里,我们使用全基因组关联研究来探索三种向日葵的局部适应模式:向日葵,向日葵,和叶柄Helianthus,每个都有大量特定物种的倒置。我们发现在与表型和环境的关联特征中发现了显著的全基因组可重复性的证据,在一个物种中具有倒置的基因组区域内特别富集。这表明,虽然倒置可能有助于局部适应,至少一些基因座仍然可以携带突变,这些突变在缺乏分离倒置的物种中没有重组抑制的好处。虽然大量的基因组区域显示出重复适应的证据,大多数最强的关联特征仍然倾向于特定于物种,表明这些物种局部适应的大量基因型冗余。
在植物中,就像人类一样,DNA被排列成称为基因的部分,这些部分又被组织成称为染色体的结构。改变这些基因活性的突变可以帮助植物物种适应新的环境或干旱等极端条件。然而,成功的适应通常需要改变许多不同的基因。如果这些基因在同一染色体上彼此靠近,任何突变都可能一起传给下一代。如果基因位于更远的地方,甚至在不同的染色体上,相反,它们可能被单独继承,这样下一代就不会从适应中受益那么多。染色体倒位-当染色体的一部分断裂并以相反的方式重新连接时-可以增加同一染色体上的突变集将一起遗传的可能性。许多先前的研究发现,染色体倒位倾向于通过将影响相同特征的突变保持在一起来驱动物种适应不同环境的能力。然而,目前尚不清楚反转如何影响适应的可重复性,也就是说,如果另一组密切相关的植物在它们的环境中面临同样的挑战,它们会以同样的方式进化,或者他们会做出新的回应?为了解决这个问题,Soudi,Jahanietal.使用一种称为全基因组关联研究的遗传学方法来探索三种密切相关的向日葵物种如何适应各自的环境。其中两个物种生长在美国中部和西部的各种环境中,这些环境通常又热又干,而第三种物种仅限于德克萨斯州更潮湿的沿海平原,美国。实验发现,所有三种向日葵物种中的一些关键基因都发生了变化。然而,每个物种在更大的一组独特基因中也有突变,而在其他物种中没有改变。在一个物种中,携带倒位的染色体区域倾向于在其中具有更多的关键基因,与其他基因组区域相比。对于那些地区没有倒置的物种也是如此。这表明,即使在没有倒位的情况下,受染色体倒位影响的区域中的基因仍然可以帮助植物适应环境的变化。向日葵因其可食用的油性种子而被广泛种植。在未来,这项工作中确定的一些关键基因可能是植物育种的有用候选基因,以提高向日葵对干旱的抵抗力,高温和其他环境挑战。
Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating
inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to
inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while
inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.
In plants, like in humans, DNA is arranged into sections known as genes that are in turn organised into structures called chromosomes. Mutations that modify the activity of these genes can help plant species to adapt to a new environment or to extreme conditions such as drought. However, successful adaptation often requires changes in many different genes. If these sets of genes are located close to each other on the same chromosome, any mutations will likely be passed onto the next generation together. If the genes are located further away, or even on different chromosomes, they may instead be inherited separately so that the next generation does not benefit as much from the adaptation. A chromosome inversion – when a segment of chromosome breaks off and reattaches the other way around – can increase the likelihood that sets of mutations on the same chromosome will be inherited together. Many previous studies have found that chromosome inversions tend to drive the ability of species to adapt to different environments by keeping together mutations that affect the same characteristics. However, it is not clear how inversions affect the repeatability of the adaptation, that is, if another group of closely related plants faced the same challenge in their environment would they evolve in the same way, or would they evolve a new response? To address this question, Soudi, Jahani et al. used a genetics approach known as a genome wide association study to explore how three closely related species of sunflower have adapted to their respective environments. Two of the species grow in various environments across the centre and west of the USA that are often hot and dry, whereas the third species is restricted to the more humid coastal plain of Texas, USA. The experiments found that a few key genes had changed in all three sunflower species. However, each species also had mutations in a larger set of unique genes that were not changed in the other species. Regions of chromosomes harbouring inversions in one of the species tended to have more of the key genes within them, compared to other genomic regions. This was also true for species that did not have
inversions in those regions. This demonstrates that genes in regions affected by chromosome inversions can still help plants adapt to changes in the environment even in the absence of
inversions. Sunflowers are widely grown for their edible oily seeds. In the future, some of the key genes identified in this work may be useful candidates for plant breeding to improve the resilience of sunflowers to drought, high temperatures and other environmental challenges.