The rhizome is an important organ through which many perennial plants are able to propagate vegetatively. Its ecological role has been thoroughly studied on many grass species while the underlying genetic basis is mainly investigated using a rhizomatous wild rice species-Oryza longistaminata. Previous studies have revealed that the rhizome trait in O. longistaminata is jointly controlled by multiple loci, yet how these loci interact with each other remains elusive. Here, an F2 population derived from Oryza sativa (RD23) and O. longistaminata was used to map loci that affect rhizome-related traits. We identified 13 major-effect loci that may jointly control rhizomatousness in O. longistaminata and a total of 51 quantitative trait loci (QTLs) were identified to affect rhizome abundance. Notably, some of these loci were found to have effects on more than one rhizome-related trait. For each trait, a genetic network was constructed according to the genetic expectations of the identified loci. Furthermore, to gain an overview of the genetic regulation on rhizome development, a comprehensive network integrating all these individual networks was assembled. This network consists of three subnetworks that control different aspects of rhizome expression. Judging from the nodes' role in the network and their corresponding traits, we speculated that qRHZ-3-1, qRHZ-4, qRHI-2, and qRHI-5 are the key loci for rhizome development. Functional verification using rhizome-free recombinant inbred lines (RILs) suggested that qRHI-2 and qRHI-5, two multi-trait controlling loci that appeared to be critical in our network analyses, are likely both needed for rhizome formation. Our results provide more insights into the genetic basis of rhizome development and may facilitate identification of key rhizome-related genes.

中文翻译：

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长雄稻根茎发育的遗传网络。

根茎是许多多年生植物能够无性繁殖的重要器官。它的生态作用已在许多草种上进行了深入研究，而其潜在的遗传基础主要使用根茎野生稻物种 - Oryza longistaminata 进行了研究。先前的研究表明，长雄花的根茎性状由多个基因座共同控制，但这些基因座如何相互作用仍然难以捉摸。在这里，来自 Oryza sativa (RD23) 和 O. longistaminata 的 F2 群体用于绘制影响根茎相关性状的基因座。我们确定了 13 个主要影响基因座，这些基因座可能共同控制 O. longistaminata 的根茎性，并且总共确定了 51 个数量性状基因座 (QTL) 来影响根茎丰度。尤其，发现其中一些基因座对不止一种根茎相关性状有影响。对于每个性状，根据已识别基因座的遗传预期构建遗传网络。此外，为了全面了解根茎发育的遗传调控，组装了一个整合所有这些单独网络的综合网络。该网络由控制根茎表达不同方面的三个子网络组成。从节点在网络中的作用及其对应的特征来看，我们推测qRHZ-3-1、qRHZ-4、qRHI-2和qRHI-5是根茎发育的关键位点。使用无根茎重组自交系 (RIL) 的功能验证表明 qRHI-2 和 qRHI-5，这两个多性状控制基因座似乎在我们的网络分析中至关重要，根茎形成可能都需要。我们的研究结果为根茎发育的遗传基础提供了更多见解，并可能有助于识别关键的根茎相关基因。