ABSTRACT

Many efforts have been made to select and isolate naturally occurring animal-friendly Epichloë strains for later reinfection into elite cultivars. Often this process involves large-scale screening of Epichloë-infected wild grass populations where strains are characterized and alkaloids measured. Here, we describe for the first time the use of genotyping-by-sequencing (GBS) on a collection of 217 Epichloë-infected grasses (7 S. arundinaceum, 4 L. perenne, and 206 S. pratensis). This genotyping strategy is cheaper than complete genome sequencing, is suitable for a large number of individuals, and, when applied to endophyte-infected grasses, conveniently genotypes both organisms. In total, 6273 single nucleotide polymorphisms (SNPs) in the endophyte data set and 38 323 SNPs in the host data set were obtained. Our findings reveal a composite structure with three distinct endophyte clusters unrelated to the three main S. pratensis gene pools that have most likely spread from different glacial refugia in Eurasia. All three gene pools can establish symbiosis with E. uncinata. A comparison of the endophyte clusters with microsatellite-based fingerprinting of the same samples allows a quick test to discriminate between these clusters using two simple sequence repeats (SSRs). Concentrations of loline alkaloids and mycelial biomass are correlated and differ significantly among the plant and endophyte subpopulations; one endophyte strain has higher levels of lolines than others, and one specific host genotype is particularly suitable to host E. uncinata. These findings pave the way for targeted artificial inoculations of specific host-endophyte combinations to boost loline production in the symbiota and for genome association studies with the aim of isolating genes involved in the compatibility between meadow fescue and E. uncinata.

摘要

为了选择和分离对动物友好的天然存在的Epichloë菌株，已经作了许多努力，以便以后再感染到优良品种中。通常，此过程涉及大规模筛选受Epichloë感染的野草种群，并在其中鉴定菌株并测量生物碱。在这里，我们首次描述了按序列进行基因分型（GBS）在217种感染埃希波（Epichloë）感染的草（7. arundinaceum，4 L. perenne和206 S. pratensis）上的使用。）。这种基因分型策略比完整的基因组测序便宜，适用于大量个体，并且当应用于内生菌感染的草时，可以方便地对两种生物进行基因分型。总共获得了内生菌数据集中的6273个单核苷酸多态性（SNP）和宿主数据集中的38 323个SNP。我们的发现揭示了一个复合结构，该结构具有三个与三个主要S.pratensis基因库无关的内生菌簇，这三个基因库最有可能从欧亚大陆的不同冰川避难所传播。所有这三个基因库都可以建立与大肠杆菌的共生关系。将内生菌簇与相同样品的基于微卫星的指纹图谱进行比较，可以使用两个简单的序列重复（SSR）快速测试以区分这些簇。在植物和内生菌亚群中，Loline生物碱和菌丝体生物量的浓度是相关的，并且存在显着差异。一种内生菌菌株的lolines水平高于其他内生菌菌株，并且一种特定的宿主基因型特别适合于宿主E. uncinata。这些结果铺平道路的特定主机内生菌组合有针对性的人工接种，以提升loline产量symbiota并与隔离参与草甸羊茅之间的相容性基因的目的基因组关联研究E. uncinata。