UMR INRA-UHP Interactions Arbres/Micro-Organismes, INRA-Nancy, 54280 Champenoux, France.
Fungal Genet Biol. 2011 Jun;48(6):592-601. doi: 10.1016/j.fgb.2010.10.007. Epub 2010 Oct 20.
The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexa-nucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.
多年来，人们一直在争论佩里戈尔黑松露（Tuber melanosporum Vittad.）的遗传多样性和遗传结构水平，主要是因为缺乏合适的遗传标记。微卫星或简单重复序列（SSR）对基因组组织、表型多样性很重要，是最受欢迎的分子标记之一。在这项研究中，我们（1）调查了 T. melanosporum 基因组，以描述其 SSR 模式；（2）将其与在 48 种其他真菌和 3 种卵菌基因组中发现的 SSR 模式进行比较；（3）鉴定用于群体遗传学的新多态性 SSR 标记。T. melanosporum 基因组富含 SSR，有 22425 个 SSR，其中单核苷酸是最常见的基序。SSR 存在于所有基因组区域，尽管它们在非编码区域（内含子和基因间区）中更为频繁。在法国、意大利和西班牙的 139 个 T. melanosporum 分离株中，对 135 个 PCR 扩增的单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸进行了分析，其中 60 个（44%）具有多态性。随机选择并分析了 27 个 SSR，并在法国、意大利和西班牙的 139 个 T. melanosporum 分离株中进行了分析。等位基因数从 2 到 18 不等，预期杂合度从 0.124 到 0.815。从 139 个 T. melanosporum 分离株中鉴定出 132 种不同的多位点基因型，基因型多样性很高（0.999）。在担子果和外生菌根调控基因的 UTR 调控区发现了多态性 SSR，表明它们可能在表型变异中发挥作用。总之，本研究中开发的 SSR 高度多态性，我们的研究结果表明，T. melanosporum 是一个遗传多样性非常重要的物种，这与它最近发现的异宗交配系统是一致的。
