Tanhuanpää Pirjo, Erkkilä Maria, Kalendar Ruslan, Schulman Alan Howard, Manninen Outi
Green Technology, Natural Resources Institute Finland (Luke), Myllytie 1, FI-31600 Jokioinen, Finland.
Internal Expert Services, Natural Resources Institute Finland (Luke), Humppilantie 14, FI-31600 Jokioinen, Finland.
Hereditas. 2016 Apr 26;153:5. doi: 10.1186/s41065-016-0009-x. eCollection 2016.
Timothy ( L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers.
Using four primer combinations, 533 REMAP markers were analyzed, compared with 464 polymorphic alleles in the 13 SSR loci previously. The average marker index, which describes information obtained per experiment (per primer combination or locus) was over six times higher with REMAPs. Most of the variation found was within accessions, with somewhat less, 89 %, for REMAPs, than for SSR, with 93 %.
SSRs revealed differences in the level of diversity slightly better than REMAPs but neither marker type could reveal any clear clustering of accessions based on countries, vegetation zones, or different cultivar types. In our study, reliable evaluation of SSR allele dosages was not possible, so each allele had to be handled as a dominant marker. SSR and REMAP, which report from different mechanisms of generating genetic diversity and from different genomic regions, together indicate a lack of population structure. Taken together, this likely reflects the outcrossing and hexaploid nature of timothy rather than failures of either marker system.
梯牧草（ Timothy (L.)）是一种冷季型六倍体多年生植物，是北欧最重要的饲草品种。早期利用SSR标记对96份梯牧草基因库种质的遗传多样性进行分析，结果显示多样性水平较高，但未能解析群体结构。因此，我们利用基于反转录转座子的REMAP标记对51份种质进行了检测，并将多样性分析结果与SSR标记的结果进行比较。
使用4对引物组合，共分析了533个REMAP标记，而之前在13个SSR位点检测到464个多态性等位基因。描述每个实验（每个引物组合或位点）所获得信息的平均标记指数，REMAP标记的该指数比SSR标记高出6倍多。发现的大部分变异存在于种质内，其中REMAP标记检测到的种质内变异比例为89%，略低于SSR标记检测到的93%。
SSRs在揭示多样性水平差异方面略优于REMAPs，但两种标记类型均无法基于国家、植被带或不同品种类型揭示种质的任何明显聚类。在我们的研究中，无法对SSR等位基因剂量进行可靠评估，因此每个等位基因都必须作为显性标记处理。SSR和REMAP分别从产生遗传多样性的不同机制和不同基因组区域进行检测，二者共同表明不存在群体结构。综合来看，这可能反映了梯牧草的异交和六倍体性质，而非两种标记系统存在缺陷。
