Development and transferability analysis of SSR primers in wild rice Zizania latifolia (Poaceae)
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摘要: 利用数据库中已有的部分菰（Zizania latifolia Turcz.）核基因组序列，采用in silico方法开发其SSR引物，并选取我国不同纬度的5个菰野生种群，对合成的64对引物进行筛选。结果显示：64对引物中有15对至少在一个种群中表现出多态性；共发现84个等位基因，每个位点平均有5.6个等位基因。在5个种群中，观察杂合度为0.000~0.941，预期杂合度为0.072~0.625。种群间的基因流（Nm=0.576）水平较低导致了种群间表现出较高的遗传分化（FST=0.432）。进一步对稻族其他物种的通用性检测发现，15个多态位点中，有8个位点在亚洲栽培稻（Oryza sativa L.）中得到扩增，有9个位点在普通野生稻（O. rufipogon Griff.）中得到扩增。
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关键词:
- 微卫星标记 /
- 参照基因组 /
- 简单重复序列(SSR) /
- 野生稻 /
- 菰
Abstract: Zizania latifolia Turcz., also known as Manchurian wild rice, is a member of the tribe Oryzeae, and a major wild ecological and genetic resource. In this study, nuclear SSR primers were developed in silico based on part of the existing genome sequences of Z. latifolia. Five wild populations of the species from different regions across China were selected to screen 64 developed primers. Results showed that 15 primer pairs were polymorphic in at least one population. In addition, we identified a total of 84 alleles, with an average of 5.6 alleles per locus. For the different populations, the level of observed and expected heterozygosity ranged from 0.000 to 0.941 and 0.072 to 0.625, respectively. Relatively high genetic differentiation between populations (FST=0.432) was found, as evidenced by low levels of gene flow (Nm=0.576) among populations. These newly developed markers will facilitate further study of the level and pattern of genetic diversity, and the development of germplasm resource conservation strategies for natural extant Z. latifolia populations. In the cross-species transferability test, eight and nine of the 15 loci were successfully amplified in Oryza sativa L. and O. rufipogon Griff., respectively. -
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