High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species
High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species
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DOI：
10.1007/s11295-015-0944-0
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发表时间：
2015-12-01
影响因子：
2.4
通讯作者：
Isagi, Yuji
中科院分区：
文献类型：
--
作者：
Sakaguchi, Shota;Sugino, Takeshi;Isagi, Yuji
白色柏松（Callitris glaucophylla）是一种耐旱万年青针叶树，是澳大利亚C.柱状种复合体。该复合体由五个密切相关的形态种组成，它们发生在澳大利亚广泛的生物气候区域。复杂的生态基因组学提供了一个机会，以确定与环境适应相关的标记，并有望扩大我们的物种形成过程的理解。本研究采用单树连锁作图法，结合高通量限制性位点相关DNA（RAD）测序和表达序列标签-简单序列重复（EST-SSR）基因分型技术，构建了一张C.灰叶所构建的连锁图由4284个标记组成，分布在11个连锁群上，对应于马蹄莲属的单倍体染色体数目（2n= 22）。标记的空间分布不均匀，与随机预期相比，在一些连锁群的中心位置有显著的聚集，这可能与着丝粒周围区域的重组冷点有关。等位基因分离被证明是扭曲的四个连锁群的特定区域，在那里选择可能已经操作的活力基因，在周围的连锁标记的等位基因失真。然后，我们测试了RAD单核苷酸多态性（RAD-SNP）标记的回收率和可转移性的连锁图谱的人口基因组数据收集的相关物种，细马蹄莲。在连锁图标记中，有1257个标记（约1000个）被标记。30%）在C.灰叶遗传多样性和分化评估使用映射标记反映了确定的偏见略有下降的Hs（绝对差异-0.018）的一个相关的物种（C。gracilis）和C. glaucophylla和C.股薄肌（+0.018）。虽然应注意考虑到这种偏见，在跨物种转移，这项研究表明，RAD-SNP为基础的连锁图谱是非常有用的，结合人口基因组分析，这针叶树谱系。
White cypress pine (Callitris glaucophylla) is a drought-tolerant evergreen conifer, which is a member of the Australian C. columellaris species complex. The complex is comprised of five closely related morphospecies that occur in a wide range of bioclimatic regions in Australia. Ecological genomics of the complex provides an opportunity to identify markers associated with environmental adaptation and is expected to broaden our understanding of its speciation process. We adopted a single-tree linkage mapping approach combined with high-throughput restriction site associated DNA (RAD) sequencing and expressed sequence tag-simple sequence repeat (EST-SSR) genotyping to set up a baseline genetic map for C. glaucophylla. The generated linkage map consisted of 4284 markers positioned on 11 linkage groups, corresponding to the haploid chromosome number of Callitris (2n= 22). The spatial distribution of markers was uneven compared to random expectation with significant clustering in central positions of some linkage groups, which may be associated with recombination cold spots of pericentromere regions. Allelic segregation was shown to be distorted in particular regions of four linkage groups, where selection may have operated on viability genes, leaving allelic distortion in surrounding linked markers. We then tested RAD single nucleotide polymorphisms (RAD-SNP) marker recovery and transferability of the linkage map to population genomic data collected for a related species, Callitris gracilis. Of the linkage map markers, 1257 markers (ca. 30 %) were recovered in independent RAD sequencing of population samples of C. glaucophylla. Genetic diversity and differentiation evaluated using mapped markers reflected ascertainment bias slightly; a decrease in Hs (absolute difference of -0.018) for a related species (C. gracilis) and an increase in F-ST between C. glaucophylla and C. gracilis (+0.018) were detected. Although care should be taken given such biases in cross-species transfer, this study demonstrated that the RAD-SNP-based linkage map is essentially useful when combined with population genomic analysis of this conifer lineage.