Development of nuclear gene-derived molecular markers linked to legume genetic maps
Development of nuclear gene-derived molecular markers linked to legume genetic maps
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DOI：
10.1007/s00438-006-0118-8
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发表时间：
2006-07-01
影响因子：
3.1
通讯作者：
Cook, Douglas R.
中科院分区：
文献类型：
--
作者：
Choi, Hong-Kyu;Luckow, Melissa A.;Cook, Douglas R.
系统地识别相关生物的同源特征极大地促进了比较基因组学，包括基因组进化和比较遗传图谱的研究。在这项研究中，我们选择了274个独特的基因序列，用于在15个豆科植物基因组中建立基于PCR的遗传标记，这些基因组代表了来自拟态和反向重复缺失分支(IRLC)的6个作物或模式豆科植物。DNA序列分析表明，129个扩增片段在大多数目标二倍体基因组中表现为单拷贝位点。这些标记大多是内含子跨越标记(70.5%)，并与豆科植物遗传图谱连锁(85.3%)。这些标记主要分为四类：(1)内含子相对保守，(2)内含子跨越发散，(3)外显子衍生保守，(4)外显子衍生发散。每一类别内的序列差异程度表明，相应的标记可能在不同但重叠的分类水平上评估系统发育关系。我们测试了以前没有取样的基因组的标记性能，代表了跨越豆科多样性的95个不同物种。系统发育分析支持扩增序列的正交学，但显著的例外是莲花与IRLC和相体分支的联系不明确。
The systematic identification of the orthologous features of related organisms greatly facilitates comparative genomics, including research on genome evolution and comparative genetic mapping. In this study, we selected 274 unique gene sequences for the development of PCR-based genetic markers across fifteen legume genomes, representing six crop or model legume species from the phaseoloid and inverted repeat loss clades (IRLC). DNA sequence analysis demonstrated that 129 of the amplified fragments represented single copy loci across most target diploid genomes. The majority of these markers are intron-spanning (70.5%) and linked to legume genetic maps (85.3%). The markers were grouped into four main categories: (1) intron-spanning relatively conserved, (2) intron-spanning diverged, (3) exon-derived conserved, and (4) exon-derived diverged. The extent of sequence divergence within each category indicates that the corresponding markers may have utility for assessing phylogenetic relationships at different, but overlapping, taxonomic levels. We tested marker performance on genomes that had not been previously sampled, representing 95 different species that span the diversity of the Fabaceae. Phylogenetic analyses support the orthology of amplified sequences, with the notable exception of an ambiguous affiliation of Lotus relative to the IRLC and phaseoloid clades.