Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes
Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes
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DOI：
10.1007/s11295-006-0049-x
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发表时间：
2007-01-01
影响因子：
2.4
通讯作者：
Karp, A.
中科院分区：
文献类型：
--
作者：
Hanley, S. J.;Mallott, M. D.;Karp, A.
杨属（Populus）和柳属（Salix）的柳树是杨柳科（Salicaceae）的成员，杨柳科（Salicaceae）是一个含有柔荑花序的树木、灌木和亚灌木的科。白杨被认为是树木生物学研究的模式系统，近年来已经获得了大量的遗传和基因组资源。将信息转移到目前可用资源较少的杨柳的研究将非常有益。然而，白杨和杨柳基因组之间的保守程度尚未得到广泛的研究。为了解决这个问题，我们构建了一个连锁图的基础上，杨柳的大作图群体来自两个柳viminalis x（S。viminalis x S. spanverind）杂交同胞，并将其与公开可得的白杨基因组序列比对。选择一组全基因组表达的白杨序列，并用于设计有效扩增杨柳同源区域的引物组。杨柳产物的直接测序证实了在大多数情况下与白杨靶标的同源性，并允许鉴定用于定位这些基因座的单核苷酸多态性（SNP）。总共使用202个扩增片段长度多态性（AFLP）、75个微卫星和79个SNP构建了一个杨柳共有图谱，该图谱跨度为1，856.7 cM，标记之间的平均间隔为6.3 cM。鉴定了与所绘制的杨柳微卫星位点同源的白杨序列，并且除了SNP标记之外，还使用这些序列将除了两个次要连锁群之外的所有连锁群与白杨基因组序列进行比对。揭示了高度的宏观共线性。
Poplars (genus Populus) and willows (genus Salix) are members of the Salicaceae, a family of catkinbearing trees, shrubs and sub-shrubs. Poplar is considered the model system for biological studies in trees and considerable genetic and genomic resources have become available in recent years. The transfer of information to research studies in willow, for which fewer resources are currently available, would be highly beneficial. However, the extent of conservation between poplar and willow genomes has not yet been extensively studied. To address this, we have constructed a linkage map of willow based on a large mapping population derived from a cross between two Salix viminalis x (S. viminalis x S. schiverind) hybrid sibs, and aligned this to the publicly available poplar genome sequence. A set of genome-wide, expressed poplar sequences was selected and used to design primer sets that efficiently amplified homeologous regions in willow. Direct sequencing of the willow products confirmed homology with the poplar target in the majority of instances and allowed identification of single nucleotide polymorphisms (SNPs) that were used to map these loci. In total, 202 amplified fragment length polymorphisms (AFLPs), 75 microsatellites and 79 SNPs were used to construct a willow consensus map that spanned 1,856.7 cM with an average interval between markers of 6.3 cM. Poplar sequences homologous to those of the mapped willow microsatellite loci were identified and used in addition to the SNP markers to putatively align all but two minor linkage groups to the poplar genome sequence. A high degree of macrosynteny was revealed.