High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.
High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.
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DOI：
10.1186/1471-2164-11-129
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发表时间：
2010-02-23
期刊：
影响因子：
4.4
通讯作者：
Rönnberg-Wästljung AC
中科院分区：
文献类型：
--
作者：
Berlin S;Lagercrantz U;von Arnold S;Ost T;Rönnberg-Wästljung AC
柳树和杨树是杨柳科植物，它们具有许多共同的生态、遗传和基因组特征。人们对利用柳树进行生物质生产的兴趣与日俱增，这给适应不同环境的高产抗病无性系育种带来了越来越大的压力。本研究的主要目的是开发高密度遗传连锁图谱，用于柳树产量和抗性相关性状的定位。以毛果杨基因组为材料，提取等间距标记，对柳树基因组中的同源基因座进行定位。这两个基因组中的标记位置被用来研究基因组进化，因为这两个谱系的分化约为45万。我们构建了覆盖柳树19个连锁群的两个连锁图谱。最详细的共识图谱S1包含495个标记，总遗传距离为2477 cM，标记间平均距离为5.0 cM。S3一致图谱包含221个标记，总遗传距离为1793 cM，标记间平均距离为8.1 cM。我们发现柳树和杨树具有高度的同步性和基因序列保守性。然而，有证据表明，杨树Lg I和XVI和柳树Lg Ib存在两个主要的染色体间重排，表明其中一个谱系发生了分裂或融合，以及五个染色体内倒位。同源基因之间的沉默替换数量(中位数：0.12)比同源基因之间的(中位数：0.37-0.41)低三倍。杨树和柳树之间的基因组变化速度相对较慢，这意味着杨树的基因组资源将在柳树基因组研究中发挥最大的作用，例如确定重要性状的QTL基因。我们的数据表明，全基因组复制发生在这两个属的分化之前很久，到目前为止，这两个事件一直被认为是当代的。估计沉默替代率分别为1.28×10-9和1.68×10-9，接近其他多年生植物的替代率，但远低于一年生植物的替代率。
Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya. We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41). The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 × 10-9 and 1.68 × 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.
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影响因子：
2.3
作者：
Manchester, Steven R.;Judd, Walter S.;Handley, Bruce
通讯作者：
Handley, Bruce
DOI：
10.1073/pnas.0900906106
发表时间：
2009-04-07
影响因子：
11.1
作者：
Fawcett, Jeffrey A.;Maere, Steven;Van de Peer, Yves
通讯作者：
Van de Peer, Yves
影响因子：
2.4
作者：
Hanley, S. J.;Mallott, M. D.;Karp, A.
通讯作者：
Karp, A.
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
影响因子：
3.5
作者：
Azaiez, Aida;Boyle, Brian;Seguin, Armand
通讯作者：
Seguin, Armand