Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon
Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon
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DOI：
10.1007/s00122-011-1598-4
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发表时间：
2011-08-01
影响因子：
5.4
通讯作者：
Vogel, John Philip
中科院分区：
文献类型：
--
作者：
Huo, Naxin;Garvin, David F.;Vogel, John Philip
小型一年生草二穗短柄草（Brachypodium distachyon）正迅速成为一个强大的模型系统，以研究独特的草。短柄草属植物资源丰富，包括全基因组测序、高效转化和大量种质资源。我们利用单核苷酸多态性（SNP）标记和476个个体的F-2作图群体构建了短柄草属植物的遗传连锁图。通过单拷贝基因组序列的靶向重测序鉴定SNP。使用Illumina GoldenGate基因分型平台，我们将558个标记放置到对应于短柄草属的五条染色体的五个连锁群中。异常长的总遗传图谱长度，1，598厘米摩根（cM），表明短柄草作图群体具有高重组率。通过比较基因图谱和基因组特征，我们发现重组率与基因密度呈正相关，与保留着丝粒重复序列的祖先染色体融合的重复区域和位点呈负相关。相邻基因组区域的重组率高与低的比较显示，种间同线性和重组率之间呈正相关。
The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. Many Brachypodium resources have been developed including a whole genome sequence, highly efficient transformation and a large germplasm collection. We developed a genetic linkage map of Brachypodium using single nucleotide polymorphism (SNP) markers and an F-2 mapping population of 476 individuals. SNPs were identified by targeted resequencing of single copy genomic sequences. Using the Illumina GoldenGate Genotyping platform we placed 558 markers into five linkage groups corresponding to the five chromosomes of Brachypodium. The unusually long total genetic map length, 1,598 centiMorgans (cM), indicates that the Brachypodium mapping population has a high recombination rate. By comparing the genetic map to genome features we found that the recombination rate was positively correlated with gene density and negatively correlated with repetitive regions and sites of ancestral chromosome fusions that retained centromeric repeat sequences. A comparison of adjacent genome regions with high versus low recombination rates revealed a positive correlation between interspecific synteny and recombination rate.