USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA.
Theor Appl Genet. 2011 Aug;123(3):455-64. doi: 10.1007/s00122-011-1598-4. Epub 2011 May 20.
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.
一年生草本植物短柄草（Brachypodium）正迅速成为研究禾本科特有问题的强大模式系统。已经开发了许多短柄草资源，包括全基因组序列、高效转化和大量种质资源。我们利用单核苷酸多态性（SNP）标记和一个由 476 个个体组成的 F2 作图群体，开发了短柄草的遗传连锁图谱。通过对单拷贝基因组序列的靶向重测序，鉴定了 SNPs。我们使用 Illumina GoldenGate 基因分型平台，将 558 个标记分配到五个连锁群中，对应于短柄草的五个染色体。异常长的总遗传图谱长度为 1598 厘摩（cM），表明短柄草作图群体具有高重组率。通过将遗传图谱与基因组特征进行比较，我们发现重组率与基因密度呈正相关，与重复区域和保留着着丝粒重复序列的祖先染色体融合位点呈负相关。比较具有高重组率和低重组率的相邻基因组区域，发现种间同线性与重组率之间存在正相关。
