SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft Genome

Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.

巴西橡胶树（Hevea brasiliensis），又称橡胶树，是重要的经济作物，其天然乳胶产量占全球绝大多数份额。该树种的核基因组包含18条染色体，总长度约为2.15 Gb。当前已发布的橡胶树参考基因组组装结果包含1,150,326个支架序列（scaffold），长度范围为200 bp至531,465 bp，总组装长度达1.1 Gb，其中仅有143个支架序列（总长度7.6 Mb）被锚定至连锁群中。本研究对6个橡胶树品种开展RNA测序（RNA-seq）以鉴定单核苷酸多态性（SNPs）与插入缺失多态性（InDels），并基于该序列变异信息开展目标序列富集与高通量测序，对RRIM 600与RRII 105橡胶树杂交组合的149个后代个体进行SNP基因型分型。基于上述分型数据，我们构建了一套遗传连锁图谱，将来自3,009个支架序列的24,424个重叠群（contig）锚定至18个连锁群中，该锚定区域总长度为115 Mb，占已发布参考基因组序列的10.4%。每个连锁群包含319至1,367个SNP位点，对应60至194个非冗余标记位点，遗传长度范围为156 cM至336 cM。该遗传连锁图谱覆盖了橡胶树预测基因总数69,300中的20,143个，可用于后续遗传定位研究并助力参考基因组组装的优化完善。