Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

Abstract

Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.

High-resolution genetic map and QTL analysis of growth-related traits ofHevea brasiliensiscultivated under suboptimal temperature and humidity conditions

“…Regions with a low marker density in the base map (i.e., LG13 and LG15), with gaps up to 24.2 cM 418 and 32.5 cM, were saturated. As in other linkage mapping studies using large-scale genotyping 419 methodologies for H. brasiliensis (Pootakham et al, 2015;Shearman et al, 2015), substantial 420 intervals (≥ 10 cM) were observed, supporting the results obtained in different plant species 421 (Guajardo et al, 2015;Marubodee et al, 2015;Boutet et al, 2016;McCallum et al, 2016). The 422 remaining gaps are common and even expected using GBS, mainly due to centromeric regions, 423…”

“…brasiliensis for several years (Pootakham et al, 2015;Shearman et al, 2015), no studies on the 420 beneficial effects of SSR markers, such as those performed on Brassica species (Yang et al, 2016), 421 have been performed for Hevea. 422…”

“…Because increasing marker densities in low-409 resolution regions can be beneficial for traditional mapping approaches and QTL mapping, GBS has 410 become a valid and interesting alternative. Although GBS technology has been available for H. 411 brasiliensis for several years (Pootakham et al, 2015;Shearman et al, 2015), no studies on the 412 beneficial effects of SSR markers, such as those performed on Brassica species , 413 have been performed for Hevea. 414…”

Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

“…In recent years, advances in next-generation sequencing technology (NGS) have lowered the cost of 72 DNA sequencing to the point that genotyping-by-sequencing (GBS) (Elshire et al, 2011) is now 73 feasible for high-diversity, large-genome species, and a genetic map has been developed using the 74 GBS approach (Pootakham et al, 2015). GBS utilizes restriction enzymes to capture a reduced 75…”

Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis)

“…A recently developed genotyping-by-sequencing (GBS) approach employs restriction endonucleases to ensure that homologous portions of the genome from multiple individuals are targeted for sequencing (Elshire et al 2011). GBS has been demonstrated to be quick, affordable, and highly robust across a range of species (Gao et al 2015; Poland et al 2013; Pootakham et al 2015b; Russell et al 2013). The key advantage of GBS is that the technique can be applied to crop species with poorly characterized genome.…”