Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon

Abstract

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P < 0.05) segregation distortion across all 11 chromosomes, and 513 (83.3 %) of these distorted loci showed distortion in favor of the elite watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.

Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico

“…After evaluation, we found an overall genotyping error for the obtained SNP markers close to 4 %, which is similar to what has been previously reported for NGS derived data [37]. The number of exploitable SNPs, repeatability and missing data is similar to what has been obtained using the same technique with other crops [22, 38, 39]. The obtained SNP markers seem to be located mostly in gene-rich parts of the genome, making them an excellent resource for traditional gene mapping or even association mapping assays in coffee trees.…”

Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

“…The Pst I-compatible (forward) adapter incorporated an Illumina flowcell attachment region, sequencing primer sequence and a varying length barcode region [58, 62]. The reverse adapter also contained a flowcell attachment region, and was compatible with the Sph I cut-site overhang.…”

“…Samples were processed in batches of 94, with 15% of all samples in a batch randomly selected for replication, to provide a basis for assessing region recovery and genotyping reproducibility. Target “mixed” fragments [62], containing both Sph I and Nla III cut-sites were selectively amplified using custom designed primers for each sample, under the following PCR conditions: initial denaturation at 94 °C for 1 min, then 30 cycles of 94 °C for 20s, 58 °C for 30s and 72 °C for 45 s, followed by a final extension step at 72 °C for 7 min. Amplified samples were subsequently cleaned using a GenElute PCR Clean-up Kit (Sigma-Aldrich, cat.# NA1020-1KT), on a TECAN Freedom EVO150 automated liquid handler.…”

Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

“…The many advantages of DArTseq include no prior knowledge about sequencing of the plant genome and the capacity to produce high-density results, scoring thousands of unique genomic-wide DNA fragments in one single experiment with low-cost genotype information (Jaccoud et al, 2001;Kilian et al, 2016). The DArTseq method is used to discriminate diverse species for population studies, genetic diversity studies, germplasm characterization (Cruz et al, 2013), association studies (Courtois et al, 2013;Phuong Phung et al, 2014), and genetic mapping (Ren et al, 2015). To date, DArTseq genotyping has also been used for genetic analysis in species genomes, including Sorghum bicolor (Mace et al, 2008), rye (Bolibok-Brągoszewska et al, 2009), Lesquerella and related species (Cruz et al, 2013), japonica rice (Courtois et al, 2013), watermelon (Ren et al, 2015), and pineapple (Kilian et al, 2016).…”