High-Resolution Genetic Map for Understanding the Effect of Genome-Wide Recombination Rate on Nucleotide Diversity in Watermelon

Abstract

We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima’s D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.

Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L

“…Genomic DNA was isolated using the DNeasy plant mini kit (QIAGEN, Germany), and GBS was as described4445. Briefly, genome complexity was reduced by digesting total genomic DNA from individual samples with the ApeKI, a type II restriction endonuclease that recognizes a degenerate 5-bp sequence (GCWGC, where W is A or T), which creates a 5′ overhang (3 bp) and is partially methylation-sensitive (will not cut if the 3′ base of the recognition sequence on both strands is 5-methylcytosine).…”

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

“…Using an integrated high-density genetic map (Ren et al, 2014), 90.3% (378.7 Mb) of the 'Charleston Gray' assembly were anchored to 11 linkage groups, and 90.5% of the anchored scaffolds (342.8 Mb) were oriented. We assigned orientation to an additional of 9.9 Mb of scaffolds, according to two other recently developed genetic maps (Branham et al, 2017;Reddy et al, 2014). Furthermore, based on the genome synteny between '97103' and 'Charleston Gray', an additional 26.6 Mb of the 'Charleston Gray' scaffolds were oriented, and 3.8 Mb of scaffolds were anchored.…”

Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers

“…The described system is implemented in the interactive user-friendly software MultiPoint-UDM (MUDM) for building ultradense genetic maps for controlled crosses (backcross, doubled haploids, F2, RIL populations); further development will also include F1 progeny of outbred species and multi-parental populations. Our approach for premapping filtering, together with previously developed algorithms (Mester et al 2003;Ronin et al 2010) implemented in the MultiPoint software, enable quality genetic maps to be built, with realistic map length and reliable marker orders (e.g., Avni et al 2014;Reddy et al 2014). A trial version for Windows with simulated examples can be downloaded using the link: http://evolution.haifa.ac.il/images/ stories/Software/MultiPointUltradense_Demo.zip.…”