Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

Abstract

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

“…The reduced cost of the new genotyping by sequencing (GBS) techniques has facilitated the development of highly dense genetic maps in aquaculture fish species, 3 , 17–19 including turbot 21 . Here, we combined for the first time a high number of markers and families for a deep mapping analysis aimed at integrating genetic and physical map resources in turbot to understand its genome organisation and variation, a study not performed to date in fish 23 , 58 .…”

“…High-density (HD) genetic maps provide information on genome organisation by establishing the cartography of thousands of markers, which can aid to disentangle the genetic architecture of productive or evolutionary traits. Moreover, these maps represent an essential tool for comparative genomics and can facilitate whole genome assembly 2 , 3 . The advent of next generation sequencing (NGS) has dramatically reduced the cost and time required for genomic analysis, 4 , 5 thus contributing to a fast increase of genomic resources.…”

Meta‐analysis of chromosome‐scale crossover rate variation in eukaryotes and its significance to evolutionary genomics

“…Studies estimating CO rates from linkage disequilibrium in population samples, presenting information from a single chromosome only, or performed with low marker resolution (fewer than ~20 markers per chromosome on average) were ignored. In a single case (Nunes et al., ), we considered a marker‐dense data set presenting genetic map position against marker order (instead of Mb position in a physical assembly). Visually comparing patterns of cM vs. Mb to cM vs. marker order in another organism in which both data types were available (Dohm et al., , ) confirmed that the latter data type also reliably captures broad‐scale CO patterns (see also Nachman & Churchill, ).…”

“…Next, we defined the length of each chromosome as the Mb position of the terminal marker interval mid‐point, calculated mean CO periphery‐bias and chromosome length across the chromosomes within each species and assessed if chromosome length predicted the CO distribution when using species as data points. This was carried out using Spearman's rank correlation (hereafter simply “correlation” because we always applied the Spearman method to quantify the strength of association between variables) and included all species except the single one lacking physical chromosome positions (Nunes et al, ). The correlation between CO periphery‐bias and chromosome length was further explored within species (i.e., using chromosomes as data points).…”

Genetic Applications in the Conservation of Neotropical Freshwater Fish

“…Hybrid fish originating from serrasalmid species such as the pacu (P. mesopotamicus), tambaqui (C. macropomum) and pirapitinga (P. brachypomus), or from pimelodid species such as the pintado (P. corruscans) and cachara (Pseudoplatystoma reticulatum), are considered commercially valuable and have high growth rates and have other characteristics that are useful to the commercial sector such as resistance and better reproductive performance [199]. The interest in hybrid production may be due to the lack of knowledge about the pure species, mainly in genetic breeding approaches [200].…”