Abstract
Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper, we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and were selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups (LGs). Around one-third of the LGs showed a different recombination rate between sexes, with the female being greater than the male map by a factor of 1.2 (1632.9 to 1359.6 cM, respectively), with most LGs displaying a sigmoid recombination profile. Finally, the sex-determining locus was mapped to position 40.53 cM on LG23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasively measured traits in Nile tilapia.
Highlights
Nile tilapia (Oreochromis niloticus) is an important fresh-water aquaculture species farmed in more than 100 countries including many developing countries in which the species is an essential source of dietary protein (ADB, 2005)
Most of the commercial and farmed Nile tilapia strains are derived from the genetically improved farmed tilapia (GIFT) base strain established in the early 1990s (Eknath et al, 1993)
Nile tilapia breeding programs have relied on traditional breeding approaches based on measurable phenotypes such as weight and length, and have just recently started to implement modern genome-based strategies, such as marker-assisted and genomic selection
Summary
Nile tilapia (Oreochromis niloticus) is an important fresh-water aquaculture species farmed in more than 100 countries including many developing countries in which the species is an essential source of dietary protein (ADB, 2005). Aquaculture has been slower to adopt genomebased selection tools largely due to a lack of genomic resources such as reference genomes, SNP arrays, and linkage maps. Resistance against Bacterial Coldwater Disease (BCWD) (Vallejo et al, 2015a,b, 2017b), infectious pancreatic necrosis (IPN) (Yoshida et al, 2018) and Piscirickettsia salmonis (Yoshida et al, 2017a) in rainbow trout; Piscirickettsia salmonis (Bangera et al, 2017) and resistance against sea lice (Ødegård et al, 2014; Tsai et al, 2016; Correa et al, 2017a) in Atlantic salmon; Piscirickettsia salmonis in coho salmon (Barría et al, 2018); and juvenile growth rate in common carp (Tsai et al, 2015b; Palaiokostas et al, 2018). Lots of GWAS studies have been conducted in these species, primarily for disease resistance (Correa et al, 2015; Liu et al, 2015; Palti et al, 2015; Vallejo et al, 2017a; Barría et al, 2018), resistance against sea lice (Davidson and Yáñez, 2016; Correa et al, 2017b), sexual maturity (Ayllon et al, 2015; Gutierrez et al, 2015) and some carcass quality traits (Sodeland et al, 2013; Tsai et al, 2015a; Gonzalez-Pena et al, 2016; Yoshida et al, 2017b)
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