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

Abstract

Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.

Figure 1.

Families selected for linkage analysis in S. maximus. Male (M) × female (F) crosses and the number of offspring per family are indicated. Note the presence of several half-sib families sharing the father or the mother.

Figure 2.

Consensus genetic map of S. maximus using the three most informative full-sib families; genetic distance in cM in the left bar; the position of centromeres (C) or genetic markers far from centromere (T) in acrocentric chromosomes are indicated.

Figure 3.

Correspondence between physical (abscissae) and genetic (ordinates) maps showing the dispersion of dots around the centromere at LG11 (A) and the difference between male and female maps at LG11 (B). The vertical bar in both figures show the position of the centromere according to Martínez et al. (2008). Genetic markers corresponding to different scaffolds are shown in different colors.

Figure 4.

Particular drawings denoting the lack of collinearity between two individual genetic maps of S. maximus: Female Fam09 vs Male Fam07 maps; consecutive LGs are represented in different colours from LG01 (left bottom) to LG23 (right top).

Figure 5.

LASTZ plots between S. maximus linkage groups (LG) and chromosomes (Chr) of P. olivaceus and C. semilaevis: (A) LG02 vs Chr06 and 14 of P. olivaceus; (B) LG02 vs Chr13 and 14 of C. semilaevis; (C) LG04 vs Chr07 of P. olivaceus; (D) LG04 vs Chr05 C. semilaevis. The gross vertical bar points the position of centromeres according to Martínez et al. (2008) and the light ones the limits between consecutive scaffolds.