Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G.; Dunham, Rex A.; Liu, Zhanjiang

doi:10.1093/dnares/dsu038

Cited by 76 publications

(81 citation statements)

References 64 publications

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“…A remarkable RF difference was observed between males and females around heterochromatic structures, especially the centromeres, where females hardly showed RF decay. This fact is the main responsible for the length difference between male and female maps of turbot, as reported previously in other fish species 58 , 66–68 . It is tempting to ascribe the different RF between males and females observed in fish 19 , 66 to different crossing-over patterns around heterochromatic blocks.…”

Section: Discussionsupporting

confidence: 75%

“…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 . The average number of SNPs in the 31 full-sib families analysed in our work was in the upper range reported in the most recent linkage mapping studies (5–6k SNPs) and ∼40 individuals were genotyped at each family.…”

Section: Discussionmentioning

confidence: 99%

“…Genetic maps of bony fish reported to date have been based on a few families, 19 , 38 , 58 and thus, the presence of inter-individual rearrangements affecting marker order has been scarcely addressed. Previous information showed that, despite a general macrosyntenic 1:1 pattern in Acanthopterygii 38 and specifically in Pleuronectiformes, a huge intrachromosomal reorganisation (mainly inversions) has taken place along flatfish evolution 9 , 34 .…”

Section: Discussionmentioning

confidence: 99%

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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

Maroso¹,

Hermida

Millán³

et al. 2018

DNA Research

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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.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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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

Maroso¹,

Hermida

Millán³

et al. 2018

DNA Research

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“…A high-density genetic linkage map was generated for channel catfish, Ictalurus punctatus and integrated with a physical map by application of genotyping of families with the 250K SNP array Li et al, 2015). Over 50 000 SNPs were placed on this linkage map, which covered 90% (867) Mb of the catfish genome.…”

Section: Linkage Mapsmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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“…Besides in model species, investigations of recombination in non-model species are also needed in order to clarify both the general and species-specific patterns of recombination [17]. Due to the importance in genetic studies, high-density genetic maps have been constructed in a few economically important teleosts [18], e.g., Atlantic salmon [19–21], Coho salmon [22], channel catfish [23] and Japanese flounder [24], European sea bass [25], Nile tilapia [26], rainbow trout [27] and lake whitefish [28]. …”

Section: Introductionmentioning

confidence: 99%

Construction of high-resolution recombination maps in Asian seabass

et al. 2017

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BackgroundA high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing.ResultsA high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males.ConclusionsThese high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users.

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Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Cited by 76 publications

References 64 publications

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

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

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Construction of high-resolution recombination maps in Asian seabass

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