Second-generation Genetic Linkage Map of Catfish and Its Integration with the BAC-based Physical Map

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2012 Oct 11

PMID 23050234

Citations 28

Authors

Parichart Ninwichian

Eric Peatman

Hong Liu

Huseyin Kucuktas

Benjaporn Somridhivej

Shikai Liu

Ping Li

Yanliang Jiang

Zhenxia Sha

Ludmilla Kaltenboeck

Jason W Abernathy

Wenqi Wang

Fei Chen

Yoona Lee

Lilian Wong

Shaolin Wang

Jianguo Lu

Zhanjiang Liu

Affiliations

Soon will be listed here.

Abstract

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ~52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds.

Citing Articles

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Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in .

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Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish.

Shi H, Zhou T, Wang X, Yang Y, Wu C, Liu S Mol Genet Genomics. 2018; 293(6):1365-1378.

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