Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map.
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.
The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama 36849, USA.
Parichart
P
Ninwichian
Eric
E
Peatman
Hong
H
Liu
Huseyin
H
Kucuktas
Benjaporn
B
Somridhivej
Shikai
S
Liu
Ping
P
Li
Yanliang
Y
Jiang
Zhenxia
Z
Sha
Ludmilla
L
Kaltenboeck
Jason W
JW
Abernathy
Wenqi
W
Wang
Fei
F
Chen
Yoona
Y
Lee
Lilian
L
Wong
Shaolin
S
Wang
Jianguo
J
Lu
Zhanjiang
Z
Liu
D000818:Animals; D002397:Catfishes / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D005260:Female; D008040:Genetic Linkage; D023281:Genomics; D008297:Male; D018895:Microsatellite Repeats; D020161:Physical Chromosome Mapping; D040641:Quantitative Trait Loci