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Catfishes of the family Pangasiidae are an important group that contributes significantly to the fisheries of the Mekong River basin. In recent times the populations of several catfish species have declined, thought to be due to overfishing and habitat changes brought about by anthropogenic influences. The Mekong giant catfish Pangasianodon gigas Chevey, 1913 is listed as Critically Endangered on the IUCN Red List. In the present study, we assessed the level of genetic diversity of nine catfish species using sequences of the large subunit of mitochondrial DNA (16S rRNA). Approximately 570 base pairs (bp) were sequenced from 672 individuals of nine species. In all species studied, haplotype diversity and nucleotide diversity ranged from 0.118 AE 0.101 to 0.667 AE 0.141 and from 0.0002 AE 0.0003 to 0.0016 AE 0.0013, respectively. Four haplotypes were detected among 16 samples from natural populations of the critically endangered Mekong giant catfish. The results, in spite of the limited sample size for some species investigated, indicated that the level of genetic variation observed in wild populations of the Mekong giant catfish (haplotype diversity = 0.350 AE 0.148, nucleotide diversity = 0.0009 AE 0.0008) is commensurate with that of some other related species. This finding indicates that (1) wild populations of the Mekong giant catfish might be more robust than currently thought or (2) present wild populations of this species carry a genetic signature of the historically larger population(s). Findings from this study also have important implications for conservation of the Mekong giant catfish, especially in designing and implementing artificial breeding programme for restocking purposes.

Genes affecting aquaculture performance, or quantitative trait loci (QTLs), can be mapped in relation to naturally occurring genetic markers. Knowledge of linkages between marker and QTL alleles can be used for marker-assisted selection (MAS), increasing the rate of genetic progress above that for selective breeding alone. Although fish may provide an attractive system for detecting QTLs and executing MAS, QTL detection and MAS have not yet been practiced on an aquaculture species. We review the technical literature on QTL detection and MAS in other species in order to advance critical discussion of how best to pursue QTL detection and MAS in fish. Over 100 highly polymorphic markers would be needed for complete genome coverage, although a subset of QTLs might be detected with fewer markers. The need for cost-effectively screening markers suggests polymerase chain reaction-based screening of a collection of microsatellite loci or RAPDs (random amplified polymorphic DNAs). Experimental power calculations suggest that because markers will have to be screened within large progeny groups, selective or sequential genotyping or screening of bulked DNA samples are needed for cost-effective detection of QTLs. With well-designed experiments, QTL detection and MAS might prove an effective adjunct to conventional selective breeding in fishes.

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The critically endangered Pangasianodon gigas is endemic to the Mekong River. Despite its importance, little is known about its genetic diversity and conservation efforts are hampered. Ten polymorphic dinucleotide microsatellite primer pairs were developed from DNA of P. gigas . The analysis of 20 individuals from hatchery stocks using these primers resulted in two to six alleles/locus; H O = 0.05 -0.95; H E = 0.05 -0.81. All but one locus (Pg-3) conformed to Hardy-Weinberg expectation. Eight, six and seven primer pairs were amplified with the DNA from Pangasianodon hypophthalmus , Pangasius larnaudii and Pangasius sanitwongsei , respectively. These markers will be useful for genetic monitoring of wild and hatchery stocks of these pangasiids.