Total alkalinity and total hardness are familiar variables in aquatic animal production. Aquaculturists—both scientists and practitioners alike—have some understanding of the two variables and of methods for adjusting their concentrations. The chemistry and the biological effects of alkalinity and hardness, however, are more complex than generally realized or depicted in the aquaculture literature. Moreover, the discussions of alkalinity and hardness—alkalinity in particular—found in water chemistry texts are presented in a rigorous manner and without explanation of how the two variables relate to aquaculture. This review provides a thorough but less rigorous discussion of alkalinity and hardness specifically oriented toward aquaculture. Alkalinity and hardness are defined, their sources identified, and analytical methods explained. This is followed by a discussion of the roles of the two variables in aquaculture, including their relationships with carbon dioxide, pH, atmospheric pollution, ammonia, and other inorganic nitrogen compounds, phytoplankton communities, trace metals, animal physiology, and clay turbidity. Liming and other practices to manage alkalinity and hardness are explained. Changes in alkalinity and hardness concentrations that occur over time in aquaculture systems are discussed. Emphasis is placed on interactions among alkalinity, hardness, water quality, and aquacultural production.

Background: SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs.

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A genetic linkage map of the channel catfish genome (N ¼ 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

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