Construction of relatedness matrices using genotyping-by-sequencing data.

BACKGROUND: Genotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by reducing the mean sequencing depth, but this results in genotype calls of lower quality. A common analysis strategy is to filter SNPs to just those with sufficient depth, thereby greatly reducing the number of SNPs available. We investigate methods for estimating relatedness using GBS data, including results of low depth, using theoretical calculation, simulation and application to a real data set. RESULTS: We show that unbiased estimates of relatedness can be obtained by using only those SNPs with genotype calls in both individuals. The expected value of this estimator is independent of the SNP depth in each individual, under a model of genotype calling that includes the special case of the two alleles being read at random. In contrast, the estimator of self-relatedness does depend on the SNP depth, and we provide a modification to provide unbiased estimates of self-relatedness. We refer to these methods of estimation as kinship using GBS with depth adjustment (KGD). The estimators can be calculated using matrix methods, which allow efficient computation. Simulation results were consistent with the methods being unbiased, and suggest that the optimal sequencing depth is around 2-4 for relatedness between individuals and 5-10 for self-relatedness. Application to a real data set revealed that some SNP filtering may still be necessary, for the exclusion of SNPs which did not behave in a Mendelian fashion. A simple graphical method (a 'fin plot') is given to illustrate this issue and to guide filtering parameters. CONCLUSION: We provide a method which gives unbiased estimates of relatedness, based on SNPs assayed by GBS, which accounts for the depth (including zero depth) of the genotype calls. This allows GBS to be applied at read depths which can be chosen to optimise the information obtained. SNPs with excess heterozygosity, often due to (partial) polyploidy or other duplications can be filtered based on a simple graphical method.

A national survey data for the technical and economic assessment of African catfish production in Nigeria before and during the COVID-19 period.

This data article presents a dataset obtained from a national survey of African catfish production in Nigeria. The African catfish is an important aquaculture species in various regions in the world and it is, after Tilapia, the most commonly cultured fish in Africa. Nigeria's share in the global production of African catfish exceeds 67 %. The dataset encompasses data collected from ten major catfish-producing states in Nigeria, with a focus on two distinct periods: before and during the COVID-19 pandemic. A total of 609 operations were captured for the pre-COVID and 509 for the COVID period. The dataset includes a wide array of variables, covering the cost and quantities of inputs and outputs, socioeconomic factors, market dynamics, feed types, challenges faced by farmers, scale of production, and farmers' level of experience. It offers valuable insights and opportunities for various stakeholders. Researchers can utilize it to explore production performance, resilience, and adaptation strategies. Industry players, including catfish farmers and suppliers, can make data-driven decisions to enhance their operations. Policymakers can formulate evidence-based policies to support sustainable growth in the catfish farming sector. Other developing countries can draw lessons from Nigeria's experiences to bolster their aquaculture sectors.