Comparing genomic signatures of selection between the Abbassa Strain and eight wild populations of Nile tilapia (Oreochromis niloticus) in Egypt

Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time

Dissemination Strategy for Three Spotted Tilapia in Zambia

Background & Report Objectives The Zambia Aquaculture Enterprise Development Project (ZAEDP) was launched by the Government of Zambia in 2017 with funding from the African Development Bank. As part of ZAEDP, The Zambian government, with support from WorldFish as technical advisors have established a genetic improvement program for Three Spotted Tilapia, a key indigenous Tilapia species perceived to possess good potential for aquaculture production within Zambian production systems. The genetic improvement program seeks to establish the foundation for future supply of genetically improved Three Spotted Tilapia fingerlings (seed) to the Zambian aquaculture industry.This report comprises the two primary areas of scope described below. 1. Assess the status and potential of the Zambian aquaculture industry, identifying the market opportunity for genetically improved Three Spotted Tilapia seed and subsequent requirements for development of a commercially sustainable breeding program. 2. Identify appropriate industry monitoring systems, data requirements and applicable standards/protocols to support the operations and management of the hatchery sector, particularly the genetic improvement nucleus

Understanding gendered trait preferences: Implications for client-responsive breeding programs

Open Access Article; Published online: 30 Aug 2022Client-responsiveness is a foundation for effectiveness of public sector breeding programs in agriculture, aquaculture and livestock. However, there remains a considerable lack of clarity about what this means, specifically in terms of how programs can be gender-responsive. This study contributes to addressing that need. It does so through sharing higher-level insights emerging from the combined experiences of eight gendered trait preference cases from across nine countries in Asia and Africa. The cases spanned crops, fish and livestock. This study inquires into the nature of gendered trait preference information that can be generated, if there are systematic gendered preference differences and how to understand these, and implications for breeding programs seeking to be more gender-responsive. Key findings include that while not all data are immediately usable by programs, the information that is generated through mixed method, intersectional gender preference assessments usefully deepens and widens programs’ knowledge. The study evidences differences in trait preferences between women and men. It also reveals that these differences are more complex than previously thought. In doing so, it challenges binary or homogenous models of preferences, suggesting instead that preferences are likely to be overlapping and nuanced. The study applies a novel ‘Three models of gendered trait preferences’ framework and sub-framework and finds these useful in that they challenge misconceptions and enable a needed analytical nuance to inform gender-responsive breeding programs. Finally, the study highlights implications and offers a call to action for gender-responsive breeding, proposing ways forward for public breeding programs, teams and funding agencies. These include investments in interdisciplinary capabilities and considerations for navigating trade-offs while orienting to sustainable development goals

Livestock and Fish animal genetics flagship review and plans

John Benzie to the CGIAR Research Program on Livestock and Fish review and planning meeting, 23-26 March 201

Mitochondrial DNA reveals genetic differentiation between Australian and Indonesian pearl oyster Pinctada maxima (Jameson 1901) populations

A total of 234 individual silver-lipped pearl oyster (Pillctada maxima) from six populations in Australia and two\ud populations in Indonesia were analyzed for genetic variation within a 6S0-base pair region of the mitochondrial DNA COl gene using restriction fragment length polymorphism analysis. The Indonesian populations were markedly different from all Australian populations\ud examined, and the differences were greater than that expected on the basis of their geographical separation. In contrast with this broader regional pattern of genetic differentiation, the Australian populations sampled were not significantly differentiated from one another, and a high degree of connectivity was observed among Western Australian pearl oyster populations. In addition. these genetic data show that Western Australian P. maxima populations have a closer tie to those from the northern Australian coast than with populations in Indonesia. This regional pattern of genetic separation is evident despite the proximity of Indonesia to the eastern Indian Ocean locations sampled and the potential for dispersal afforded by the southward currents of the Indonesian throughflow