Tiến Sĩ Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)

LUẬN ÁN TIẾN SĨ ( Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University)
NĂM 2013

OPTIMISATION OF SELECTIVE BREEDING PROGRAM FOR NILE TILAPIA (OREOCHROMIS NILOTICUS)
Tối ưu hoá các chương trình chọn giống cho cá rô phi (Oreochromis niloticus)

Contents
5 Abstract
9 1 – General introduction
21 2 – A comparison of microsatellites and SNPs in parental assignment in the GIFT strain of Nile tilapia (Oreochromis niloticus): the power of exclusion
53 3 – Genetic parameters for reproductive traits in Nile tilapia (Oreochromis niloticus): I. Spawning success and time to spawn
77 4 – Genetic parameters for reproductive traits in Nile tilapia (Oreochromis niloticus): II. Fecundity and fertility
99 5 – Heritability and genotype by environment interaction estimates for harvest weight, growth rate, and shape of Nile tilapia (Oreochromis niloticus) grown in river cage and VAC in Vietnam
127 6 – General discussion
147 Summary
153 Samenvatting
159 Publications
163 About the author
167 Training and education
173 Acknowledgement
176 Colophon


1.1 Introduction
Nile tilapia
Tilapia is the common name used to classify three groups of Cichlidae fish: Tilapia, Sarotherodon, and Oreochromis. Among these, the Nile tilapia (Oreochromis niloticus) is the most cultured species (FAO, 2012). In Vietnam, Nile tilapia is the second most important freshwater species, after the pangasius catfish (Pangasianodon hypophthalmus) (Merican, 2011). The total production of Nile tilapia was estimated to be 20,000 tonnes in 2010 (personal communication). The Mekong Delta region in the South of Vietnam is the major tilapia production area of the country. Nile tilapia is cultured in three production environments: in river cages, in monoculture in ponds and in low-input integrated poly-culture in ponds with a mix of other fish species and livestock species (VAC1). The majority of Nile tilapia production however is conducted in cages in the Mekong river (see e.g. Merican, 2011). Production from VAC ponds is mainly for household consumption and the domestic market.
Selective breeding in Nile tilapia and the GIFT project
There have been several selective breeding programs for Nile tilapia (review by Ponzoni et al. (2011). They are the ‘Genetic Improvement of Farmed Tilapias’ (GIFT), GET-EXCEL (Tayamen, 2004), FaST (Bolivar, 1998), GST (GenoMar Supreme Tilapia) (Zimmermann and Natividad, 2004), and Hainan Progift (Thodesen et al., 2011). Among these projects, the GIFT project is the best documented one (Bentsen et al., 2012; Gjedrem, 2012; Ponzoni et al., 2011). The 10-year GIFT project was initiated in 1988 (Pullin et al., 1991), jointly by Akvaforsk (Institute of Aquaculture Research, Norway) and the International Center for Living Aquatic Resources Management (ICLARM, now renamed the WorldFish Center). The GIFT project was funded, first by the United Nation Development Programme (UNDP), and thereafter co-funded by the Asian Development Bank (ADB). The National Freshwater Fisheries Training and Research Center in Munoz, Nueva Ecija, Philippines, was selected as the location for the project. The GIFT project which was terminated in 1997, produced a vast amount of data and knowledge about tilapia breeding. To this date, not all results from this project have been published (Gjedrem, 2012). At the end of 2000, the WorldFish Center (WFC) teamed up with Acronym for ‘vườn’, ‘ao’ and ‘chuồng’ meaning garden, pond and livestock pen.

1 General introduction
the Malaysian Department of Fisheries, took over the 6th generation of GIFT, and has continued further selection to this date. In 2006, fifty full-sib families of generation 10 were transferred to the Research Institute for Aquaculture No. 2 (RIA2), to initiate the breeding program for GIFT in the Mekong Delta of Vietnam that is described in this study.
In GIFT, harvest weight has been the main trait of interest (Gjedrem, 2012; Ponzoni et al., 2011), with genetic gains for harvest weight ranging from 10 to 15 per cent per generation over 6 generations (Ponzoni et al., 2011). In addition to harvest weight, other traits have been studied in different subsets of GIFT generations including body dimension (Nguyen et al., 2007), fillet yield (Nguyen et al., 2010a), and flesh composition (Nguyen et al., 2010b).
The breeding scheme of the GIFT project is based on Best Linear Unbiased Prediction (BLUP) breeding value estimation using individual information (own performance) and information from relatives (full-sibs, half-sibs, and progeny). The BLUP selection scheme builds on controlled single pair mating to produce full- and half-sib families, and reliable pedigree identification via tagging (Gjerde, 2005).
Reproduction in the GIFT breeding program
While the GIFT breeding program resulted in considerable genetic gain, reproduction remained problematic. The GIFT breeding program applies single pair mating, that is, one male and one female are stocked into a spawning unit (‘hapa’ or tank). This single pair mating prolongs the time required for the production of full- and half-sib families. for GIFT generation 1 to 5, the time for family production ranged from 40 to 101 days in the Philippines (Bentsen et al., 2012), for GIFT 6 to 13 at the WorldFish Center in Penang, Malaysia it was 60 to 180 days (Ponzoni et al., 2011), and for GIFT 11 to 13 in Vietnam (this study) it ranged from 105 to 136 days. The prolonged time for family production increases the time for family rearing in hapas, because tagging can only be conducted when fingerlings in the last produced family reach tagging size. By the time of tagging, the differences in ages and thereby in sizes of fingerlings between- and within-families can be substantial.
For harvest weight, the main selected trait in GIFT, prolonged time for family production reduces accuracy of estimated breeding values (EBV), and increases the 12
1 General introduction
impact of environmental effects common to full-sibs (c2) (Bentsen et al., 2012). In addition, prolonged time for family production increases the generation interval by 3 to 4 months, which reduces genetic gain per generation.
It has been theorised that selection for harvest weight might lead to undesirable correlated responses in spawning success, fecundity, and fertility traits of GIFT Nile tilapia. In many livestock species, long-term selection for high production efficiency resulted in physiological, immunological and reproductive problems (Rauw et al., 1998). Typical reproductive problems are defective eggs and poor semen quality in chicken, delayed age at puberty and farrowing in pigs, and low success rates after insemination in dairy cattle (Rauw et al., 1998). However, in Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), there seems to be no strong unfavourable relationship between growth rate and age at maturity (Gjerde, 1986).