Genetic Computation Ltd.

Aquaculture and fisheries genetics breed improvement, selective breeding and genetic conservation broodstock, fry & fingerling evaluation

Tilapia, Salmon, Trout, Shrimp, Prawn, Penaeus, Litopenaeus, Macrobrachium, Oreochromis

Aquaculture and Genetic Conservation

Genetic Computation Limited (GCL) is a private consulting company in aquaculture and fisheries genetics and conservation. The emphasis is selective breeding procedures that minimize inbreeding and loss of genetic diversity, while achieving rapid genetic gain in production traits. Genetic Computation Ltd. has worked with, and is continuing to work with, some of the world's largest aquaculture companies as well as with much smaller companies to design low-cost, low inbreeding, genetic improvement systems. GCL also consults on genetic biodiversity and genetic contamination issues, breeder's rights and the economic value of indigenous aquacultural genetic resources.

The original purpose of this website was educational, to point out some important, new papers which have been published in journals that are not primarily devoted to aquaculture or fisheries. The papers give useful insights on the management of broodstock, breeding, stock and strain improvement, disease susceptibility, and genetic conservation. The journals can be hard to find in many parts of the world. The "Hard-to-find papers" button at the top of the page will take you to the titles of the publications I came across, with my notes on why they deserve notice.

The most recent posting to the Hard-to-find papers page was in late 2009. I intend to begin posting again when pressure of work eases off a bit. (This was written in October 2015.)

Guidance for small-scale genetic improvement

Macrobrachium farm

Workers collect big shrimp from a commercial crop to use as broodstock.

Guidance for super-intensive genetic improvement

Tilapia farm

Oxygen is blown into the water and CO2 is blown out into a greenhouse growing tomatoes.

Genetic erosion

African reservoirs

Genetic environmental deterioration in some African reservoirs and aquaculture broodstocks over time.

Regional genetic quality

Hatchery types

Ongoing research on sustaining genetic quality and diversity at all scales of production in complex, real-world, socio-economic environments.

Roger W. Doyle, Ph.D.

Professional background

Roger Doyle Currently President of Genetic Computation Ltd., a consulting company in aquaculture and conservation genetics. Retired Professor of Biology and Founding Director of the Marine Gene Probe Laboratory at Dalhousie University in Canada. Former President of the International Association for Aquaculture Genetics and former Coordinator of the Aquaculture Genetics Network in Asia.

MSc and PhD in Biology from Yale University, MSc in Oceanography and Hons. BSc. in Biology and Chemistry from Dalhousie University. Research and study fellowships from North Atlantic Treaty Organization (NATO: Denmark), the FAO Co-operative Program (Rome), the International Atomic Energy Agency (Vienna) and the International Development Research Centre (Singapore).

More than 100 publications in ecology and theoretical and applied genetics, plus editorial appointments, invited keynote lectures, consultancies and visiting professorships in aquaculture, fisheries, fisheries genetics and conservation genetics. Awards include the Elvira E.O. Tan Research Award (South East Asian Fisheries Development Center) and the APICS research gold medal.

Extensive research, development and commercial experience in tilapia, salmon, carp and shrimp genetics (Macrobrachium, L. vannamei, P. monodon) in the Americas, the Middle East, Africa and Asia. Ongoing research programs focus on the effect of long-term domestication on commercially important fitness traits in aquaculture, the maintenance of founder genome diversity in aquacultural broodstocks, and the estimation of inbreeding in aquacultural populations and its effect on susceptibility to disease and environmenal stress.

Publications (aquaculture & fisheries, 1990 and later)

2016 (in press). Doyle, R.W. Inbreeding and disease in tropical shrimp aquaculture: a reappraisal and caution. Aquaculture Research. Published in 2014 open access online/early doi:10.1111/are.12472, 1-15.

2015. Doyle, R.W. Is small-hold tropical aquaculture in a genetic plunge towards extinction? Pages 3 - 18 in M. R. R. Romana-Eguia, F. D. Parado-Estepa, N. D. Salayo, and M. J. H. Lebata-Ramos, editors. Proceedings of the International Workshop on Resource Enhancement and Sustainable Aquaculture Practices in Southeast Asia 2014 (RESA). Southeast Asian Fisheries Development Center, Aquaculture Department, Tigbauan, Iloilo, Philippines.

Doyle, R., Virapat, C., Kamonrat, W. National Broodstock Improvement Network – Concept For Breaking Inbreeding/Disease Feedback Loop. Global Aquaculture Advocate. 18(May/June), 34-34.

2014. Doyle, R.W. 'Big Picture' Connects Shrimp Disease, Inbreeding. Global Aquaculture Advocate. 17 (Sept/Oct), 45-46.

2012. Mandal, A., Rao, D., Karuppaiah, D., Gopalakrishnan, A., Pozhoth, J., Thampi Samraj, Y., Doyle, R.W., 2012. Population genetic structure of Penaeus monodon, in relation to monsoon current patterns in Southwest, East and Andaman coastal waters of India. Gene. 491, 149-157.

2007. Moss, D.R., Arce, S.M., Otoshi, C.A., Doyle, R.W., Moss, S.M. Effects of inbreeding on survival and growth of Pacific White Shrimp Penaeus (Litopenaeus) vannamei. Aquaculture 272 (S1):30-37.

2007. Live gene banking of endangered populations of Atlantic salmon. 2007. O'Reilly, P. T. and R. W. Doyle in E. Verspoor, L. Stradmeyer, and J. Nielsen, eds. The Atlantic Salmon: Genetics, Conservation and Management. London, Blackwell. pp 425-469

2006. Doyle, R.W., Moss, D.R., Moss, S.M. Shrimp copyright: inbreeding strategies effective against illegal copying of genetically improved shrimp. Global Aquaculture Advocate, April/May 2006, 76-79.

2005. Basiao, Z. U., A. L. Arago, and R. W. Doyle. A farmer-oriented Nile tilapia (Oreochromis niloticus) breed improvement program in the Philippines. Aquaculture Research 36:113-119. (Winner of SEAFDEC Elvira Tan award for best paper 2004-2005)

2005. Basiao, Z.U., Eguia, R.V., and R.W. Doyle. Growth response of Nile tilapia fry to salinity stress in the presence of an 'internal reference' fish. Aquaculture Research 36, 712-720.

2005. Moss, S.M., R.W. Doyle, and D.V. Lightner. Breeding shrimp for disease resistance: challenges and opportunities for improvement. In: P. Walker, R. Lester and M.G. Bondad-Reantaso (eds). Diseases in Asian Aquaculture V, pp. 379-393. Fish Health Section, Asian Fisheries Society, Manila .

2003. Li, K., C.A. Field, and R.W. Doyle. Estimation of additive genetic variance components in aquaculture populations selectively pedigreed by DNA fingerprinting.Biometrical Journal 45:61-72.

2003. Doyle, R.W. Contribution of genetics to aquaculture: a socio-economic critique. Fisheries Science 68, Supplement I: 708-713.

2001. Doyle, R.W., R. Perez-Enriquez, M. Takagi, and N. Taniguchi. Selective recovery of founder genetic diversity in aquaculture broodstocks and captive, endangered fish populations. Genetica 111: 291-304.

2001. Doyle, R.W. Increasing genetic diversity in a hatchery without bringing in new breeders. Hatchery International 2 (5):18-20.

2001. Ruzzante, D.E., C.T. Taggart, R.W. Doyle, and D. Cook. Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994. Conservation Genetics 2 (3): 257-269.

2000. Ambali, A. J. D., R. W. Doyle, and D. I. Cook. Development of polymorphic microsatellite DNA loci for characterising Oreochromis shiranus subspecies in Malawi. Journal of Applied Ichthyology 16(3):121-125.

1999. Doyle, R. W. Managing broodstock for on-farm genetic improvement: principles and examples. In Proceedings Simposio Centroamericano de Acuacultura, edited by B. W. Green, H. C. Clifford, M. McNamara and G. M. Moctezuma. San Pedro Sula, Honduras: World Aquaculture Society (C.R.S.P.). pp. 155-162.

1999. Ambali, A. J. D., R. W. Doyle, and D. I Cook. Genetic changes in Oreochromis shiranus (Trewavas) associated with the early stages of national aquaculture development in Malawi. Aquaculture Research 30: (579-588).

1999. Ambali, A.J., R. W. Doyle, and A. O. Maluwa. The potential of small waterbodies as in situ gene banks for aquaculture: a genetic assessment of the Malawian reservoirs. In Proceedings of the Committee for Inland Fisheries for Africa (CIFA): FAO/Fishing News Book. in press.

1999. Basiao, Z. and R. W. Doyle. Test of size-specific mass selection for tilapia cage farming in the Philippines. Aquaculture Research 30:373-378.

1999. Doyle, R. W., B. A. Costa-Pierce, and A. J. Ambali. Forensic aquaculture, or, do you really expect us to believe these fish came from Egypt? Aquaculture 173:7.

1999. Gadagkar, S. R., and R. W. Doyle. A genetic analysis of the growth-behaviour feedback loop in Oreochromis niloticus using DNA fingerprinting. Aquaculture 173:7.

1999. Herbinger, C. M., P. T. O'Reilly, R. W. Doyle, J. M. Wright, and F. O'Flynn. Early Growth Performance of Atlantic salmon full-sib families reared in single family tanks versus in mixed family tanks. Aquaculture 173:105-116.

1997. Costa-Pierce, B. A., and R. W. Doyle. Genetic identification and status of California regional strains in southern California. In Tilapia Aquaculture in the Americas; edited by B. A. Costa-Pierce and J. Rakocy. Baton Rouge, Louisiana: World Aqua. Soc. Books. pp. 1-17.

1997. Takagi, M., Taniguchi, N., Cook, D., and R. W. Doyle. Isolation and characterization of microsatelite loci from red sea bream Pagrus major and detection in closely related species. Fisheries Science 63(2):199-204.

1996. Doyle, R. W., C. M. Herbinger, M. Ball, and G. A. E. Gall, eds. Genetics in Aquaculture V. Amsterdam: Elsevier. 358 pp.

1995. Zhang, J, R W Doyle, X Sun, J Wang, Y Shi, Y Gong, and J Zhu. Rapid response of Jian carp (Cyprinus carpio var. Jian) to on-farm domestication selection in China. Aquaculture 137:277.

1995. Herbinger, C. M., R. W. Doyle, E. R. Pitman, D. Paquet, K. A. Mesa, D. B. Morris, and D. Cook. DNA fingerprint analysis of paternal and maternal effects on offspring growth and survival in communally-reared rainbow trout. Aquaculture 137:245-256.

1995. Doyle, R.W., C. Herbinger, C.T. Taggart, and S. Lochmann. Use of DNA microsatellite fingerprinting to analyse genetic correlations between hatchery and natural fitness. In Uses and Effects of Cultured fishes in Aquatic Ecosystems; edited by H. L. H. Schramm and R. G. Piper. Albuquerque: American Fisheries Society. pp. 205-211.

1995. Doyle, R W, and C M Herbinger. Broodstock improvement strategies based on DNA fingerprinting: examples and cost-benefit analysis. Aquaculture 137:283.

1995. Brzeski, V. J. , and R. W. Doyle. A test of an on-farm selection procedure for tilapia growth. Aquaculture 137:219-230.

1995. Uraiwan, S., Doyle, R. W., and R. Jala. Evidence of genotype environment interaction observed in selected strains of tilapia (Oreochromis niloticus Linn.) during on farm growth comparison. Aquaculture 137: 330.

1994. Ruzzante, D E, and R W Doyle. Evolution of social behaviour in a resource-rich, structured environment. Evolution 47:456-470.

1994. Doyle, R.W., and C. M. Herbinger. The use of DNA fingerprinting for high-intensity, within-family selection in fish breeding. Proceedings 5th World Congress, Genetics Applied to Livestock Production Guelph, Ontario. Canada 19:364-371.

1994. Doyle, R. W., Z. Jiansen, S. Xiaoyi, W. Jianxin, and S. Yonghong. Growth Comparison of different ages and generations of Jian carp (C. carpio). Jour. Fish. Sci. China 1(1):20-24.

1993. Doyle, R W. The use of DNA fingerprint pedigrees for conserving and increasing the productivity of locally adapted aquaculture breeds. In Conservation and Utilization of Aquatic Genetic Resources: F.A.O. Fisheries Report #491. pp. 42-51.

1992. Ruzzante, D E, and R W Doyle. Behaviour, growth and intensity of social interaction among fish. Can. Jour. Statistics 20:222-227.

1991. Doyle, R W., N. L. Shackell, Z. Basiao, S. Uraiwan, T Matricia, and A. J. Talbot. Selective diversification of aquaculture stocks: a proposal for economically sustainable genetic conservation. Can. Jour. Fish. Aquat. Sci. 48 (Suppl. 1):148-154.

1991. Shackell, N, and R W Doyle. Scale morphology as an index of developmental stability and stress resistance of tilapia (O. niloticus). Can. Jour. Fish. Aquat. Sci. 48:1662-1669.

1991. Harris, A S, S Bieger, R W Doyle, and J M Wright. DNA fingerprinting of tilapia Oreochromis niloticus and its application to aquaculture genetics. Aquaculture 92:57-163.

1991. Ruzzante, D E, and R W Doyle. Behavioural and growth responses to the intensity of intraspecific social interaction among medaka (Oryzias latipes). (Pices: Cyprinodontidae.). J. Fish Biol. 37:663-673.

1991. Ruzzante, D E, and R W Doyle. Rapid behavioral changes in medaka (Oryzias latipes) caused by selection for competitive and non-competitive growth. Evolution 45:1936-1946.

1990. Doyle, R W, C A Field, and Z U Basiao. Statistical procedures for using reference fish for comparing the growth of different genetic strains in aquaculture. Proceedings 2nd. Asian Fisheries Forum. 499-502 pp.

1990. Basiao, Z U, and R W Doyle. Interaction between test and reference populations when tilapia strains are compared by the "internal control" technique. Aquaculture 85:207-214.

1990. Eknath, A E, and R W Doyle. Effective population size and rate of inbreeding in aquaculture of Indian major carps. Aquaculture 85:293-305.

1990. Eknath, A E, and R W Doyle. Repeatability of relative size of individuals under communal stocking: implications for size-grading in aquaculture. Paper read at Proceedings 2nd. Asian Fisheries Forum. 45-48 pp.

1990. Robinson, B W, and R W Doyle. Phenotypic correlations among behaviour and growth variables in tilapia: implications for domestication selection. Aquaculture 85:177-186.

1990. Shackell, N, and R W Doyle. 1990. The coordination of growth in juvenile tilapia (Oreochromis mossambicus/hornorum). Proceedings 2nd. Asian Fisheries Forum. Manila. p. 495-498.

1990. Sinervo, B, and R W Doyle. Life-history analysis in "physiological" compared with sidereal time: an example with an amphipod (Gammarus lawrencianus) in a varying environment. Mar. Biol. 107:129-139.

1990. Basiao, Z., and R. W. Doyle. Use of internal reference population for growth rate comparison of tilapia strains. I. Crowded environments. In Proceedings 2nd. Asian Fisheries Forum. Manila: Asian Fisheries Society. pp. 503-506.