Editing Selective breeding (section)

==Selective breeding in aquaculture==
Selective breeding in aquaculture holds high potential for the genetic improvement of fish and shellfish for the process of production. Unlike terrestrial livestock, the potential benefits of selective breeding in aquaculture were not realized until recently. This is because high mortality led to the selection of only a few [[broodstock]], causing inbreeding depression, which then forced the use of wild broodstock. This was evident in selective breeding programs for growth rate, which resulted in slow growth and high mortality.<ref name=gb/>

Control of the reproduction cycle was one of the main reasons as it is a requisite for selective breeding programs. Artificial reproduction was not achieved because of the difficulties in hatching or feeding some farmed species such as eel and yellowtail farming.<ref name=g85>{{Cite journal | doi = 10.1007/BF00462124| title = Improvement of productivity through breeding schemes| journal = GeoJournal| volume = 10| issue = 3| pages = 233–241| year = 1985| last1 = Gjedrem | first1 = T. | bibcode = 1985GeoJo..10..233G| s2cid = 154519652}}</ref>
A suspected reason associated with the late realization of success in selective breeding programs in aquaculture was the education of the concerned people – researchers, advisory personnel and fish farmers. The education of fish biologists paid less attention to quantitative genetics and breeding plans.<ref name=g83>{{Cite journal | doi = 10.1016/0044-8486(83)90386-1| title = Genetic variation in quantitative traits and selective breeding in fish and shellfish| journal = Aquaculture| volume = 33| issue = 1–4| pages = 51–72| year = 1983| last1 = Gjedrem | first1 = T. | bibcode = 1983Aquac..33...51G}}</ref>

Another was the failure of documentation of the genetic gains in successive generations. This in turn led to failure in quantifying economic benefits that successful selective breeding programs produce. Documentation of the genetic changes was considered important as they help in fine tuning further selection schemes.<ref name=gb/>

===Quality traits in aquaculture===
Aquaculture species are reared for particular traits such as growth rate, survival rate, meat quality, resistance to diseases, age at sexual maturation, fecundity, shell traits like shell size, shell color, etc.
*'''Growth rate''' – growth rate is normally measured as either body weight or body length. This trait is of great economic importance for all aquaculture species as faster growth rate speeds up the turnover of production.<ref name=g83/> Improved growth rates show that farmed animals utilize their feed more efficiently through a positive correlated response.<ref name=g85/>
*'''Survival rate''' – survival rate may take into account the degrees of resistance to diseases.<ref name=g85/> This may also see the stress response as fish under stress are highly vulnerable to diseases.<ref name=g83/> The stress fish experience could be of biological, chemical or environmental influence.
*'''Meat quality''' – the quality of fish is of great economic importance in the market. Fish quality usually takes into account size, meatiness, and percentage of fat, color of flesh, taste, shape of the body, ideal oil and omega-3 content.<ref name=g85/><ref>{{cite journal|last1=Joshi|first1=Rajesh|last2=Woolliams|first2=John|last3=Meuwissen|first3=Theo MJ|title=Maternal, dominance and additive genetic effects in Nile tilapia; influence on growth, fillet yield and body size traits|journal=Heredity|volume=120|issue=5|pages=452–462|date=Jan 2018|doi=10.1038/s41437-017-0046-x|pmid=29335620|pmc=5889400|bibcode=2018Hered.120..452J }}</ref>
*'''Age at sexual maturation''' – The age of maturity in aquaculture species is another very important attribute for farmers as during early maturation the species divert all their energy to gonad production affecting growth and meat production and are more susceptible to health problems (Gjerde 1986).
*'''Fecundity''' – As the fecundity in fish and shellfish is usually high it is not considered as a major trait for improvement. However, selective breeding practices may consider the size of the egg and correlate it with survival and early growth rate.<ref name=g85/>

===Finfish response to selection===

====Salmonids====

Gjedrem (1979) showed that selection of Atlantic salmon (''Salmo salar'') led to an increase in body weight by 30% per generation. A comparative study on the performance of select Atlantic salmon with wild fish was conducted by AKVAFORSK Genetics Centre in Norway. The traits, for which the selection was done included growth rate, feed consumption, protein retention, energy retention, and feed conversion efficiency. Selected fish had a twice better growth rate, a 40% higher feed intake, and an increased protein and energy retention. This led to an overall 20% better Fed Conversion Efficiency as compared to the wild stock.<ref>{{Cite journal | doi = 10.1016/s0044-8486(99)00204-5 | title = Feed intake, growth and feed utilization of offspring from wild and selected Atlantic salmon (''Salmo salar'')| journal = Aquaculture| volume = 180| issue = 3–4| pages = 237–246| year = 1999| last1 = Thodesen | first1 = J. R. | last2 = Grisdale-Helland | first2 = B. | last3 = Helland | first3 = S. L. J. | last4 = Gjerde | first4 = B. | bibcode = 1999Aquac.180..237T}}</ref> Atlantic salmon have also been selected for resistance to bacterial and viral diseases. Selection was done to check resistance to Infectious Pancreatic Necrosis Virus (IPNV). The results showed 66.6% mortality for low-resistant species whereas the high-resistant species showed 29.3% mortality compared to wild species.<ref>{{Cite journal | doi = 10.1016/j.aquaculture.2007.08.011| title = Response to selection for resistance against infectious pancreatic necrosis in Atlantic salmon (''Salmo salar'' L.)| journal = Aquaculture| volume = 272| pages = S62–S68| year = 2007| last1 = Storset | first1 = A. | last2 = Strand | first2 = C. | last3 = Wetten | first3 = M. | last4 = Kjøglum | first4 = S. | last5 = Ramstad | first5 = A. | bibcode = 2007Aquac.272..S62S}}</ref>

Rainbow trout (''S. gairdneri'') was reported to show large improvements in growth rate after 7–10 generations of selection.<ref>{{Cite journal | doi = 10.1577/1548-8659(1955)85[93:dortbs]2.0.co;2| title = Development of Rainbow Trout Brood Stock by Selective Breeding| journal = Transactions of the American Fisheries Society| volume = 85| pages = 93–101| year = 1957| last1 = Donaldson | first1 = L. R. | last2 = Olson | first2 = P. R. }}</ref> Kincaid et al. (1977) showed that growth gains by 30% could be achieved by selectively breeding rainbow trout for three generations.<ref>{{Cite journal | doi = 10.1577/1548-8659(1977)106<621:tgosfg>2.0.co;2| title = Three Generations of Selection for Growth Rate in Fall-Spawning Rainbow Trout| journal = Transactions of the American Fisheries Society| volume = 106| issue = 6| pages = 621–628| year = 1977| last1 = Kincaid | first1 = H. L.| last2 = Bridges | first2 = W. R.| last3 = von Limbach | first3 = B.| bibcode = 1977TrAFS.106..621K}}</ref> A 7% increase in growth was recorded per generation for rainbow trout by Kause et al. (2005).<ref>{{Cite journal | doi = 10.1016/j.aquaculture.2005.02.023| title = Genetic trends in growth, sexual maturity and skeletal deformations, and rate of inbreeding in a breeding programme for rainbow trout (Oncorhynchus mykiss)| journal = Aquaculture| volume = 247| issue = 1–4| pages = 177–187| year = 2005| last1 = Kause | first1 = A. | last2 = Ritola | first2 = O. | last3 = Paananen | first3 = T. | last4 = Wahlroos | first4 = H. | last5 = Mäntysaari | first5 = E. A. | bibcode = 2005Aquac.247..177K}}</ref>

In Japan, high resistance to IPNV in rainbow trout has been achieved by selectively breeding the stock. Resistant strains were found to have an average mortality of 4.3% whereas 96.1% mortality was observed in a highly sensitive strain.<ref>{{Cite journal | doi = 10.1016/0044-8486(93)90124-h| title = Resistance of a rainbow trout strain to infectious pancreatic necrosis| journal = Aquaculture| volume = 117| issue = 1–2| pages = 71–76| year = 1993| last1 = Okamoto | first1 = N. | last2 = Tayama | first2 = T. | last3 = Kawanobe | first3 = M. | last4 = Fujiki | first4 = N. | last5 = Yasuda | first5 = Y. | last6 = Sano | first6 = T. | bibcode = 1993Aquac.117...71O}}</ref>

Coho salmon (''Oncorhynchus kisutch'') increase in weight was found to be more than 60% after four generations of selective breeding.<ref>{{Cite journal | doi = 10.1016/0044-8486(90)90018-i| title = Genetic changes in the growth of coho salmon (''Oncorhynchus kisutch'') in marine net-pens, produced by ten years of selection| journal = Aquaculture| volume = 85| issue = 1–4| pages = 187–197| year = 1990| last1 = Hershberger | first1 = W. K. | last2 = Myers | first2 = J. M. | last3 = Iwamoto | first3 = R. N. | last4 = McAuley | first4 = W. C. | last5 = Saxton | first5 = A. M. | bibcode = 1990Aquac..85..187H}}</ref> In Chile, Neira et al. (2006) conducted experiments on early spawning dates in coho salmon. After selectively breeding the fish for four generations, spawning dates were 13–15 days earlier.<ref>{{Cite journal | doi = 10.1016/j.aquaculture.2006.03.001 | url = http://www.captura.uchile.cl/bitstream/handle/2250/6068/Neira_Roberto_GeneticII.pdf?sequence=1 | title = Genetic improvement in coho salmon (''Oncorhynchus kisutch''). II: Selection response for early spawning date | journal = Aquaculture | volume = 257 | issue = 1–4 | pages = 1–8 | year = 2006 | last1 = Neira | first1 = R. | last2 = Díaz | first2 = N. F. | last3 = Gall | first3 = G. A. E. | last4 = Gallardo | first4 = J. A. | last5 = Lhorente | first5 = J. P. | last6 = Alert | first6 = A. | bibcode = 2006Aquac.257....1N | access-date = 4 September 2015 | archive-date = 5 February 2020 | archive-url = https://web.archive.org/web/20200205110444/http://repositorio.uchile.cl/?sequence=1 | url-status = dead }}</ref>

'''Cyprinids'''

Selective breeding programs for the Common carp (''Cyprinus carpio'') include improvement in growth, shape and resistance to disease. Experiments carried out in the USSR used crossings of broodstocks to increase genetic diversity and then selected the species for traits like growth rate, exterior traits and viability, and/or adaptation to environmental conditions like variations in temperature. Kirpichnikov ''et al.'' (1974)<ref>{{Cite book | doi = 10.1016/b978-0-444-81527-9.50006-3| chapter = Selection of Krasnodar common carp (''Cyprinus carpio'' L.) for resistance to dropsy: Principal results and prospects| title = Genetics in Aquaculture| pages = 7| year = 1993| last1 = Kirpichnikov | first1 = V. S.| last2 = Ilyasov | first2 = I.| last3 = Shart | first3 = L. A.| last4 = Vikhman | first4 = A. A.| last5 = Ganchenko | first5 = M. V.| last6 = Ostashevsky | first6 = A. L.| last7 = Simonov | first7 = V. M.| last8 = Tikhonov | first8 = G. F.| last9 = Tjurin | first9 = V. V.| isbn = 9780444815279}}</ref> and Babouchkine (1987)<ref name=Babouchkine/> selected carp for fast growth and tolerance to cold, the Ropsha carp. The results showed a 30–40% to 77.4% improvement of cold tolerance but did not provide any data for growth rate. An increase in growth rate was observed in the second generation in Vietnam.<ref>{{Cite journal | doi = 10.1016/0044-8486(93)90064-6| title = Selection of common carp (''Cyprinus carpio'' L.) in Vietnam| journal = Aquaculture| volume = 111| issue = 1–4| pages = 301–302| year = 1993| last1 = Mai Thien Tran| last2 = Cong Thang Nguyen| bibcode = 1993Aquac.111..301M}}</ref> Moav and Wohlfarth (1976) showed positive results when selecting for slower growth for three generations compared to selecting for faster growth. Schaperclaus (1962) showed resistance to the dropsy disease wherein selected lines suffered low mortality (11.5%) compared to unselected (57%).<ref>{{Cite journal
 | pmid = 1248737
| pmc = 1213447
| year = 1976
| last1 = Moav
| first1 = R
| title = Two-way selection for growth rate in the common carp (''Cyprinus carpio'' L.)
| journal = Genetics
| volume = 82
| issue = 1
| pages = 83–101
| last2 = Wohlfarth
| first2 = G
| doi = 10.1093/genetics/82.1.83
}}</ref>

====Channel Catfish====

Growth was seen to increase by 12–20% in selectively bred ''Iictalurus punctatus''.<ref>{{Cite journal | doi = 10.1016/0044-8486(83)90387-3| title = Response to bidirectional selection for body weight in channel catfish| journal = Aquaculture| volume = 33| issue = 1–4| pages = 73–81| year = 1983| last1 = Bondari | first1 = K.| bibcode = 1983Aquac..33...73B}}</ref> More recently, the response of the Channel Catfish to selection for improved growth rate was found to be approximately 80%, that is, an average of 13% per generation.

===Shellfish response to selection===

====Oysters====

Selection for live weight of Pacific oysters showed improvements ranging from 0.4% to 25.6% compared to the wild stock.<ref>{{Cite journal | doi = 10.1016/s0044-8486(02)00621-x| title = Yields of cultured Pacific oysters Crassostrea gigas Thunberg improved after one generation of selection| journal = Aquaculture| volume = 220| issue = 1–4| pages = 227–244| year = 2003| last1 = Langdon | first1 = C. | last2 = Evans | first2 = F. | last3 = Jacobson | first3 = D. | last4 = Blouin | first4 = M. | bibcode = 2003Aquac.220..227L}}</ref> Sydney-rock oysters (''Saccostrea commercialis'') showed a 4% increase after one generation and a 15% increase after two generations.<ref>{{Cite journal | doi = 10.1016/0044-8486(96)01328-2| title = Progress in a Sydney rock oyster, Saccostrea commercialis (Iredale and Roughley), breeding program| journal = Aquaculture| volume = 144| issue = 4| pages = 295–302| year = 1996| last1 = Nell | first1 = J. A. | last2 = Sheridan | first2 = A. K. | last3 = Smith | first3 = I. R. | bibcode = 1996Aquac.144..295N}}</ref><ref>{{Cite journal | doi = 10.1016/s0044-8486(98)00408-6| title = Third generation evaluation of Sydney rock oyster Saccostrea commercialis (Iredale and Roughley) breeding lines| journal = Aquaculture| volume = 170| issue = 3–4| pages = 195–203| year = 1999| last1 = Nell | first1 = J. A. | last2 = Smith | first2 = I. R. | last3 = Sheridan | first3 = A. K. | bibcode = 1999Aquac.170..195N}}</ref> Chilean oysters (''Ostrea chilensis''), selected for improvement in live weight and shell length showed a 10–13% gain in one generation.
Bonamia ostrea is a protistan parasite that causes catastrophic losses (nearly 98%) in European flat oyster ''Ostrea edulis'' L. This protistan parasite is endemic to three oyster-regions in Europe. Selective breeding programs show that ''O. edulis'' susceptibility to the infection differs across oyster strains in Europe. A study carried out by Culloty et al. showed that 'Rossmore' oysters in Cork harbour, Ireland had better resistance compared to other Irish strains. A selective breeding program at Cork harbour uses broodstock from 3– to 4-year-old survivors and is further controlled until a viable percentage reaches market size.<ref>{{Cite journal | doi = 10.1016/s0044-8486(01)00569-5| title = An investigation into the relative resistance of Irish flat oysters ''Ostrea edulis'' L. to the parasite ''Bonamia ostreae''| journal = Aquaculture| volume = 199| issue = 3–4| pages = 229–244| year = 2001| last1 = Culloty | first1 = S. C. | last2 = Cronin | first2 = M. A. | last3 = Mulcahy | first3 = M. I. F. }}</ref><ref>{{Cite journal | doi = 10.1016/j.aquaculture.2004.04.007| title = Potential resistance of a number of populations of the oyster ''Ostrea edulis'' to the parasite ''Bonamia ostreae''| journal = Aquaculture| volume = 237| issue = 1–4| pages = 41–58| year = 2004| last1 = Culloty | first1 = S. C. | last2 = Cronin | first2 = M. A. | last3 = Mulcahy | first3 = M. F. | bibcode = 2004Aquac.237...41C}}</ref>

Over the years 'Rossmore' oysters have shown to develop lower prevalence of ''B. ostreae'' infection and percentage mortality. Ragone Calvo et al. (2003) selectively bred the eastern oyster, ''Crassostrea virginica'', for resistance against co-occurring parasites ''Haplosporidium nelson'' (MSX) and ''Perkinsus marinus'' (Dermo). They achieved dual resistance to the disease in four generations of selective breeding. The oysters showed higher growth and survival rates and low susceptibility to the infections. At the end of the experiment, artificially selected ''C. virginica'' showed a 34–48% higher survival rate.<ref>{{Cite journal | doi = 10.1016/s0044-8486(02)00399-x| title = Dual disease resistance in a selectively bred eastern oyster, ''Crassostrea virginica'', strain tested in Chesapeake Bay| journal = Aquaculture| volume = 220| issue = 1–4| pages = 69–87| year = 2003| last1 = Ragone Calvo | first1 = L. M. | last2 = Calvo | first2 = G. W. | last3 = Burreson | first3 = E. M. | bibcode = 2003Aquac.220...69R}}</ref>

====Penaeid shrimps====
Selection for growth in Penaeid shrimps yielded successful results. A selective breeding program for ''Litopenaeus stylirostris'' saw an 18% increase in growth after the fourth generation and 21% growth after the fifth generation.<ref>{{cite journal | last1 = Goyard | first1 = E. | last2 = Patrois | first2 = J. | last3 = Reignon | first3 = J.-M. | last4 = Vanaa | first4 = V. | last5 = Dufour | first5 = R | last6 = Be | year = 1999 | title = IFREMER's shrimp genetics program | journal = Global Aquaculture Advocate | volume = 2 | issue = 6| pages = 26–28 }}</ref> ''Marsupenaeus japonicas'' showed a 10.7% increase in growth after the first generation.<ref>{{Cite journal | doi = 10.1016/S0044-8486(99)00237-9| title = Response to selection and heritability for growth in the Kuruma prawn, ''Penaeus japonicus''| journal = Aquaculture| volume = 181| issue = 3–4| pages = 215–223| year = 2000| last1 = Hetzel | first1 = D. J. S. | last2 = Crocos | first2 = P. J. | last3 = Davis | first3 = G. P. | last4 = Moore | first4 = S. S. | last5 = Preston | first5 = N. C. | bibcode = 2000Aquac.181..215H}}</ref> Argue et al. (2002) conducted a selective breeding program on the Pacific White Shrimp,'' Litopenaeus vannamei'' at The Oceanic Institute, Waimanalo, USA from 1995 to 1998. They reported significant responses to selection compared to the unselected control shrimps. After one generation, a 21% increase was observed in growth and 18.4% increase in survival to TSV.<ref>{{Cite journal | doi = 10.1016/s0044-8486(01)00830-4| title = Selective breeding of Pacific white shrimp (''Litopenaeus vannamei'') for growth and resistance to Taura Syndrome Virus| journal = Aquaculture| volume = 204| issue = 3–4| pages = 447–460| year = 2002| last1 = Argue | first1 = B. J. | last2 = Arce | first2 = S. M. | last3 = Lotz | first3 = J. M. | last4 = Moss | first4 = S. M. | bibcode = 2002Aquac.204..447A}}</ref> The Taura Syndrome Virus (TSV) causes mortalities of 70% or more in shrimps. C.I. Oceanos S.A. in Colombia selected the survivors of the disease from infected ponds and used them as parents for the next generation. They achieved satisfying results in two or three generations wherein survival rates approached levels before the outbreak of the disease.<ref>{{Cite journal | doi = 10.1016/j.aquaculture.2008.09.011| title = Breeding for disease resistance of Penaeid shrimps| journal = Aquaculture| volume = 286| issue = 1–2| pages = 1–11| year = 2009| last1 = Cock | first1 = J. | last2 = Gitterle | first2 = T. | last3 = Salazar | first3 = M. | last4 = Rye | first4 = M. | bibcode = 2009Aquac.286....1C}}</ref> The resulting heavy losses (up to 90%) caused by Infectious hypodermal and haematopoietic necrosis virus (IHHNV) caused a number of shrimp farming industries started to selectively breed shrimps resistant to this disease. Successful outcomes led to development of Super Shrimp, a selected line of ''L. stylirostris'' that is resistant to IHHNV infection. Tang et al. (2000) confirmed this by showing no mortalities in IHHNV- challenged Super Shrimp post larvae and juveniles.<ref>{{Cite journal | doi = 10.1016/s0044-8486(00)00407-5 | title = Postlarvae and juveniles of a selected line of ''Penaeus stylirostris'' are resistant to infectious hypodermal and hematopoietic necrosis virus infection| journal = Aquaculture| volume = 190| issue = 3–4| pages = 203–210| year = 2000| last1 = Tang | first1 = K. F. J. | last2 = Durand | first2 = S. V. | last3 = White | first3 = B. L. | last4 = Redman | first4 = R. M. | last5 = Pantoja | first5 = C. R. | last6 = Lightner | first6 = D. V. | bibcode = 2000Aquac.190..203T}}</ref>

===Aquatic species versus terrestrial livestock===
Selective breeding programs for aquatic species provide better outcomes compared to terrestrial livestock. This higher response to selection of aquatic farmed species can be attributed to the following:
* High fecundity in both sexes fish and shellfish enabling higher selection intensity.
* Large phenotypic and genetic variation in the selected traits.

Selective breeding in aquaculture provide remarkable economic benefits to the industry, the primary one being that it reduces production costs due to faster turnover rates. When selective breeding is carried out, some characteristics are lost for others that may suit a specific environment or situation.<ref>{{Cite web |title=What Is the Main Idea of Overproduction in Natural Selection? |url=https://sciencing.com/main-idea-overproduction-natural-selection-18000.html |access-date=2024-01-28 |website=Sciencing |date=30 July 2018 |language=en}}</ref> This is because of faster growth rates, decreased maintenance rates, increased energy and protein retention, and better feed efficiency.<ref name=gb>Gjedrem, T & Baranski, M. (2009). ''Selective breeding in Aquaculture: An Introduction''. 1st Edition. Springer. {{ISBN|978-90-481-2772-6}}</ref> Applying genetic improvement programs to aquaculture species will increase their productivity. Thus allowing them to meet the increasing demands of growing populations. Conversely, selective breeding within aquaculture can create problems within the biodiversity of both stock and wild fish, which can hurt the industry down the road. Although there is great potential to improve aquaculture due to the current lack of domestication, it is essential that the genetic diversity of the fish are preserved through proper genetic management, as we domesticate these species.<ref name=":2">{{Cite journal |last1=Lind |first1=Ce |last2=Ponzoni |first2=Rw |last3=Nguyen |first3=Nh |last4=Khaw |first4=Hl |date=August 2012 |title=Selective Breeding in Fish and Conservation of Genetic Resources for Aquaculture |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1439-0531.2012.02084.x |journal=Reproduction in Domestic Animals |language=en |volume=47 |issue=s4 |pages=255–263 |doi=10.1111/j.1439-0531.2012.02084.x |pmid=22827379 |issn=0936-6768|url-access=subscription }}</ref> It is not uncommon for fish to escape the nets or pens that they are kept in, especially in mass. If these fish are farmed in areas they are not native to they may be able to establish themselves and outcompete native populations of fish, and cause ecological harm as an invasive species.<ref name=":4">{{cite web |url=https://www.seafoodwatch.org/seafood-basics/sustainable-solutions/prevent-farmed-fish-escapes |title=Prevent farmed fish escapes |access-date=2024-02-27 |website=[[Seafood Watch]]}}</ref> Furthermore, if they are in areas where the fish being farmed are native too their genetics are selectively bred rather than being wild. These farmed fish could breed with the natives which could be problematic In the sense that they would have been bred for consumption rather than by chance. Resulting in an overall decrease in genetic diversity and rendering local fish populations less fit for survival.<ref name=":4" /> If proper management is not taking place then the economic benefits and the diversity of the fish species will falter.<ref name=":2" />