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Breeding for desired characteristics

Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant males and females will sexually reproduce and have offspring together. Domesticated animals are known as breeds, normally bred by a professional breeder, while domesticated plants are known as varieties, cultigens, cultivars, or breeds. Two purebred animals of different breeds produce a crossbreed, and crossbred plants are called hybrids. Flowers, vegetables and fruit trees may be bred by amateurs and commercial or non commercial professionals: major crops are usually the provenance of the professionals. In animal breeding artificial selection is often combined with techniques such as inbreeding, linebreeding, and outcrossing. In plant breeding, similar methods are used. Charles Darwin discussed how selective breeding had been successful in producing change over time in his 1859 book, On the Origin of Species. Its first chapter discusses selective breeding and domestication of such animals as pigeons, cats, cattle, and dogs. Darwin used artificial selection as an analogy to propose and explain the theory of natural selection but distinguished the latter from the former as a separate process that is non directed. The deliberate exploitation of selective breeding to produce desired results has become very common in agriculture and experimental biology. Selective breeding can be unintentional, for example, resulting from the process of human cultivation; and it may also produce unintended – desirable or undesirable – results. For example, in some grains, an increase in seed size may have resulted from certain ploughing practices rather than from the intentional selection of larger seeds. Most likely, there has been an interdependence between natural and artificial factors that have resulted in plant domestication.

Animals with homogeneous appearance, behavior, and other characteristics are known as particular breeds or pure breeds, and they are bred through culling animals with particular traits and selecting for further breeding those with other traits. Purebred animals have a single, recognizable breed, and purebreds with recorded lineage are called pedigreed. Crossbreeds are a mix of two purebreds, whereas mixed breeds are a mix of several breeds, often unknown. Animal breeding begins with breeding stock, a group of animals used for the purpose of planned breeding. When individuals are looking to breed animals, they look for certain valuable traits in purebred stock for a certain purpose, or may intend to use some type of crossbreeding to produce a new type of stock with different, and, it is presumed, superior abilities in a given area of endeavor. For example, to breed chickens, a breeder typically intends to receive eggs, meat, and new, young birds for further reproduction. Thus, the breeder has to study different breeds and types of chickens and analyze what can be expected from a certain set of characteristics before he or she starts breeding them. Therefore, when purchasing initial breeding stock, the breeder seeks a group of birds that will most closely fit the purpose intended. Purebred breeding aims to establish and maintain stable traits, that animals will pass to the next generation. By "breeding the best to the best," employing a certain degree of inbreeding, considerable culling, and selection for "superior" qualities, one could develop a bloodline superior in certain respects to the original base stock. Such animals can be recorded with a breed registry, the organization that maintains pedigrees and/or stud books. However, single trait breeding, breeding for only one trait over all others, can be problematic. In one case mentioned by animal behaviorist Temple Grandin, roosters bred for fast growth or heavy muscles did not know how to perform typical rooster courtship dances, which alienated the roosters from hens and led the roosters to kill the hens after mating with them. The observable phenomenon of hybrid vigor stands in contrast to the notion of breed purity. However, on the other hand, indiscriminate breeding of crossbred or hybrid animals may also result in degradation of quality. Studies in evolutionary physiology, behavioral genetics, and other areas of organismal biology have also made use of deliberate selective breeding, though longer generation times and greater difficulty in breeding can make these projects challenging in such vertebrates as house mice.

The process of plant breeding has been used for thousands of years, and began with the domestication of wild plants into uniform and predictable agricultural cultigens. These high yielding varieties have been particularly important in agriculture. As crops improved, humans were able to move from hunter gatherer style living to a mix of hunter gatherer and agriculture practices. Although these higher yielding plants were derived from an extremely primitive version of plant breeding, this form of agriculture was an investment that the people who grew them were planting then could have a more varied diet. This meant that they did not completely stop their hunting and gathering immediately but instead over time transition and ultimately favored agriculture. n addition, the ability for humans to stay within one place for food and create permanent settlements made the process move along faster. During this transitional period, crops began to acclimate and evolve with humans encouraging humans to invest further into crops. Over time this reliance on plant breeding has created problems, as highlighted by the book Botany of Desire where Michael Pollan shows the connection between basic human desires through four different plants: apples for sweetness, tulips for beauty, cannabis for intoxication, and potatoes for control. In a form of reciprocal evolution humans have influenced these plants as much as the plants have influenced the people that consume them, is known as coevolution. Selective plant breeding is also used in research to produce transgenic animals that breed "true" (i. e., are homozygous) for artificially inserted or deleted genes.

Growth was seen to increase by 12–20% in selectively bred Iictalurus punctatus. 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.

Selection for live weight of Pacific oysters showed improvements ranging from 0.4% to 25.6% compared to the wild stock. Sydney rock oysters (Saccostrea commercialis) showed a 4% increase after one generation and a 15% increase after two generations. 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. 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.

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. Marsupenaeus japonicas showed a 10.7% increase in growth after the first generation. 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. 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. 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.

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. This is because of faster growth rates, decreased maintenance rates, increased energy and protein retention, and better feed efficiency. 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. 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. 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. Additionally, selective breeding can lead to a variety of issues including reduction of genetic diversity or physical problems. The process of selective breeding can create physical issues for plants or animals such as dogs selectively bred for extremely small sizes dislocating their kneecaps at a much more frequent rate then other dogs. An example in the plant world is the Lenape potatoes were selectively bred for their disease or pest resistance which was attributed to their high levels of toxic glycoalkaloid solanine which are usually present only in small amounts in potatoes fit for human consumption. When genetic diversity is lost it can also allow for populations to lack genetic alternatives to adapt to events. This becomes an issue of biodiversity, because attributes are so wide spread they can result in mass epidemics. As seen in the Southern Corn leaf blight epidemic of 1970 that wiped out 15% of the United States corn crop due to the wide use of a type of Texan corn strain that was artificially selected due to having sterile pollen to make farming easier. At the same time it was more vulnerable to Southern Corn leaf blight.