Mutation breeding

From Wikipedia, the free encyclopedia

Mutation breeding, sometimes referred to as "variation breeding", is the process of exposing seeds to chemicals or radiation in order to generate mutants with desirable traits to be bred with other cultivars. Plants created using mutagenesis are sometimes called mutagenic plants or mutagenic seeds. From 1930 to 2014 more than 3200 mutagenic plant varieties were released that have been derived either as direct mutants (70%) or from their progeny (30%). Crop plants account for 75% of released mutagenic species with the remaining 25% ornamentals or decorative plants. However, although the FAO/IAEA reported in 2014 that over 1,000 mutant varieties of major staple crops were being grown worldwide, it is unclear how many of these varieties are currently used in agriculture or horticulture around the world, as these seeds are not always identified or labeled as being mutagen or having a mutagenic provenance.

Process

There are different kinds of mutagenic breeding such as using chemical mutagens like ethyl methanesulfonate and dimethyl sulfate, radiation and transposons are used to generate mutants. Mutation breeding is commonly used to produce traits in crops such as larger seeds, new colors, or sweeter fruits, that either cannot be found in nature or have been lost during evolution.

Radiation breeding

Exposing plants to radiation is sometimes called radiation breeding and is a sub class of mutagenic breeding. Radiation breeding was discovered in the 1920s when Lewis Stadler of the University of Missouri used X-rays on maize and barley. In the case of barley, the resulting plants were white, yellow, pale yellow and some had white stripes. In 1928, Stadler first published his findings on radiation-induced mutagenesis in plants. During the period 1930–2004, radiation-induced mutant varieties were developed primarily using gamma rays (64%) and X-rays (22%).


Radiation breeding may take place in atomic gardens; and seeds have been sent into orbit in order to expose them to more cosmic radiation.

Use of chemical mutagens

High rates of chromosome aberrations resulting from ionizing radiation and the accompanied detrimental effects made researchers look for alternate sources for inducing mutations. As a result, an array of chemical mutagens has been discovered. The most widely used chemical mutagens are alkylating agents. Ethyl methanesulfonate (EMS) is the most popular because of its effectiveness and ease of handling, especially its detoxification through hydrolysis for disposal. Nitroso compounds are the other alkylating agents widely used, but they are light-sensitive and more precautions need to be taken because of their higher volatility. EMS has become a commonly used mutagen for developing large numbers of mutants for screening such as in developing TILLING populations. Although many chemicals are mutagens, only few have been used in practical breeding as the doses need to be optimised and also because the effectiveness is not high in plants for many.

History

According to garden historian Paige Johnson

After WWII, there was a concerted effort to find 'peaceful' uses for atomic energy. One of the ideas was to bombard plants with radiation and produce lots of mutations, some of which, it was hoped, would lead to plants that bore more heavily or were disease or cold-resistant or just had unusual colors. The experiments were mostly conducted in giant gamma gardens on the grounds of national laboratories in the US but also in Europe and countries of the former USSR.

Comparison to other agronomic techniques

In the debate over genetically modified foods, the use of transgenic processes is often compared and contrasted with mutagenic processes. While the abundance and variation of transgenic organisms in human food systems, and their effect on agricultural biodiversity, ecosystem health and human health is somewhat well documented, mutagenic plants and their role on human food systems is less well known, with one journalist writing "Though poorly known, radiation breeding has produced thousands of useful mutants and a sizable fraction of the world's crops...including varieties of rice, wheat, barley, pears, peas, cotton, peppermint, sunflowers, peanuts, grapefruit, sesame, bananas, cassava and sorghum." In Canada crops generated by mutation breeding face the same regulations and testing as crops obtained by genetic engineering. Mutagenic varieties tend to be made freely available for plant breeding, in contrast to many commercial plant varieties or germplasm that increasingly have restrictions on their use such as terms of use, patents and proposed genetic user restriction technologies and other intellectual property regimes and modes of enforcement.

Unlike genetically modified crops, which typically involve the insertion of one or two target genes, plants developed via mutagenic processes with random, multiple and unspecific genetic changes have been discussed as a concern but are not prohibited by any nation's organic standards. Reports from the US National Academy of Sciences state that there is no scientific justification for regulating genetic engineered crops while not doing so for mutation breeding crops.

Several organic food and seed companies promote and sell certified organic products that were developed using both chemical and nuclear mutagenesis. Several certified organic brands, whose companies support strict labeling or outright bans on GMO-crops, market their use of branded wheat and other varietal strains which were derived from mutagenic processes without any reference to this genetic manipulation. These organic products range from mutagenic barley and wheat ingredient used in organic beers to mutagenic varieties of grapefruits sold directly to consumers as organic.

New mutagen techniques

Restriction endonucleases

Interest in the use of bacterial restriction endonucleases (RE) to study double-stranded breaks in plant DNA began in the mid-nineties. These breaks in DNA, otherwise known as DSBs, were found to be the source of much chromosomal damage in eukaryotes, causing mutations in plant varieties. REs induce a result on plant DNA similar to that of ionizing radiation or radiomimetic chemicals. Blunt ended breaks in the DNA, unlike sticky ended breaks, were found to produce more variations in chromosomal damage, making them the more useful type of break for mutation breeding. While the connection of REs to chromosomal aberrations is mostly limited to research on mammalian DNA, success in mammalian studies caused scientists to conduct more studies of RE-induced chromosomal and DNA damaged on barley genomes. Due to restriction endonucleases' ability to facilitate damage in chromosomes and DNA, REs have the capability of being used as a new method of mutagenesis to promote the proliferation of mutated plant varieties.

Space-breeding

The ability of plants to develop and thrive is dependent on conditions such as microgravity and cosmic radiation in space. China has been experimenting with this theory by sending seeds into space, testing to see if space flights will cause genetic mutations. Since 1987, China has cultivated 66 mutant varieties from space through their space-breeding program. Chromosomal aberrations greatly increased when seeds were sent into aerospace compared to their earth-bound counterparts. The effect of space flight on seeds depends on their species and variety. For example, space-bred wheat saw a large growth in seed germination in compared to its Earth-bound control, but space-bred rice had no visible advantage compared to its control. For the varieties that were positively mutated by space flight, their growth potential exceeded that of not only their Earth-grown counterparts, but also their irradiated counterparts on Earth. Compared to traditional mutagenic techniques, space-bred mutations have greater efficacy in that they experience positive effects on their first generation of mutation, whereas irradiated crops often see no advantageous mutations in their first generations. Though multiple experiments have shown the positive effects of space flight on seed mutation, there is no clear connection as to what aspect of aerospace has produced such advantageous mutations. There is much speculation around cosmic radiation being the source of chromosomal aberrations, but so far, there has been no concrete evidence of such connection. Though China's space-breeding program has been shown to be very successful, the program requires a large budget and technological support that many other countries are either unwilling or unable to provide, meaning this program is unfeasible outside of China. Due to such restraints, scientists have been trying to replicate space condition on Earth in order to promote the same expedient space-born mutations on Earth. One such replication is a magnetic field-free space (MF), which produces an area with a weaker magnetic field than that of Earth. MF treatment produced mutagenic results, and has been used to cultivate new mutant varieties of rice and alfalfa. Other replications of space conditions include irradiation of seeds by a heavy 7 Li-ion beam or mixed high-energy particles. These space-bred varieties are already being introduced to the public. In 2011, during the National Lotus Flowers Exhibition in China, a mutant lotus, called the "Outer Space Sun", was shown at the flower show.

Ion beam technology

Ion beams mutate DNA by deleting multiple bases from its code. Compared to traditional sources of radiation, like gamma rays and X-rays, ion beams have been shown to cause more severe breaks in DNA that are more difficult to weave back together, causing the change in DNA to be more drastic than changes caused by traditional irradiation. Ion beams change DNA in a manner that makes it look vastly different than its original makeup, more so than when traditional irradiation techniques are used. Most experimentation, using ion beam technology, has been conducted in Japan. Notable facilities using this technology are TIARA of the Japan Atomic Energy Agency, RIKEN Accelerator Research Facility, and various other Japanese institutions. During the process of ion beam radiation, seeds are wedged between two kapton films and irradiated for roughly two minutes. Mutation frequencies are notably higher for ion beam radiation compared to electron radiation, and the mutation spectrum is broader for ion beam radiation compared to gamma ray radiation. The broader mutation spectrum was revealed through the largely varied amount of flower phenotypes produced by ion beams. Flowers mutated by the ion beams exhibited a variety of colors, patterns, and shapes. Through ion beam radiation, new varieties of plants have been cultivated. These plants had the characteristics of being ultraviolet light-B resistant, disease resistant, and chlorophyll-deficient. Ion beam technology has been used in the discovery of new genes responsible for the creation of more robust plants, but its most prevalent use is commercially for producing new flower phenotypes, like striped chrysanthemums.

Mature pollen treated with gamma radiation

Gamma radiation is used on mature rice pollen to produce parent plants used for crossing. The mutated traits in the parent plants are able to be inherited by their offspring plants. Because rice pollen has a very short lifespan, researchers had to blast gamma rays at cultured spikes from rice plants. Through experimentation, it was revealed that there was a greater variety of mutation in irradiated pollen rather than irradiated dry seeds. Pollen treated with 46Gy of gamma radiation showed an increase in grain size overall and other useful variations. Typically, the length of each grain was longer after the crossing of irradiated parent rice plants. The rice progeny also exhibited a less chalky visage, improving on the appearance of the parent rice plants. This technique was used to develop two new rice cultivars, Jiaohezaozhan and Jiafuzhan, in China. Along with facilitating the creation of these two rice cultivars, the irradiation of mature rice pollen has produced roughly two hundred mutant rice lines. Each of these lines produce rice grains of both a higher quality and larger size. The mutations produced by this technique vary with each generation, meaning further breeding of these mutated plants could produce new mutations. Traditionally, gamma radiation is used on solely adult plants, and not on pollen. The irradiation of mature pollen allows mutant plants to grow without being in direct contact with gamma radiation. This discovery is in contrast to what was previously believed about gamma radiation: that it could only elicit mutations in plants and not pollen.

Notable mutagen varieties

 Argentina

• Colorado Irradiado groundnut (mutant created with X-rays; high fat content and yield, 80% of groundnuts grown in Argentina in the 1980s was Colorado Irradiado)
• Puita INTA-CL rice mutant (herbicide resistance and good yield; also grown in Bolivia, Brazil, Costa Rica and Paraguay)

 Australia

• Amaroo rice mutant variety (60-70% of rice grown in Australia was Amaroo in 2001)

 Bangladesh

• Binasail, Iratom-24 and Binadhan-6 rice mutants 
• Binamoog-5 mung bean mutant variety

 Cuba

• Maybel tomato mutant (excellent drought resistance)
• GINES rice mutant (created using proton radiation; grows well in salty conditions)

 People's Republic of China

• Henong series soybean mutants
• Jiahezazhan and Jiafuzhan rice (mutations obtained by pollen irradiation; high yield and quality, very adaptable, resistant to plant hopper and blast)
• Lumian Number 1 cotton
• Purple Orchard 3 Sweet potato
• Tiefeng 18 soybean
• Yangdao Number 6 rice
• Yangmai 156 wheat
• Zhefu 802 rice mutant (irradiated with gamma rays; resistant to rice blast, good yield even in poor conditions, the most planted rice variety between 1986-1994)
• 26Zhaizao indica rice mutant (created with gamma rays)

 Czech Republic

• Diamant barley (high yield, short height mutant created with X-Rays)

 Egypt

• Giza 176 and Sakha 101 high yield rice mutants

 Finland

• Balder J barley mutant (better drought resistance, yield and sprouting)
• Puhti and Ryhti stiff straw oat mutants

 France

• High oleic sunflowers (covering more than 50 % of the sunflower acreage)

 Germany

• Trumpf barley

 Ghana

• Tek bankye mutant cassava (good poundability and increased dry matter content)

 India

• Co-4, Pant Mung-2, and TAP mung bean mutants
• MA-9 cotton - the world's first mutant cotton, released in 1948 (X-ray radiation; drought tolerance, high yielding)
• PNR-381 Rice
• Pusa 408 (Ajay), Pusa 413 (Atul), Pusa 417 (Girnar), and Pusa 547 chickpea mutants (resistant to Ascochyta blight and wilt diseases, and have high yields)
• Sharbati Sonora wheat
• Tau-1, MUM 2, BM 4, LGG 407, LGG 450, Co4, Dhauli (TT9E) and Pant moong-1 blackgram (YMC, (Yellow mosaic virus) resistance)
• TG24 and TG37 groundnut mutants

 Italy

• Durum wheat (especially Creso mutant, created with thermal neutrons)

 Japan

• Osa Gold Pear (disease resistance) 
• Most rice varieties grown in Japan have the sd1 mutant allele from the Reimei rice variety

 Myanmar

• Shwewartun rice mutant (created by irradiating IR5 rice to give better yield, grain quality and earlier maturity)

 Pakistan

• Basmati 370 short height rice mutant
• NIAB-78 cotton mutant (high yielding, heat tolerant, early maturing)
• CM-72 chickpea mutant (created with 150Gy of gamma rays; high yielding, blight resistant)
• NM-28 mungbean mutant (short height, uniform and early maturing, high seed yield)
• NIAB Masoor 2006 lentil mutant (created with 200Gy of radiation; early maturing, high yield, resistant to disease)

 Peru

• UNA La Molina 95 barley mutant (developed in 1995 for growing above 3,000 m)
• Centenario Amarinth "kiwicha" mutant (high quality grain and exported as a certified organic product)
• Centenario II barley mutant (developed for growing in the Andean highlands with high yield, high quality flour and tolerance to hail)

 Sudan

• Albeely banana mutant (better quality, high yield and better stand)

 Thailand

• RD15 and RD6 aromatic indica rice mutants (created with gamma rays and released in 1977-8; RD 15 is early ripening, RD6 has a valuable glutinous endosperm) Thailand is the biggest exporter of aromatic rice in the world

 United Kingdom

• Golden Promise barley (semi-dwarf, salt tolerant mutant created with gamma rays) Is used to make beer and whisky

 United States

• Calrose 76 Rice (short height rice induced with gamma rays)
• Luther and Pennrad barley (high yield mutant varieties; Pennrad also resistant to winter)
• Murray Mitcham Peppermint (Verticillium wilt tolerance)
• Sanilac bean (X-ray radiation; high yielding mutant - also the Gratiot and Sea-way bean varieties were cross-bred from Sanilac)
• Stadler wheat (high yield mutant with resistance to loose smut and leaf rust and earlier maturity)
• Star Ruby and Rio red varieties of the Rio Star Grapefruit (created using thermal neutron techniques)
• Todd's Mitcham Peppermint (Verticillium wilt tolerance)

 Vietnam

• VND 95-20, VND-99-1 and VN121 rice mutants (increased yield, improved quality, resistance to disease and pests)
• DT84, DT96, DT99 and DT 2008 soybean mutants (developed using gamma rays to grow three crops a year, tolerance to heat and cold and resistance to disease)

In 2014, it was reported that 17 rice mutant varieties, 10 soybean, two maize and one chrysanthemum mutant varieties had been officially released to Vietnamese farmers. 15% of rice and 50% of soybean was produced from mutant varieties.

Release by nation

As of 2011 the percentage of all mutagenic varieties released globally, by country, were:

• (25.2%)  People's Republic of China
• (15.0%)  Japan
• (11.5%)  India
• (6.7%)  Russia
• (5.5%)  Netherlands
• (5.3%)  Germany
• (4.3%)  United States
• (2.4%)  Bulgaria
• (1.7%)  Vietnam
• (1.4%)  Bangladesh

Selective breeding

From Wikipedia, the free encyclopedia

A Belgian Blue cow. The defect in the breed's myostatin gene is maintained through linebreeding and is responsible for its accelerated lean muscle growth.

This Chihuahua mix and Great Dane shows the wide range of dog breed sizes created using selective breeding.

Selective breeding transformed teosinte's few fruitcases (left) into modern maize's rows of exposed kernels (right).

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, or cultivars. 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, techniques such as inbreeding, linebreeding, and outcrossing are utilized. 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 a springboard to introduce and support the theory of natural selection.

The deliberate exploitation of selective breeding to produce desired results has become very common in agriculture and experimental biology.

Selective breeding can be unintentional, e.g., 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.

History

Selective breeding of both plants and animals has been practiced since early prehistory; key species such as wheat, rice, and dogs have been significantly different from their wild ancestors for millennia, and maize, which required especially large changes from teosinte, its wild form, was selectively bred in Mesoamerica. Selective breeding was practiced by the Romans. Treatises as much as 2,000 years old give advice on selecting animals for different purposes, and these ancient works cite still older authorities, such as Mago the Carthaginian. The notion of selective breeding was later expressed by the Persian Muslim polymath Abu Rayhan Biruni in the 11th century. He noted the idea in his book titled India, which included various examples.

The agriculturist selects his corn, letting grow as much as he requires, and tearing out the remainder. The forester leaves those branches which he perceives to be excellent, whilst he cuts away all others. The bees kill those of their kind who only eat, but do not work in their beehive.

— Abu Rayhan Biruni, India

Selective breeding was established as a scientific practice by Robert Bakewell during the British Agricultural Revolution in the 18th century. Arguably, his most important breeding program was with sheep. Using native stock, he was able to quickly select for large, yet fine-boned sheep, with long, lustrous wool. The Lincoln Longwool was improved by Bakewell, and in turn the Lincoln was used to develop the subsequent breed, named the New (or Dishley) Leicester. It was hornless and had a square, meaty body with straight top lines.

These sheep were exported widely, including to Australia and North America, and have contributed to numerous modern breeds, despite the fact that they fell quickly out of favor as market preferences in meat and textiles changed. Bloodlines of these original New Leicesters survive today as the English Leicester (or Leicester Longwool), which is primarily kept for wool production.

Bakewell was also the first to breed cattle to be used primarily for beef. Previously, cattle were first and foremost kept for pulling ploughs as oxen, but he crossed long-horned heifers and a Westmoreland bull to eventually create the Dishley Longhorn. As more and more farmers followed his lead, farm animals increased dramatically in size and quality. In 1700, the average weight of a bull sold for slaughter was 370 pounds (168 kg). By 1786, that weight had more than doubled to 840 pounds (381 kg). However, after his death, the Dishley Longhorn was replaced with short-horn versions.

He also bred the Improved Black Cart horse, which later became the Shire horse.

Charles Darwin coined the term 'selective breeding'; he was interested in the process as an illustration of his proposed wider process of natural selection. Darwin noted that many domesticated animals and plants had special properties that were developed by intentional animal and plant breeding from individuals that showed desirable characteristics, and discouraging the breeding of individuals with less desirable characteristics.

Darwin used the term "artificial selection" twice in the 1859 first edition of his work On the Origin of Species, in Chapter IV: Natural Selection, and in Chapter VI: Difficulties on Theory:

Slow though the process of selection may be, if feeble man can do much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the co-adaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection.

— Charles Darwin, On the Origin of Species

We are profoundly ignorant of the causes producing slight and unimportant variations; and we are immediately made conscious of this by reflecting on the differences in the breeds of our domesticated animals in different countries,—more especially in the less civilized countries where there has been but little artificial selection.

— Charles Darwin, On the Origin of Species

Animal breeding

Three generations of "Westies" in a village in Fife, Scotland

Animals with homogeneous appearance, behavior, and other characteristics are known as particular 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 such projects challenging in vertebrates.

Plant breeding

Researchers at the USDA have selectively bred carrots with a variety of colors.

Plant breeding has been used for thousands of years, and began with the domestication of wild plants into uniform and predictable agricultural cultigens. High-yielding varieties have been particularly important in agriculture.

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.

Selective breeding in aquaculture

Selective breeding in aquaculture holds high potential for the genetic improvement of fish and shellfish. 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.

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. A suspected reason associated with the late realisation 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.

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.

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 colour, 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. Improved growth rates show that farmed animals utilize their feed more efficiently through a correlated response.
• Survival rate – survival rate may take into account the degrees of resistance to diseases. This may also see the stress response as fish under stress are highly vulnerable to diseases. 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, colour of flesh, taste, shape of the body, ideal oil and omega-3 content.
• 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.

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. 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.

Rainbow trout (S. gairdneri) was reported to show large improvements in growth rate after 7–10 generations of selection. Kincaid et al. (1977) showed that growth gains by 30% could be achieved by selectively breeding rainbow trout for three generations. A 7% increase in growth was recorded per generation for rainbow trout by Kause et al. (2005).

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.

Coho salmon (Oncorhynchus kisutch) increase in weight was found to be more than 60% after four generations of selective breeding. 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.

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) and Babouchkine (1987) 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. 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%).

Channel Catfish

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%, i.e., 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. 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.

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. 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.

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. This is because of faster growth rates, decreased maintenance rates, increased energy and protein retention, and better feed efficiency. Applying such genetic improvement program to aquaculture species will increase productivity to meet the increasing demands of growing populations.

Advantages and disadvantages

Selective breeding is a direct way to determine if a specific trait can evolve in response to selection. A single-generation method of breeding is not as accurate or direct. The process is also more practical and easier to understand than sibling analysis. Selective breeding is better for traits such as physiology and behavior that are hard to measure because it requires fewer individuals to test than single-generation testing.

However, there are disadvantages to this process. Because a single experiment done in selective breeding cannot be used to assess an entire group of genetic variances, individual experiments must be done for every individual trait. Also, because of the necessity of selective breeding experiments to require maintaining the organisms tested in a lab or greenhouse, it is impractical to use this breeding method on many organisms. Controlled mating instances are difficult to carry out in this case and this is a necessary component of selective breeding.

Domestication

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Dogs and sheep were among the first animals to be domesticated.

Domestication is a sustained multi-generational relationship in which one group of organisms assumes a significant degree of influence over the reproduction and care of another group to secure a more predictable supply of resources from that second group.

Charles Darwin recognized the small number of traits that made domestic species different from their wild ancestors. He was also the first to recognize the difference between conscious selective breeding in which humans directly select for desirable traits, and unconscious selection where traits evolve as a by-product of natural selection or from selection on other traits. There is a genetic difference between domestic and wild populations. There is also such a difference between the domestication traits that researchers believe to have been essential at the early stages of domestication, and the improvement traits that have appeared since the split between wild and domestic populations. Domestication traits are generally fixed within all domesticates, and were selected during the initial episode of domestication of that animal or plant, whereas improvement traits are present only in a proportion of domesticates, though they may be fixed in individual breeds or regional populations.

The dog was the first domesticated vertebrate, and was established across Eurasia before the end of the Late Pleistocene era, well before cultivation and before the domestication of other animals. The archaeological and genetic data suggest that long-term bidirectional gene flow between wild and domestic stocks – including donkeys, horses, New and Old World camelids, goats, sheep, and pigs – was common. Given its importance to humans and its value as a model of evolutionary and demographic change, domestication has attracted scientists from archaeology, palaeontology, anthropology, botany, zoology, genetics, and the environmental sciences. Among birds, the major domestic species today is the chicken, important for meat and eggs, though economically valuable poultry include the turkey, guineafowl and numerous other species. Birds are also widely kept as cagebirds, from songbirds to parrots. The longest established invertebrate domesticates are the honey bee and the silkworm. Terrestrial snails are raised for food, while species from several phyla are kept for research, and others are bred for biological control.

The domestication of plants began at least 12,000 years ago with cereals in the Middle East, and the bottle gourd in Asia. Agriculture developed in at least 11 different centres around the world, domesticating different crops and animals.

Overview

Succulents like this jelly bean plant (Sedum rubrotinctum) need infrequent watering, making them convenient as houseplants.

Domestication, from the Latin domesticus, 'belonging to the house', is "a sustained multi-generational, mutualistic relationship in which one organism assumes a significant degree of influence over the reproduction and care of another organism in order to secure a more predictable supply of a resource of interest, and through which the partner organism gains advantage over individuals that remain outside this relationship, thereby benefitting and often increasing the fitness of both the domesticator and the target domesticate." This definition recognizes both the biological and the cultural components of the domestication process and the impacts on both humans and the domesticated animals and plants. All past definitions of domestication have included a relationship between humans with plants and animals, but their differences lay in who was considered as the lead partner in the relationship. This new definition recognizes a mutualistic relationship in which both partners gain benefits. Domestication has vastly enhanced the reproductive output of crop plants, livestock, and pets far beyond that of their wild progenitors. Domesticates have provided humans with resources that they could more predictably and securely control, move, and redistribute, which has been the advantage that had fueled a population explosion of the agro-pastoralists and their spread to all corners of the planet.

Houseplants and ornamentals are plants domesticated primarily for aesthetic enjoyment in and around the home, while those domesticated for large-scale food production are called crops. Domesticated plants deliberately altered or selected for special desirable characteristics are cultigens. Animals domesticated for home companionship are called pets, while those domesticated for food or work are known as livestock.

This biological mutualism is not restricted to humans with domestic crops and livestock but is well-documented in nonhuman species, especially among a number of social insect domesticators and their plant and animal domesticates, for example the ant–fungus mutualism that exists between leafcutter ants and certain fungi.

Domestication syndrome is the suite of phenotypic traits arising during domestication that distinguish crops from their wild ancestors. The term is also applied to vertebrate animals, and includes increased docility and tameness, coat color changes, reductions in tooth size, changes in craniofacial morphology, alterations in ear and tail form (e.g., floppy ears), more frequent and nonseasonal estrus cycles, alterations in adrenocorticotropic hormone levels, changed concentrations of several neurotransmitters, prolongations in juvenile behavior, and reductions in both total brain size and of particular brain regions.

The domestication of animals and plants began with the wolf (Canis lupus) at least 15,000 years before present (YBP), which then led to a rapid shift in the evolution, ecology, and demography of both humans and numerous species of animals and plants. The sudden appearance of the domestic dog (Canis lupus familiaris) in the archaeological record was followed by livestock and crop domestication, and the transition of humans from foraging to farming in different places and times across the planet. Around 10,000 YBP, a new way of life emerged for humans through the management and exploitation of plant and animal species, leading to higher-density populations in the centers of domestication, the expansion of agricultural economies, and the development of urban communities.

A 2018 domestication study looked at the reasons why the archeological record that is based on the dating of fossil remains often differed from the genetic record contained within the cells of living species. The study concluded that our inability to date domestication is because domestication is a continuum and there is no single point where we can say that a species was clearly domesticated using these two techniques. The study proposes that changes in morphology across time and how humans were interacting with the species in the past needs to be considered in addition to these two techniques.

Animals

Theory

Karakul sheep and shepherds in Iran. Photograph by Harold F. Weston, 1920s

The domestication of animals is the mutual relationship between animals with the humans who have influence on their care and reproduction. Charles Darwin recognized the small number of traits that made domestic species different from their wild ancestors. He was also the first to recognize the difference between conscious selective breeding in which humans directly select for desirable traits, and unconscious selection where traits evolve as a by-product of natural selection or from selection on other traits. There is a genetic difference between domestic and wild populations. There is also such a difference between the domestication traits that researchers believe to have been essential at the early stages of domestication, and the improvement traits that have appeared since the split between wild and domestic populations. Domestication traits are generally fixed within all domesticates, and were selected during the initial episode of domestication of that animal or plant, whereas improvement traits are present only in a proportion of domesticates, though they may be fixed in individual breeds or regional populations.

Domestication should not be confused with taming. Taming is the conditioned behavioral modification of an animal to reduce its natural avoidance of humans, and to accept the presence of humans. Domestication is the permanent genetic modification of a bred lineage that leads to an inherited predisposition towards humans. Certain animal species, and certain individuals within those species, make better candidates for domestication than others because they exhibit certain behavioral characteristics: (1) the size and organization of their social structure; (2) the availability and the degree of selectivity in their choice of mates; (3) the ease and speed with which the parents bond with their young, and the maturity and mobility of the young at birth; (4) the degree of flexibility in diet and habitat tolerance; and (5) responses to humans and new environments, including flight responses and reactivity to external stimuli.

Mammals

The beginnings of animal domestication involved a protracted coevolutionary process with multiple stages along different pathways. It is proposed that there were three major pathways that most animal domesticates followed into domestication: (1) commensals, adapted to a human niche (e.g., dogs, cats, fowl, possibly pigs); (2) prey animals sought for food (e.g., sheep, goats, cattle, water buffalo, yak, pig, reindeer, llama and alpaca); and (3) targeted animals for draft and nonfood resources (e.g., horse, donkey, camel). The dog was the first domesticant, and was established across Eurasia before the end of the Late Pleistocene era, well before cultivation and before the domestication of other animals. Humans did not intend to domesticate animals from, or at least they did not envision a domesticated animal resulting from, either the commensal or prey pathways. In both of these cases, humans became entangled with these species as the relationship between them, and the human role in their survival and reproduction, intensified, leading eventually to a formalised animal husbandry. Although the directed pathway proceeded from capture to taming, the other two pathways are not as goal-oriented and archaeological records suggest that they took place over much longer time frames.

Unlike other domestic species which were primarily selected for production-related traits, dogs were initially selected for their behaviors. The archaeological and genetic data suggest that long-term bidirectional gene flow between wild and domestic stocks – including donkeys, horses, New and Old World camelids, goats, sheep, and pigs – was common. One study has concluded that human selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars into pigs and created domestication islands in the genome. The same process may also apply to other domesticated animals.

Birds

The red junglefowl of Southeast Asia was domesticated, apparently for cockfighting, some 7,000 years ago.

Domesticated birds principally mean poultry, raised for meat and eggs: some Galliformes (chicken, turkey, guineafowl) and Anseriformes (waterfowl: duck, goose, swan). Also widely domesticated are cagebirds such as songbirds and parrots; these are kept both for pleasure and for use in research. Domestic pigeon is known as a messenger, research suggests it was domesticated as early as 10,000 years ago. Chickens were domesticated at least 7,000 years ago, with fossils in China from c. 5400 BC. The chicken's wild ancestor is Gallus gallus, the red junglefowl of Southeast Asia, and another species, probably the grey junglefowl of India. It appears to have been kept initially for cockfighting rather than for food.

Invertebrates

Sericulturalists preparing silkworms for spinning of the silk

Two insects, the silkworm and the western honey bee, have been domesticated for over 5,000 years, often for commercial use. The silkworm is raised for the silk threads wound around its pupal cocoon; the western honey bee, for honey, and, lately, for pollination of crops.

Several other invertebrates have been domesticated, both terrestrial and aquatic, including some such as Drosophila melanogaster fruit flies and the freshwater cnidarian Hydra for research into genetics and physiology. Few have a long history of domestication. Most are used for food or other products such as shellac and cochineal. The phyla involved are Cnidaria, Platyhelminthes (for biological control), Annelida, Mollusca, Arthropoda (marine crustaceans as well as insects and spiders), and Echinodermata. While many marine molluscs are used for food, only a few have been domesticated, including squid, cuttlefish and octopus, all used in research on behaviour and neurology. Terrestrial snails in the genera Helix and Murex are raised for food. Several parasitic or parasitoidal insects including the fly Eucelatoria, the beetle Chrysolina, and the wasp Aphytis are raised for biological control. Conscious or unconscious artificial selection has many effects on species under domestication; variability can readily be lost by inbreeding, selection against undesired traits, or genetic drift, while in Drosophila, variability in eclosion time (when adults emerge) has increased.

Plants

The initial domestication of animals impacted most on the genes that controlled their behavior, but the initial domestication of plants impacted most on the genes that controlled their morphology (seed size, plant architecture, dispersal mechanisms) and their physiology (timing of germination or ripening).

Farmers with wheat and cattle - Ancient Egyptian art 1,422 BC

The domestication of wheat provides an example. Wild wheat shatters and falls to the ground to reseed itself when ripe, but domesticated wheat stays on the stem for easier harvesting. This change was possible because of a random mutation in the wild populations at the beginning of wheat's cultivation. Wheat with this mutation was harvested more frequently and became the seed for the next crop. Therefore, without realizing, early farmers selected for this mutation. The result is domesticated wheat, which relies on farmers for its reproduction and dissemination.

History

The earliest human attempts at plant domestication occurred in the Middle East. There is early evidence for conscious cultivation and trait selection of plants by pre-Neolithic groups in Syria: grains of rye with domestic traits have been recovered from Epi-Palaeolithic (c. 11,050 BCE) contexts at Abu Hureyra in Syria, but this appears to be a localised phenomenon resulting from cultivation of stands of wild rye, rather than a definitive step towards domestication.

By 10,000 BCE the bottle gourd (Lagenaria siceraria) plant, used as a container before the advent of ceramic technology, appears to have been domesticated. The domesticated bottle gourd reached the Americas from Asia by 8000 BCE, most likely due to the migration of peoples from Asia to America.

Cereal crops were first domesticated around 9000 BCE in the Fertile Crescent in the Middle East. The first domesticated crops were generally annuals with large seeds or fruits. These included pulses such as peas and grains such as wheat. The Middle East was especially suited to these species; the dry-summer climate was conducive to the evolution of large-seeded annual plants, and the variety of elevations led to a great variety of species. As domestication took place humans began to move from a hunter-gatherer society to a settled agricultural society. This change would eventually lead, some 4000 to 5000 years later, to the first city states and eventually the rise of civilization itself.
Continued domestication was gradual, a process of intermittent trial and error. Over time perennials and small trees including the apple and the olive were domesticated. Some plants, such as the macadamia nut and the pecan, were not domesticated until recently.

In other parts of the world very different species were domesticated. In the Americas squash, maize, beans, and perhaps manioc (also known as cassava) formed the core of the diet. In East Asia millet, rice, and soy were the most important crops. Some areas of the world such as Southern Africa, Australia, California and southern South America never saw local species domesticated.

Differences from wild plants

Domesticated plants may differ from their wild relatives in many ways, including

• the way they spread to a more diverse environment and have a wider geographic range;
• different ecological preference (sun, water, temperature, nutrients, etc. requirements), different disease susceptibility;
• conversion from a perennial to annual;
• loss of seed dormancy and photoperiodic controls;
• simultaneous flower and fruit, double flowers;
• a lack of shattering or scattering of seeds, or even loss of their dispersal mechanisms completely;
• less efficient breeding system (e.g. lack normal pollinating organs, making human intervention a requirement), smaller seeds with lower success in the wild, or even complete sexual sterility (e.g. seedless fruits) and therefore only vegetative reproduction;
• less defensive adaptations such as hairs, thorns, spines, and prickles, poison, protective coverings and sturdiness, rendering them more likely to be eaten by animals and pests unless cared by humans;
• chemical composition, giving them better palatability (e.g. sugar content), better smell, and lower toxicity

edible part larger, and easier separated from non-edible part (e.g. freestone fruit).

Traits that are being genetically improved

There are many challenges facing modern farmers, including climate change, pests, soil salinity, drought, and periods with limited sunlight.

Drought is one of the most serious challenges facing farmers today. With shifting climates comes shifting weather patterns, meaning that regions that could traditionally rely on a substantial amount of precipitation were, quite literally, left out to dry. In light of these conditions, drought resistance in major crop plants has become a clear priority. One method is to identify the genetic basis of drought resistance in naturally drought resistant plants, i.e. the Bambara groundnut. Next, transferring these advantages to otherwise vulnerable crop plants. Rice, which is one of the most vulnerable crops in terms of drought, has been successfully improved by the addition of the Barley hva1 gene into the genome using transgenetics. Drought resistance can also be improved through changes in a plant's root system architecture, such as a root orientation that maximizes water retention and nutrient uptake. There must be a continued focus on the efficient usage of available water on a planet that is expected to have a population in excess of nine-billion people by 2050.

Another specific area of genetic improvement for domesticated crops is the crop plant's uptake and utilization of soil potassium, an essential element for crop plants yield and overall quality. A plant's ability to effectively uptake potassium and utilize it efficiently is known as its potassium utilization efficiency. It has been suggested that first optimizing plant root architecture and then root potassium uptake activity may effectively improve plant potassium utilization efficiency.

Crop plants that are being genetically improved

Cereals, rice, wheat, corn, and barley, make up a huge amount of the global diet across all demographic and social scales. These cereal crop plants are all autogamous, i.e. self- fertilizing, which limits overall diversity in allelic combinations, and therefore adaptability to novel environments. To combat this issue the researchers suggest an "Island Model of Genomic Selection". By breaking a single large population of cereal crop plants into several smaller sub-populations which can receive "migrants" from the other subpopulations, new genetic combinations can be generated.

The Bambara groundnut is a durable crop plant that, like many underutilized crops, has received little attention in an agricultural sense. The Bambara Groundnut is drought resistant and is known to be able to grow in almost any soil conditions, no matter how impoverished an area may be. New genomic and transcriptomic approaches are allowing researchers to improve this relatively small-scale crop, as well as other large-scale crop plants. The reduction in cost, and wide availability of both microarray technology and Next Generation Sequencing have made it possible to analyze underutilized crops, like the groundnut, at genome-wide level. Not overlooking particular crops that don't appear to hold any value outside of the developing world will be key to not only overall crop improvement, but also to reducing the global dependency on only a few crop plants, which holds many intrinsic dangers to the global population's food supply.

Challenges facing genetic improvement

The semi-arid tropics, ranging from parts of North and South Africa,Asia especially in the South Pacific, all the way to Australia are notorious for being both economically destitute and agriculturally difficult to cultivate and farm effectively. Barriers include everything from lack of rainfall and diseases, to economic isolation and environmental irresponsibility. There is a large interest in the continued efforts, of the International Crops Research Institute for the Semi-Arid Tropics (ICRSAT) to improve staple foods. some mandated crops of ICRISAT include the groundnut, pigeonpea, chickpea, sorghum and pearl millet, which are the main staple foods for nearly one billion people in the semi-arid tropics. As part of the ICRISAT efforts, some wild plant breeds are being used to transfer genes to cultivated crops by interspecific hybridization involving modern methods of embryo rescue and tissue culture. One example of early success has been work to combat the very detrimental peanut clump virus. Transgenetic plants containing the coat protein gene for resistance against peanut clump virus have already been produced successfully. Another region threatened by food security are the Pacific Island Countries, which are disproportionally faced with the negative effects of climate change. The Pacific Islands are largely made up of a chain of small bodies of land, which obviously limits the amount of geographical area in which to farm. This leaves the region with only two viable options 1.) increase agricultural production or 2.) increase food importation. The latter of course runs into the issues of availability and economic feasibility, leaving only the first option as a viable means to solve the region's food crisis. It is much easier to misuse the limited resources remaining, as compared with solving the problem at its' core.

Working with wild plants to improve domestics

Work has also has been focusing on improving domestic crops through the use of crop wild relatives. The amount and depth of genetic material available in crop wild relatives is larger than originally believed, and the range of plants involved, both wild and domestic, is ever expanding. Through the use of new biotechnological tools such as genome editing, cisgenesis/intragenesis, the transfer of genes between crossable donor species including hybrids, and other omic approaches.

Wild plants can be hybridized with crop plants to form perennial crops from annuals, increase yield, growth rate, and resistance to outside pressures like disease and drought. It is important to remember that these changes take significant lengths of time to achieve, sometimes even decades. However, the outcome can be extremly successful as is the case with a hybrid grass variant known as Kernza. Over the course of nearly three decades, work was done on an attempted hybridization between an already domesticated grass strain, and several of its wild relatives. The domesticated strain as was more uniform in its orientation, but the wild strains were larger and propagated faster. The resulting Kernza crop has traits from both progenitors: uniform orientation and a linearly vertical root system from the domesticated crop, along with increased size and rate of propagation from the wild relatives.

Fungi

Button mushrooms are widely cultivated for food.

Several species of fungi have been domesticated for use directly as food, or in fermentation to produce foods and drugs. The white button mushroom Agaricus bisporus is widely grown for food. The yeast Saccharomyces cerevisiae have been used for thousands of years to ferment beer and wine, and to leaven bread. Mould fungi including Penicillium are used to mature cheeses and other dairy products, as well as to make drugs such as antibiotics.

Effects

On domestic animals

Selection of animals for visible "desirable" traits may have undesired consequences. Captive and domesticated animals often have smaller size, piebald color, shorter faces with smaller and fewer teeth, diminished horns, weak muscle ridges, and less genetic variability. Poor joint definition, late fusion of the limb bone epiphyses with the diaphyses, hair changes, greater fat accumulation, smaller brains, simplified behavior patterns, extended immaturity, and more pathology are among the defects of domestic animals. All of these changes have been documented by archaeological evidence, and confirmed by animal breeders in the 20th century. In 2014, a study proposed the theory that under selection, docility in mammals and birds results partly from a slowed pace of neural crest development, that would in turn cause a reduced fear–startle response due to mild neurocristopathy that causes domestication syndrome. The theory was unable to explain curly tails nor domestication syndrome exhibited by plants.

A side effect of domestication has been zoonotic diseases. For example, cattle have given humanity various viral poxes, measles, and tuberculosis; pigs and ducks have given influenza; and horses have given the rhinoviruses. Many parasites have their origins in domestic animals. The advent of domestication resulted in denser human populations which provided ripe conditions for pathogens to reproduce, mutate, spread, and eventually find a new host in humans.

Paul Shepard writes "Man substitutes controlled breeding for natural selection; animals are selected for special traits like milk production or passivity, at the expense of overall fitness and nature-wide relationships...Though domestication broadens the diversity of forms – that is, increases visible polymorphism – it undermines the crisp demarcations that separate wild species and cripples our recognition of the species as a group. Knowing only domestic animals dulls our understanding of the way in which unity and discontinuity occur as patterns in nature, and substitutes an attention to individuals and breeds. The wide variety of size, color, shape, and form of domestic horses, for example, blurs the distinction among different species of Equus that once were constant and meaningful."

On society

Jared Diamond in his book Guns, Germs, and Steel describes the universal tendency for populations that have acquired agriculture and domestic animals to develop a large population and to expand into new territories. He recounts migrations of people armed with domestic crops overtaking, displacing or killing indigenous hunter-gatherers, whose lifestyle is coming to an end.

Some anarcho-primitivist authors describe domestication as the process by which previously nomadic human populations shifted towards a sedentary or settled existence through agriculture and animal husbandry. They claim that this kind of domestication demands a totalitarian relationship with both the land and the plants and animals being domesticated. They say that whereas, in a state of wildness, all life shares and competes for resources, domestication destroys this balance. Domesticated landscape (e.g. pastoral lands/agricultural fields and, to a lesser degree, horticulture and gardening) ends the open sharing of resources; where "this was everyone's", it is now "mine". Anarcho-primitivists state that this notion of ownership laid the foundation for social hierarchy as property and power emerged. It also involved the destruction, enslavement, or assimilation of other groups of early people who did not make such a transition.

On diversity

Industrialized wheat harvest - North America today

In 2016, a study found that humans have had a major impact on global genetic diversity as well as extinction rates, including a contribution to megafaunal extinctions. Pristine landscapes no longer exist and have not existed for millennia, and humans have concentrated the planet's biomass into human-favored plants and animals. Domesticated ecosystems provide food, reduce predator and natural dangers, and promote commerce, but have also resulted in habitat loss and extinctions commencing in the Late Pleistocene. Ecologists and other researchers are advised to make better use of the archaeological and paleoecological data available for gaining an understanding the history of human impacts before proposing solutions.