Genomic selection

Genomic selection in animal breeding means that genomic information is used together with phenotypic information to calculate estimated breeding values. Genomic information in itself is rather useless. It only shows what genetic markers, QTLs, SNPs or microsatellites one animal has. Only by connecting those markers to wanted traits can we select the animal with the "right" markers. For example, we may know that a marker X1 is connected with high milk yield, and X2 with susceptibility to metabolic illnesses. Then we can choose animals with X1 but not X2. Genetic mapping is the key to connect genetic information with phenotypic observations. However, once the traits have been linked with genetic markers, pure genotype information is enough to value an animal. In practice, genomic estimated breeding value GEBV always combines genotypic data with pedigree information.

Using genomic information increases accuracy in all traits.

Single nucleotide polymorphisms, SNPs, are used in genomic selection. At one time, current genotyping technology can identify up to 800 000 SNPs from a given DNA sample. Those SNPs are evenly distributed to the DNA strand. SNPs are known to be connected to productive traits. Animals are genotyped, their genes are valued based on the SNPs, and then best animals are selected for breeding. We don't need to know where or what the actual wanted genes are - we just know which SNPs are connected to them, and use those as a basis for selection. It's a bit like orienteering: you see from the map where you are and where you have to go, even if you have no clue in which city or country you're in!


Illumina is a manufacturer of bead chips, chips which are used to identify SNPs from a genome. For example, the  PorcineSNP60 chip has 65000 evenly spaced probes for recognizing SNPs. It can be used for four pig breeds: Duroc, Landrace, Pietran, and Large White. More information about the chip can be found from the product information sheet.

Simulations

There are two ways for evaluating genetic variation in quantitative traits: simulations and experimental genetics. Simulations are cheap and easy to repeat, but the assumptions used in the simulation may not be realistic.Experimental genetics uses real data, but is more cost and labour intensive. Simulations are carried out with different computer programs. They estimate population evolution under different conditions. Each simulation is based on real data about

• allele and genotype frequencies
• linkages between markers and genes
• population and family structure
• effective population size
• reproduction parameters
• selection (if any)
• isolated / open population
• DNA alteration parameters

Simulations work with four basic forces of evolution: mutation, recombination, selection and genetic drift. Mutation adds diversity, recombination creates new combinations of alleles and breaks linkage between chromosomal regions, selection favours some genotypes with selective advantage and genetic drift makes allele frequencies fluctuate over generations. The key for simulations is that the researcher can change the underlying variables, and study the impact of (for example) population size or family structures to genetic evolution. For a free simulation software, you can try QMsim by Sargolzaei and Schenkel (http://www.aps.uoguelph.ca/~msargol/qmsim).

4N_eμ is an important term in simulations. According to professor Alban Bouquet, in a mutation drift equilibrium the SNP (or allele) frequency depends on the variable 4N_eμ.  If 4N_eμ < 1, the distribution is U-shaped. Large % of markers are fixed, and diversity is low. When 4N_eμ  = 1, the distribution is uniform, and when it's > 1, the distribution is curved out: only a few markers are fixed, and there's high diversity. In most mammals 4N_eμ is about 0,001, so most loci are fixed at MDE and many markers need to be simulated.

Comparing the effectiveness of genomic and traditional selection

(c) informedfarmers.com

In animal breeding, there are four selection pathways: sire of bull, sire of cow, dam of cow and dam of bull. Each pathway has their own selection intensity i, accuracy r_TI and generation interval L. For bovines, dams of bulls have the highest selection intensity (around 2 %), because only the best of the best are chosen. A few more sires of bulls are chosen, about 5 %, while as much as 80 % may be chosen for dams of cows. With strict selection and reliable genomic information the genetic gain is largest when dams and sires are selected at one year of age. In such a juvenile scheme (JS), genetic gain increases while rate of inbreeding decreases. Genetic gain increases the most with strictest selection intensities, but rate of  inbreeding is also higher. (Bouquet & Juga 2012)

The study by Bouquet and Juga (2012) showed that with JS, using a multiple-ovulation embryo transfer (MOET) herd of 75 heifers genetic gain is significantly increased.  MOET does not significantly increase inbreeding rates if over 33 AI sires used. Doubling the number of flushed heifers may change response to selection with over 50 AI sires, but only if the number of genotyped females is increased as well. Increasing the number of flushings per heifer from 2 to three increases both genetic and rate of inbreeding, and may not thus be advisable. All in all, MOET and JS combined impact production traits very strongly, but functional traits only little. Compared to traditional pedigree-based selection, the variance of response is slightly increased in JS schemes whereas genetic gain istremendously increased.

(c) eadgene.info

For pigs genome information also increases the accuracy of breeding values. In a study by Tribout, Larzul and Phocas (2012) a simulation generated 39% - 58% more accurate EBVs with genomic breeding schemes. Annual genetic gain increased 63% - 128%. There was variation in the results between different traits. Rate of inbreeding was reduced 49% - 60%.  They conclude that genomic breeding schemes can increase accuracy and genetic gain while decreasing rate of inbreeding without a need to modify current breeding scheme structures. 

Piglet production

The aim of piglet producing is to have as many piglets per sow per year with as little costs as possible. Approximately sows give birth 2,3 times a year. One farrow has 10-17 piglets, of which a few often die at birth or soon after. Between birth and weaning, the mortality can rise up to 13 %. About 11 piglets are weaned from each farrow, and 21 piglets / sow / year.

The efficiency of piglet production is affected by four main factors:

• Length of lactation period: Reducing the lactation time reduces fertility and number of piglets born. However, the sooned the piglets are weaned, the sooner the sow comes into heat and can be inseminated. 
• Time from weaning to insemination: Sows come into heat twice after weaning. First heat is two days after weaning, but insemination at that time does not lead to fertilization. The other heat is 4-7 days after weaning. If the sow is not inseminated then, it takes three weeks before it comes into heat again.
• Mortality of piglets: Reducing mortality directly increases piglet production. More piglets die in large farrows, so increasing farrow size is not the only solution.
• Number of piglets in a farrow: To avoid  high mortality, large farrows must be evened out between lactating sows. Mortality rate can be over 40% in farrows of 18 piglets or more.  Each sow has fourteen teats, so they cannot nurse more piglets than that. Breed of the sow also affects its "efficiency". Mixed breed sows (local breed + yorkshire) have larger farrows and have their first farrow younger than purebreds. 

Pigs to be used as parents are selected at the weight of 80-90 kilos. They need more space than finishing pigs so they can develop strong muscles, and they should be fed more freely. Abundantly fed sows grow more, release more egg cells per ovulation, come into heat earlier and have their first farrow at a younger age, but their feeding costs are higher than limited-fed sows. Growing gilts need almost as much feed as growing pigs. Young boars are fed 10% less than growing pigs. Both gilts and young boards nees as much amino acids as growing pigs.

The ideal time to inseminate a sow for the first time is at 210-230 days of age. The sow's heat lasts 20-72 hours, usually 36-48 hours. Ovulation occurs 30-36 hours after the heat begins, but the eggs live only 8 hours after ovulation. Sows should be serviced (inseminated or mated) 10-30 hours after the heat starts, before the ovulation. Sperm cells need six hours in the uterus to adapt, before they can fertilize the eggs. If the sow is serviced during the optimum time, she will have a better chance of getting pregnant and a to have larger farrow.

Young sows release 10-20 eggs in one ovulation, and older sows 15-25 eggs. Free feeding before service increases the amount of eggs released. Eggs, which are fertilized, stay 12 days floating free in the uterus. Up to 30 % of the fertilized eggs will die during this phase.This phase is called preimplantation. The implantation phase is on days 13-40 from insemination. During implantation the eggs attach to the uterus,  the placenta develops and fetuses are formed. The fetus phase lasts until the end of the pregnancy. Sows are pregnant "3/3/3": three months, three weeks and three days. Approximately 115 days after the insemination the sow will give birth.

In intensive production unproductive sows are easily culled. Culling unproductive sows is done to ensure profitability, but also to avoid unhealthy piglets. Sows are often removed, if

• they haven't come into heat at 8,5 months of age
• less than 18 piglets are weaned from their two first farrows
• the sum of days it takes for the sow to come into heat after two first farrowings is over 21 days
• it isn't pregnant after service during two heats
• it has farrowed twice or more, but produces less than 20 piglets a year
• the sow is ill, doesn't nurse the piglets, has feet problems or loses much weight during lactation
• there have been malformed or weak piglets in several farrows
• their estimated breeding value decreases
• they have farrowed more than six times, after which the litter size decreases

Nutrition of a pregnant and lactating sow

Gestating sows must get enough feed and especially protein for the fetuses to develop. If the sow gains too much weight during gestation, it will eat less after farrowing and lose a lot weight during lactation. Weightloss reduces fertility in the next heats. The condition score at insemination should be 3,5, and 3 right after weaning. Condition score is evaluated after second insemination (gilts) or after weaning (older sows).

Each sow should be fed individually during gestation. In practice they follow two phase diet. During gestation, they need 40-43 MJ ME/day, gilts needing more than older sows. Sows with a lot of moving space need slightly more feed. The feed must be fibrous, so the sows need to spend time eating and feel more satiated. It should have 5 g of intestinally digestable lysine per feed unit, or 12-14 % of crude protein. The feed can be "lactation feed" which has been diluted with grains. Young sows need more feed than old, because they still grow themselves.Thin sows (condition score 2 or 3) can be given 3 units a day. Five days before farrowing the amount of feed is cut drastically to less than 2 units a day. This will empty the intestines of the sow, making farrowing easier. Hay or straw should be given freely to avoid constipation.

(c) DonkeyHotey / Flickr

Lactating sows can be fed little during the first few days after farrowing, when their appetite is usually very low. Otherwise the feed will just spoil. After that sows are fed according to recommendations. Gilts need 80 MJ ME/day, but when the piglets grow, the amount is raised up to 93 ME MJ/day before weaning. Older sows (farrowed five times or more) need 85-98 ME MJ/day. Piglet feed can be mixed to the sow's lactation feed to ensure palatability and energy content. The feed should have 15-18 % of crude protein, and 42-51 grams of lysine a day. Protein need depends on farrow size and lactation phase. Sows also need enough calcium (8 g / feed unit), 6 g of P and 4 g of salt. Vitamins, magnesium, iron, zinc, copper, iodine and selenium are also important, and easily gained from a premix or concentrate. Feed for lactating sows must be palatable, and can be given several times a day to ensure adequate eating.

Inadequate feeding during lactation increases the dry matter content of the milk, but decreases total milk yield and protein content. Underfed sows also lose more body fat and muscle. Their piglets grow less, and have less protein and more fat than piglets from an  ideally fed sow. It is more effective for a sow to get energy using its own tissues than from feed, so some weight loss is likely even for an ideally fed sow.

See details from Formulating farm-specific swine diets (University of Minnesota).

Caring for piglets

Piglets are born without any immunity or ability to thermoregulate ( = to regulate their body temperature). The temperature inside the sow's womb is nearly 40 C, but only 20 C in the piggery, so piglets are cold and need a heat source to stay warm. The pen has to be clean, desinfected and have enough straw or other dry litter. New-born piglets weigh about 1,5 kilograms. 50-70 % of new-born piglets weighing less 800 g die soon after birth.

First born piglets get to the sow's teats sooner than others, and usually grow faster. They need colostrum during the first hours to build immunity, and to get energy for maintaining body heat. Colostrum is also rich in fat, lactose, vitamins, minerals and proteins. Piglets cannot mobilize their own tissues to get energy. Lack of milk causes the blood glucose level to drop, which makes the piglets drowsy and weak, and unable to seek nutrition. As their body heat and glucose levels continue to decrease, the piglets will fall into come and die.  Weak and last-born piglets can be guided to the teats.

(c) Organicpork.co.uk

Piglets suckle 20-23 times a day, about 5 minutes at a time. Most of time is spent butting the udder so the milk is released from the alveols. Suckling piglets get milk only for half a minute, about 0,6 dl each. The milk yield increases at each parturition from 8 to 10 kg / day. Number of piglets increases the milk yield as well, but only little, so each piglet gets less milk if the farrow is large. The sow calls the piglets for suckle with low grunts. If the piggery is noisy, the piglets cannot hear the sow, and will die soon of malnutrition. Noisy piggery also prevents the sow to hear its piglets screaming if she accidentally is laying down or sitting on them, making it impossible for her to watch out for her young.

After the first week solid food should be offered to the piglets. For some piglets this becomes an important source of nutrition. Their intestinal epithelium, enzymatic activity and stomach acid formation develop faster if they get solid food in addition to milk. At weaning these piglets are better prepared to eat only solid feed. Their chance to get diarrhea and lose weight is decreased. They also may be calmer if they've used the feed as a stimulus. Best ingredients for piglet feed are wheat and peeled oats. Small amounts of oats, barley, and whey can also be used.

At three weeks of age the piglet starts to develop its own immune system, and is no longer dependent on milk. This is also the time they are weaned, and the stress combined with low level of immunity often causes diarrhea and even deaths. If the piglets are weak or small, it is recommended to postpone weaning until the piglets are four or five weeks old.

(c) newlandpoultry.com

Legumes, rapeseed and grains in pig nutrition

This text considers the usage of legumes and rapeseed as protein source in pig nutrition. Various species of legumes are discussed, and their digestibility and nutrition contents are compared. Finally minerals are discussed, why are they needed and how to make sure inbdoors-raised pigs get all the needed minerals from their feed.

Legumes

Legumes are shrubs, herbs and trees that grow multi-leaf stalks and reproductive flowers that produce pod-shaped fruit. The pods typically house the pulses, which are are the seeds of a legume. Legumes are part of the pea, bean and lentil families. From legumes, only seeds are used in pig nutrition. Pulses can be used to replace soybean meal, which is the most common protein source in pig nutrition. Pulses are grinded to fit either solid or liquid feed. The most common pulses used in Europe are pea, broad bean, lupine, rape, and chickling. By-products of alcohol and bakery industries are also used as protein source.

Growing legumes diversify crop rotation, bind nitrogen and improve soil. Using pulses in pig feed usually needs no additional equipment or machinery, and can be used to increase self-sufficiency in protein feeds. However, they are sensitive to weather, and only the seeds are usable for pig feed. Most of the biomass thus goes to waste. It may also be difficult to find commercial complementary feeds for home-made pulse feed.

Nutritional content and toxic agents
Grain legume (pea, broad bean and lupines) pulses contain mainly water-soluble protein, which has a digestibility of 85 %. They have a lot of lysine, but may lack sulphurous amino acids methionine and cystine.The higher the crude protein content in a pulse, the lower the amount of sulphurous amino acids. Compared to soy bean meal, all pulses have about 50 % less lysine and 60% less methionine and tryptophan. Intestinal digestibility of lupines equals that of soybean meal, but other pulses fall slightly behind.

Soybean meal has much as much starch as lupines. Lupines are higher in cellulose content, and may cause mild diarrhea due to their high fibre content. Faba beans and peas have seven times more starch but less sucrose than soybean.

Lupines have a much higher fat content than other pulses, soybeans included. All pulses have much polyunsaturated fatty acids, which soften the lard (pig fat) if fed in high amounts. While soft lard is healthier for humans, it makes handling and processing the carcass more difficult.

Pulses have several toxic agents. Lectines are protease inhibitors, inhibiting protein-degrading enzymes from working and lowering the digestibility.They bind into the epitelial cells of the small intestine, damaging the mucuous membrane and affecting the immune system. Peas and faba beans have much less lectines than soybean meal. Other protease-inhibitors affect the pancreatic enzymes trypsine and chymotrypsine, which split amino acids from proteins. Soybeans are high in protease-inhibitors. Heat-processing the pulses destroys the inhibitors. Tannines may bind proteins to themselves, which inreases endogenous excretion and decreases protein digestibility. Tannines also negatively affect the taste of the feed. White-flowered legumes have no tannines. Pulses from legumes with colored flowers should be peeled, since tannines are located in the husk of the seed. Alkaloids are toxic amines found only in lupines. They disrupt the central nervous system, decrease digestibility of all nutrients, decrease fertility and cause the feed to taste bitter. No feed should have more than 0,2-0,3 grams of alkaloids per kilogram of dry matter. ODAP can be found only in chickling fetch/grass pea (Lathyrys sativus). It is a neurotoxine, which in high amounts causes permanent paralysis. ODAP content can be lowered by soaking, fermenting and heat-processing the seeds. Overall, contaminants are not a concern when using white-flowered legumes.

Less serious contaminants are vicine, saponines and alfa-galactosides. Vicine and covicine are typical for faba beans, and may affect fertility in sows. Saponines are found in legumes with colored flowes, and they taste bitter but cause no severe problems. Alfa-galactosides are carbohydrates, which pigs cannot digest at all. They are used by microbes in the colon, increasing gas production.

Using pulses in pig nutrition
Due to variable nutritional content and many contaminants, the use of pulses in pig feed must be limited. The food for sows should have a maximum of 10 % of any pulse. Piglets under 25 kg can be fed 5-15 % of pulses. Finishing pigs over 50 kg can have up to 40 % of pea, 20 % faba bean and 15 % of blue lupine in their daily feed.

Rapeseed

There are two subspecies of rapeseed: Turnip rape (Brassica rapa) and rape (Brassica napus).  They are usually not separated in processing, and thus rape products may include turnip rape as well. Here both are referred to as rapeseed. Rapeseed is used in pig nutrition as compressed cakes, powdered seeds or groats. Organic production relies heavily on rapeseed for protein, and they also include a lot of necessary phosphorus and healthy fatty acids. Organic producers cannot however use rapeseed meals which are produced using ether extraction. Rapeseeds are high in fibre content, so they fit especially well for sows.

Rapeseeds contain two toxic agents: glucosinolates and erucic acid. Only the so-called 00-variants of rape are free from both compounds. Glucosinolates are sulphurous, aliphatic compounds found in cruciferous plants. Glucosinolates cause bitter taste, decrease the metabolism of iodine in the thryroid gland and may damage the liver if their amount in feed exceeds 7 μmol/g. Crops cultivated in cool and humid environment develop less toxic agents than crops in hot and dry environments. When rapeseeds are processed, most of the glucosinolates stay in the pressed cakes.They can also be partially destroyed by heat-processing. The effects of erucic acid  are controversial and not very well known.

Soybean meals can be entirely replaced with rapeseed groats or heat-processed, pressed rapeseed cakes for growing meat pigs. Only a third of soy can be replaced with rapeseed for sows. Rapeseed-fed sows lose less weight after parturition and their piglets weigh more when born and when weaned.

Minerals

From minerals, calcium and phosphorus are the most important for pigs since they are needed for muscle contractions, nervous system, energy metabolism and blood clotting. Strong bones require the right ratio of Ca and P. Phosphorus is absorbed from the small intestine with the help of Na-transferrers, which again need vitamin D to work. Absorption of Calcium aso needs vitamin D. If the animal gets more phosphorus than it needs or the phosphorus is in an insoluble form, the excess will be secreted in urine.

Sheep with inherited rickets. (c) Dittmer, Thompson, Blair 2009

Lack of Ca, P and vitamin D causes rickets in young animals and osteomalacia in old. Pigs need to get 1,2-1,4 times more Ca than P. Exceeding the needed amount of Ca decreases the absorbancy of zinc and can cause skin problems for young pigs. Pregnant sows with calcium deficiency have weak contractions, and piglets are born with oxygen-deficieny and covered in feces. The probability of uterus infection is also increased.

50-90 % of the phosphorus in plants exists as phytic acid (inositol hexakisphosphate). Compressed rapeseed and rapeseed groats contain most free phosphorus, approximately 11 g P / kg dry matter (DM), but as much as 32 grams of phytic acid in a kilogram of DM. Barley, wheat and oats contain only 3,5 g P / kg DM and 10 g phytic acid / kg DM. Phytic acid exists as K- and Mg-salts, and forms complexes with other positively charged ions. Monogastric animals like swine cannot digest phytic acid. They need an enzyme called phytase to remove phosphate from the inositol ring in the phytate molecule. Often phytase is added to pig feed, because the natural phytase in plants is destroyed in heat-processing. Some by-products of alcohol industry (barley protein feed) have almost only free P, since the phytic acid denaturates in the ethanol creation process.

Grains

Grains, and especially barley, is the most important component in pig nutrition in Europe. Barley can be given to pigs of all ages, and without mixing it to other ingredients. Oats are very fibrous, and are used mostly for sows to replace 50% of the barley. For meat pigs, the diet must contain less than 50% of wheat and oats to avoid softening the lard. Rye is not commonly used at all, but may be used in small proportions for growing pigs.

All grains must be fed either dried or as silage, but the grains must be flattened, grinded or powdered before feeding. Grinded grains preserved with propionic acid are safe to feed, since the acid is a natural product of the gastric system, and it keeps the grain free from spores, fungi and mold. Anaerobic preservation can also be used. Grains must always be clean and in good condition before feeding. Moldy grains cause gastric problems or other severe effects, and sprouted and very light grains have only low nutritional value. Moldy grains cannot be given to sows and piglets at all.

All grains contain roughly the same amount of starch, ash and crude protein. Whole-grain oats and barley have the most crude carbohydrates (hemicellulose, cellulose and lignin), but peeled oats and barley have less CC than whole-grain wheat and rye. Compared to soybean meals, grains contains approximately 2/3 less protein. The amino acids in grains have intestinal digestibility of 60-90 depending on the amino acid. Grains fertilized with nitrogen contain 2 % more protein, but less lysine than non-nitrogen-fertilized grains.

Grains must be harvested at the right time and silaged and grinded properly. Good grains are clean, bright-colored and smell fresh. A hectolitre of barley should weight over 66 kgs and oat over 56 kgs. Lighter grains have less organic matter and considerably more neutral detergent fibres, which make the grains less digestible. All grains must be dried to 14 % of moisture immediately after harvesting to ensure microbiological quality. The protein content must be analyzed and found to be around 12-13 %. Barley must contain over 59 % of starch (in dry matter). Grains should be stored so that birds, pigs or pests cannot contaminate them with feces.

More information

Plants poisonous to livestock (Cornell University): http://www.ansci.cornell.edu/plants/php/plants.php?action=display&ispecies=swine

Jezierny, D.; Mosenthin, R.; Bauer, E. 2010. The use of grain legumes as a protein source in pig nutrition: A review.  Animal Feed Science and Technology vol. 157 issue 3-4 May 11, 2010. p. 111-128

Partanen K., Valaja J., Jalava T., Siljander-Rasi H. 2001. Composition, ileal amino acid digestibility and nutritive value of organically grown legume seeds and conventional rapeseed cakes for pigs. Agricultural and food science in Finland, Vol 10 (2001): 309-322.

Pig nutrition: minerals and vitamins

Minerals are inorganic elements, which are divided into trace elements (or microminerals) and macrominerals depending on how much of each is present in the animal body. Trace elements are those elements, which the animal needs less than 0,01 % of the dry matter weight of it's tissues. Minerals are needed for three tasks ( (T) after the element name denotes it's a trace element):

• Building tissues

• Calcium
• Phosphorus
• Magnesium
• Silicon (T)
•  Fluorine (T)
• Sulphur

• Regulating osmotic pressure and permeability of cell membranes

• Sodium
• Potassium
• Chlorine
• Calcium
• Magnesium

• Catalyzing enzymatic and hormonal regulation

• Iron (T)
• Cobalt (T)
• Zinc (T)
• Manganese (T)
• Molybden (T)
• Selenium (T)

Vitamins are biologically active, organic compounds, which are necessary for normal bodily functions, and cannot be replaced with any other compound. Many vitamins are a part of an enzyme. Vitamins have five basic functions: antioxidant activity, proton/electron recipient, hormonal activity, coenzymatic activity and participation in genetic transcription.

Pigs need to get most of their vitamins from the feed. The vitamin content of feeds decrease during storage and processing,  so especially highly productive animals need vitamin additions. Age, health, stress, diet composition, gender and physiological state affect the need for vitamins. Vitamins of the K- and B-groups are formed in the color by microbes, but absorbancy may be weak. The minimum dose is where no symptoms of deficiency are apparent. The optimum need is the amount of vitamins needed to secure as high a production as possible, health, resistance against illnesses and adequate vitamin reserves.Exceeding the optimum need is costly, since the excess is secreted out from the body. Vitamins may also have toxic effects if the dosage is greatly exceeded for a long period of time.

Pigs are often raised indoors, so they cannot synthetize D vitamin from sunlight at all. Normally pigs could get K and B vitamins from feces, but if there's grating on the floor, this too becomes impossible. The most often needed vitamins are already added to commercial pig feeds and concetrates: A, D and E vitamins, niacin (B3), pantothenic acid (B5), riboflavin (B2) and B12.  Basic vitamin need stays the same for the entire life of a meat pig, but sows and and boars need more vitamin A and D than growing pigs and piglets. Sows and boars also need added choline, folic acid and K-vitamin.

The details of the different vitamins are discussed in another post about vitamins. Some vitamins have specific effects on  pigs:

• Vitamin E: increases litter size, prevents milk fever, increases immunity on sows and piglets
• Choline: increases fertility of sows and the amount of piglets born alive. Pigs can synthetize choline from methionine.
• Vitamin K: additions are needed for pregnant sows, so the vitamin can permeate the placenta and also absorb into the colostrum
• Biotine: may improve claw health

Defining breeding targets and trait values

An animal breeding is not just about calculating breeding values and creating statistics. It starts with a difficult task: defining what "best animals" are like, and what to measure. Only that which is measured can also be improved.Good breeding goals are

• well defined
• reliable, easy and cheap to measure and record
• aim to the future (help the animals adapt to the coming changes.

Goals can also be ethical, political or biological, and either global, national or areal. For example, national policy may dictate that local breeds are to be conserved, which prevents cross-breeding. Biological goal could be the need to improve fertility, and ethical goals such as breeding only healthy animals is (or should be) a global target. Also,  breeding can only target traits which have genetic variation. If every animal already has long horns, it's not feasible to aim at short horns.

Once a list of breeding goals has been made, the goals need to be weighed. Every goal cannot be the most important. Factors influencing the weighing process are

• defining efficiency: biological and economical views
• target of selection: maximizing profit or minimizing costs
• production system: developing animals / herds / breeds
• limiting factors: Limiting production inputs, number of animals
• range of planning: what needs to be inmproved first, and what later
• different roles in the food production chain: slaughterhouses have different goals than piggeries or animal welfare professionals

Example: values of fertility and udder health

 Animal breeding for farm animals targets mostly at better income for the farmer. Each trait can be given an economic value based on how it increases profits or decreases costs. Better fertility decreases medical costs, while inreased milk/meat yield increases profits and decreases cost of milk liter/cow.. A profit function has been defined to describe changes in net profit as a function of modifiable parameters (physical, biological and economical). For breeding to be profitable, the changes leading to better revenues must be caused by genetic improvement. But focus on profits has its downside. Animals are culled as soon as their production decreases, even if their best production seasons would still be ahead. Increased production is a heavy stress on metabolism and health, causing a variety of ailments on the animals.

Costs of traits for pigs have been valued to show how much an improvement of one unit of standard deviantion increases the price of pig meat. In one study, the most profitable trait was the size of litterm which increased the price of pig meat  2 cents / kg. The least profitable traits was the size of the first litter. Some breeding programmes like the Northern European NAV has defined clear values for different traits, as can be seen in the picture below.

Values of traits in NAV. (c) http://www.nordicebv.info

Calculating estimated breeding values

An estimated breeding value (EBV) is simply the value of an animal's additive genetic effects. It is the value of the genes which the animal may transfer to its offspring. Animal's BV is half of the BV of it's parent, or twice the value of the BV of it's offspring. Note that BVs are always only estimates - even if they are referred shortly as "breeding values".

The most important concepts related to EBV are shortly described below.

• Heritability, h2: The part of the difference between animals which is due to difference in breeding values. It's always between 0 and 1. h2 = Var(A)/Var(P) = σ_A² / σ_P²
• Â_i denotes the animal's EBV
• Accuracy r_TI: is the level of confidence we have for a given EBV. Accuracy is calculated as correlation between A and Â, where A is the actual BV. Accuracy increases as the amount of results (=number of offspring) and/or the heritability increase.
• Error of estimation, ε : The difference between the real and estimated BV. ε = Â - A. Usually it is 0, because we don't know A, so A = Â. The variance of ε is called PEV and calculated as Var(ε) = (1– r_TI²)Var(A) = Var(A) - Var(Â)
• BLUP: Best Linear Unbiased Prediction, currently the most used and reliable method of calculating EBVs. BLUP has three models:

• Animal model: Concerns all animals in the population, linked by their relations
• Sire model: Calculates EBVs based on the male relatives of the animal's sire
• Sire - Dam of sire -model: Corrects the EBV of the other parent by using the parent's sire's information.

A parent's EBV is two times
the EBV of its offspring.
(c) Linda Lester / betterphoto.com

EBV is calculated using one of three possible methods. First, an individual estimation considers only the animal's own results for one or several traits. Second, an estimation based on relatives considers results from the animal's relatives for one or several traits. Results are weighed based on how close a relative they're from. Factors affecting the weight are genetic relationships, genetic parameters of the trait and availability of other records. Finally, a combination uses both the animal's and its relative's information. The combination gives the most reliable EBVs, because it combines information from many sources, increasing accuracy. An excellent example of this is the international bull comparison index INTERBULL.

EBV formulas

The formula for calculating EBV varies depending on the method of estimation used. EBV based on animal's own results is calculated as

(Â_i - A) = b * (P_i - P)

and EBV for animal's relatives' results as

I = 2 b (P_i - P)
where b = (n * h²) / ((n-1) * h² + 4)

Â_i : EBV for the animal
A: Actual breeding value
b: correlation efficient
P_i: Average result of the animal's offspring
P: Average result of the comparison group
h²: heritability for the trait
n: number of offspring.

Estimating BV for a trait x using results from another, linked trait y:

 âix = b (y-μy)

where b = cov(a_x,_y) / var(y)

'
In this case, accuracy depends on genetic correlation and heritability of the measured trait y:

rax,ay = cov(a_x, _y)/ σ_axσ_y = r_axy h_y

 

Energy and protein metabolism in pigs

Metabolism is defines as the chemical changes in living cells by which energy is provided for vital processes and activities and new material is assimilate, as the sum of the processes by which a particular substance is handled in the living body and as the sum of the metabolic activities taking place in a particular environment. This text describes the metabolism of energy and proteins in pigs.

Energy metabolism

A pig needs energy for maintenance (necessary bodily functions) and for production (growth, lactation, piglet production). Pigs get energy from all organic compunds which they can digest, absorb and which their metabolic routes can use.  Energy is gained from carbohydrates, proteins, fats and organic acids. Carbohydrates are the most important energy source, but pigs can digest only starch and sugars, no cellulose or lignin.

Levels of energy (c) Evonik.com

Only a part of the energy gained is used for maintenance or production. Loss of energy happens in three stages:

• Gross energy: all the energy gained from feed
• Digestible energy: gross energy - energy in feces
• Metabolizable energy: digestible energy -
  - the energy in urine and metabolic gases
• Net energy: metabolizable energy - energy of heat produced by basic metabolism (heat increment)

Of these levels, net energy (NE) is the actual amount of energy the animal can use for production. It is only approximately 60 % of the gross energy (GE). Most energy is lost in heat (~20 %) and feces (~18 %). Chemically, oxidizing one mole of glucose (2870 kJ) produces 1976 kJ, so only 69 % is used as energy and 30 % lost as heat.

Energy is used primarily for maintenance. If a pig gets less energy than it needs for the maintenance, it utilizes its tissues and loses weight. When the energy gain exceeds the maintenance level (over 10 ME / day) , a pig is able to retain proteins and water into its tissues, building muscles. If plenty of energy is still available, pigs will convert the extra energy as body fat, which is not desirable in meat production. A pig growing 850g a day uses 3,8 MJ to gain 160g of protein for its muscles, 4,1 MJ to gain 105 of fat and 6,7 MJ for metabolism.

Nutrients can be either used as energy or in building body tissues. If fatty acids are used for energy, 66 % of the energy can be utilized. When using fatty acids for creating adipose tissue, the transformation efficiency is 90 %. For glucose the percentages are 68 % (for energy) and 74 % (for fat). From carbohydrates, starch, saccharose and glucose are most effective with 67 % of energy utilized as ATP. 

The amount and type of fibres in the feed affect the digestibility of carbohydrates. Pig feed must have enough sugar and starch to provide the needed energy.The more dietary fibre the feed has, the less energy is metabolizable. If the feed has 50 % of fibre, ~55 % of energy is metabolized. Neutral-detergent fibre (NDF) cannot be used by pigs, so the more NDF a feed has, the less energy pigs can get. High amounts of fibre also increase microbial fermentation in the colon, which increases loss of energy in gases.

Energy contents of nutrients and different feeds.

Protein metabolism 

Pigs need protein for several functions: own muscle growth, milk production and muscle growth for piglets, creation of enzymes and other proteins in the body, etc.

Animals don't actually need proteins but amino acids, which are the building blocks of proteins. Most important amino acids for pigs are lycine and metionine, but there are 9 essential amino acids in all. These amino acids can be mixed directly to the feed either as pure amino acids or as a part of a premix. The composition of amino acids in a feed determines its value as a protein source. When using home-made feeds, the amino acid composition must be determined with tests. It is also important to determine the intestinal digestibility of the amino acids. The need for amino acids can be scientifically determined by measuring production parameters (growth, carcass composition) and metabolic parameters (nitrogen in urine, urine and amino acids in plasma). The optimal composition of amino acids is called the "ideal protein", where every amino acid is present at the same time and at the correct ratio.

Animals can build non-essential amino acids only if they get enough of the essential ones at the same time. Essential amino acids cannot be synthetized at all. Unused or spare amino acids are fermented into ammonia by microbes in the colon, and the ammonia is then transferred into the liver and secreted as nitrogen. Pigs can only use amino acids which are absorbed from the small intestine. Excretion is an energy-consuming process, and increases the nitrogen emissions from pig production.

Comparing common feeds to the ideal protein gives an estimate on which amino acids and how much should be added to the feed. Barley meal lacks lysine and threonine the most,while soybean meal has almost enough of every amino acid, some even in excess. Maize lacks especially lysine and tryptophan, peas methionine and cysteine and fish meal histidine, phenylalanine and tyrosine. Digestibility trials show that adding lysine increases meat production in sows and hogs alike.

Proteins, which pigs get from their feed, are first denaturated to peptides in the stomach by HCl and pepsin. The peptides continue into the intestine, where several pancreatic enzymes break them further into oligopeptides. The intestinal wall secretes dipeptidase and aminopeptidase, which split the oligopeptides into amino acids. Amino acids are absorbed through the intestinal wall against the concentration gradient. Small peptides are also absorbed and hydrolysed. Blood stream carries the peptides and amino acids into different tissues, where they are used for protein synthesis and as energy. 

Different feeds induce a different amount of endogenous secretion: the secretion of mucus, microbe material and other nitrogenous compounds in the feces. Endogenous excretion must be taken into account when doing digestibility and metabolization trials. True digestibility excludes endogenous excretion, while apparent digestibility includes it. The digestibility of amino acids also varies between meals. Lysine is digested best from soybean meal and maize, and least from beet pulp and wheat. 

Soybean, fish and corn meals. (c)http://fomicanimalmeal.en.ec21.com

The need for protein can be calculated using a simple formula:

I = a (M + R/e)

where
I = need of amino acids from feed
a = utilization efficiency of amino acids
M = protein need for maintenance
R = protein need for muscle growth
e = degree of utilization