Questions & explanations
1. Explain how genomic selection can be integrated into a nucleus breeding program that already uses artificial insemination and performance testing.
In a nucleus program, all candidate boars and gilts are performance-tested for traits like growth rate, backfat, and loin depth. They are also genotyped with a SNP chip. The genomic predictions are combined with their own performance records and pedigree information using a method called single-step genomic BLUP (best linear unbiased prediction). This produces a single genomic enhanced breeding value (GEBV). The top-ranked animals are selected for breeding. For boars, they enter the AI stud; for gilts, they are mated to produce the next generation. The reference population is updated each year by adding newly genotyped animals with reliable phenotypes. The program runs on a 12-month cycle: birth, genotyping, performance test, selection, and mating. Over time, the rate of genetic gain increases by 30-50% compared to traditional selection.
2. What is the main disadvantage of using a two-breed rotational crossbreeding system compared to a three-breed terminal system?
A two-breed rotational system maintains only about 67% of maximum heterosis, while a three-breed terminal system can achieve 100% heterosis in the market pigs. In a two-breed rotation, the same two breeds are alternated, so the offspring are always 50% of one breed and 50% of the other, but heterosis is lower because the breeds are not all different. Additionally, a two-breed rotation does not allow for breed complementarity as effectively; both breeds must be good for both maternal and terminal traits, which is rare. The terminal system uses specialized maternal and paternal lines, giving better overall performance. However, the terminal system requires purchasing replacement gilds from a separate multiplier herd, which adds cost.
3. What challenges might a breeding company face when implementing genomic selection in a commercial swine operation?
The main challenge is the initial cost of genotyping thousands of animals with SNP chips to build a reference population. Each SNP chip costs $30-50, so a reference set of 10,000 animals costs $300,000-500,000. Another challenge is data management: the company must collect accurate phenotypes (like growth rate, feed intake, carcass traits) on the reference animals. In commercial farms, recording individual feed intake is difficult and expensive. Additionally, the prediction equations need to be updated every few generations as the population changes. There is also a risk of inbreeding if selection is too intense on a few high-GEBV animals. Finally, staff training is needed to understand and trust genomic predictions.
4. Give an example of breed complementarity in a terminal crossbreeding system.
In a terminal cross, a maternal breed (e.g., Yorkshire or Landrace) is used for the sow because of its excellent mothering ability, large litter size, and good milk production. The sow is mated to a terminal sire breed like Duroc or Pietrain, which contributes fast growth, high lean meat percentage, and superior meat quality. The resulting crossbred offspring grow quickly, have good feed conversion, and produce a high-quality carcass. All offspring are sold for meat, so the maternal breed's traits are not needed in the market pigs. This system maximizes the strengths of each breed: the sow is a good mother, and the sire produces fast-growing, lean pigs. It is the most common system in large commercial operations.
5. What is parthenogenesis in silkworms?
Parthenogenesis is when an egg develops into an embryo without being fertilized by sperm. In silkworms, this happens naturally in some strains. The offspring are always female because they get two Z chromosomes from the mother. The mother's egg has a Z chromosome, and it duplicates to become ZZ (male) or sometimes ZW? Actually, in silkworms, natural parthenogenesis produces only females because the egg becomes diploid by retaining the second polar body, resulting in ZW females. Wait, correction: In silkworms, natural thelytokous parthenogenesis produces females (ZW). The egg undergoes automixis to restore diploidy. So all offspring are female clones of the mother. This is rare but can be induced artificially.
6. What is genomic selection in swine breeding?
Genomic selection uses DNA markers called single nucleotide polymorphisms (SNPs, pronounced 'snips') to predict an animal's genetic merit for traits like growth rate or meat quality. A SNP chip is a tool that reads thousands of these markers across the genome. By comparing an animal's SNP profile to a reference population with known performance, breeders can estimate its breeding value without waiting for its own offspring data. This speeds up genetic progress because selection decisions can be made early in life. It is especially useful for traits that are hard or expensive to measure, like disease resistance. Genomic selection is now common in nucleus herds to identify the best young boars and gilts.
7. What is crossbreeding and why is it used in swine production?
Crossbreeding is mating pigs from different breeds, such as a Duroc boar with a Landrace sow. The main reason is to take advantage of heterosis, also called hybrid vigor. Heterosis means that crossbred offspring perform better than the average of their purebred parents. For example, crossbred pigs often grow faster, have better survival rates, and produce more piglets per litter. Crossbreeding also allows breed complementarity, where each breed contributes its strengths. For instance, a maternal breed like Yorkshire is good for mothering ability, while a terminal breed like Duroc provides superior meat quality. Most commercial pork production uses a three-breed cross system to maximize heterosis.
8. How can bakery waste be used in swine diets and what are the risks?
Bakery waste includes unsold bread, cookies, pastries, and dough. It is high in energy (starch and sugar) and low in fiber, making it a good substitute for corn. It can be included at up to 30% of the diet, but it must be processed to prevent spoilage. The waste is often dried and ground into a meal to ensure uniform mixing. Risks include variability in nutrient content (different batches may have different ingredients), potential mold growth, and high salt content from salted products. Mycotoxins from mold can harm pigs. Also, bakery waste may contain chocolate or other ingredients toxic to pigs (theobromine). Therefore, sourcing from reliable suppliers and testing for mycotoxins is essential.
9. Compare genomic selection with traditional pedigree-based selection. Which gives more accurate predictions for a young boar?
Genomic selection is more accurate because it uses actual DNA marker information rather than just the average of relatives. Traditional pedigree-based selection assumes that full siblings share exactly 50% of their genes, but in reality they may share more or less. Genomic selection measures the true proportion of shared DNA using SNP chips. For a young boar, genomic prediction can achieve accuracy of 0.5-0.7 for traits like backfat thickness, while pedigree-based accuracy is often below 0.3. The extra accuracy comes from capturing Mendelian sampling variation—the random shuffling of genes from parents. Therefore, genomic selection identifies superior individuals within a litter more reliably.
10. Give an example of how genomic selection can improve a low-heritability trait like litter size in pigs.
Litter size has low heritability (about 0.1), meaning only 10% of the differences between animals are genetic. Traditional selection is slow because you must wait for sows to have several litters to get accurate records. With genomic selection, a young boar can be genotyped and his GEBV for litter size is predicted from the SNP effects estimated in a large reference population of sows with litter records. Breeders can then select boars with high GEBV for litter size and use them via artificial insemination. Their daughters will have, on average, 0.5-1 more piglets per litter than daughters of unselected boars. This accelerates genetic gain for a trait that was previously difficult to improve.
11. How is embryo transfer performed in pigs and what are its benefits?
Embryo transfer (ET) involves collecting fertilized eggs (embryos) from a donor sow and transferring them into recipient sows. The donor is superovulated with hormones (e.g., PMSG and hCG) to produce multiple eggs, then artificially inseminated. About 6-7 days later, embryos are flushed from the donor's uterus using a catheter and sterile medium. The embryos are evaluated under a microscope for quality, and 10-15 good embryos are transferred surgically or non-surgically into a synchronized recipient sow. Benefits include moving genetics without transporting live animals, reducing disease risk, and multiplying valuable genetics quickly. ET also allows old or injured sows to produce offspring.
12. Compare surgical and non-surgical embryo transfer in pigs. Which is more practical for commercial use?
Surgical embryo transfer requires opening the abdomen (laparotomy) to access the uterus, which is invasive, requires anesthesia, and has risks of infection and adhesions. It is mainly used in research or for valuable donors. Non-surgical transfer uses a catheter passed through the cervix into the uterus, similar to artificial insemination. It is less invasive, faster, and can be done on farm without surgery. However, non-surgical transfer in pigs has lower pregnancy rates (40-60%) compared to surgical (60-80%) because the catheter may not deposit embryos correctly. For commercial use, non-surgical is more practical because it is simpler and cheaper, but success rates need improvement.