QA Informed Breeding

1. What is the main difference between genomic selection and genome wide association analyses ?
   1. Association analyses uses only rare markers
   2. Bothe techniques use simple linear regression to select markers with large and small effects
   3. Genomic selection is used for prediction, association mapping is used for gene mapping
   4. Explanation
      1. In genomic selection all markers are used for prediction.
      2. Association mapping concentrates on markers with significant effects
      3. Association analyses is for complex traits with heritability close to one.
2. Select one main advantage of genomic selection over phenotypic selection ?
   1. Genomic selection can not be combined with phenotypic selection
   2. Genomic selection os for mapping genes using complex statistical models
   3. Genomic selections makes the breeding cycle shorter
   4. Explanation:
      1. By using markers breeding values of unobserved individuals can be predicted without the need to phenotype them.
      2. Phenotypic selections is for mapping genes using complex statistical models
3. Define genotype x environment interaction ?
   1. Genes with differential response under different environmental conditions
   2. Explanation:
      1. Environments module genes and thus making some genes to response differently under differential environmental stimulus
      2. Genes acting in an additive action in all the environments.
      3. Genes acting additive in some environments and dominance in other environments.
      4. Genomic regions acting similarly in all the environments.
4. What is the difference between QTL and Association mapping?
   1. QTL analysis is performed in constructed bi-parental populations using contrasting parents, therefore only one recombination event is recorded in the population. Association mapping considers the use of natural populations or panels with diverse cultivars with the purpose of recording more recombination events that contributes to a higher resolution to find regions associated to traits.
   2. Bi-parental QTL mapping: uses crosses between tolerant and susceptible parents (contrasts for the trait of interest) and then phenotype and genotype (with molecular markers) progeny populations to determine QTL (marker trait associations (MTA). Association mapping (AM): or linkage disequilibrium (LD) mapping or Genome-Wide Association Mapping (GWAS) is an alternative approach.
   3. With GWAS associations are made between genotypes based on molecular markers and phenotypes of various traits in reference germplasm sets. Theoretically, this technique can be applied to any set of germplasm and detect QTL for as many traits that show variation.
5. What is type 1 Error in AM ?
   1. GWAS has some limitations including Type I error (false positives), because of population structure.
6. What is the difference between GWAS, QTL mapping, and linkage analysis?
   1. linkage mapping/recombination mapping/positional cloning - rely on known markers (typically SNPs) that are close to the gene responsible for a disease or trait to segregate with that marker within a family. Works great for high-penetrance, single gene traits and diseases.
   2. QTL mapping/interval mapping - for quantitative traits like height that are polygenic. Same as linkage mapping except the phenotype is continuous and the markers are put into a scoring scheme to measure their contribution - i.e. "marker effects" or "allelic contribution". Big in agriculture.
   3. GWAS/linkage disequilibrium mapping - score thousands of SNPs at once from a population of unrelated individuals. Measure association with a disease or trait with the presumption that some markers are in LD with, or actually are, causative SNPs.
   4. So linkage mapping and QTL mapping are similar in that they rely on Mendelian inheritance to isolate loci. QTL mapping and GWAS are similar in that they typically measure association in terms of log-odds along a genetic or physical map and do not assume one gene or locus is responsible. And finally, linkage mapping and GWAS are both concerned with categorical traits and diseases.
7. Major allele vs Minor allele
   1. Minor allele frequency. Minor allele frequency (MAF) refers to the frequency at which the second most common allele occurs in a given population. widely used in population genetics studies because it provides information to differentiate between common and rare variants in the population.
8. Forward vs Backward selection