| Chiasmata | Cross overs. 1 recombination per generation per chromosome |
| Self Recombination Inbred Lines | Plants after F6 get rid of heterozygous |
| Mapping stages | 1) Calculate all pairwise recombination frequencies
2) Assign markers to linkage groups = chromosomes
3) Determine marker order within each linkage group
4) Decide on the identity of each linkage group
5) Decide on the orientation of each linkage group |
| Mapping traits (phenotype) | Simple traits: Controlled by a single gene, close to 100% penetrance of the trait, Mapped in the same way as a genetic marker.
Quantative traits: Controlled by two or more genes – most traits of interest to plant breeders, mapped using Quantitative Trait Locus (QTL) analysis |
| Transgressive segregation | The formation of extreme phenotypes, or transgressive phenotypes, observed in segregated hybrid populations compared to phenotypes observed in the parental lines. |
| What are the aims of QTL mapping? | 1) To map the phenotypic variation to regions of the genome controlling it
2) To assign a confidence interval to the position of the QTL
3) To determine the proportion of the variation in the trait that can be explained by the QTL
4) Determine which parent is contributing to increasing or decreasing trait values
5) Identify interactions between different QTLs |
| What do we need in order to perform QTL mapping? | A suitable population varying for the trait of interest, usually the parents of the population also differed.
The trait scores.
The genotypes of all the lines that were phenotyped.
A genetic map for the markers used for genotyping. |
| Trait evaluation | Variation in a trait in a population is caused by Genetic and Environmental contributions: Vp=Vg+Ve.
Variation due to genotype is the heritability of the trait: Heritability H^2 = VG/VP (usually H<50%). Variation resulting from the environment is large |
| The advantages of homozygous lines | Homozygous lines mean that multiple individuals of the same genotype can be grown in an experiment. Estimate proportion. Determine environmental effects in genotypes. |
| Expression QTLs (e-QTLs) | Using microarrays or transcriptome sequence.
Using gene expression data as trait. |
| Metabolite QTLs | Screen levels of wide range of metabolites across the lines in a population. To explore regulation of biochemical
pathways. This is in the realms of Systems Biology |
| A perfect storm | Mass migration, conflict and public unrest |
| Sustainable crop production | GMO, genome editing, MAS. They increase yield. |
| Breeding requires genetic variation | Natural allelic variation within the genepool: Elite varieties, breeder’s germplasm, Landraces, Undomesticated wild species.
How can we generate new variation: Mutations, Genetic modification |
| Domestication | Accumulation of mutations, selective sweeps of domestication alleles, modern crops with narrow genetic base. |
| Landraces | Dynamic pop of a cultivated plant that has historical origin, distinct identity and locks formal crop improvement |
| Recombinant Inbreds Pros: | No question of dominance.
Immortal lines.
Powerful data accumulation.
Reproducibility.
GxE experiments possible.
Inter-mating inbreds, to test genetic models. |
| Bean seed colour: Summary of Evidence | Cellular: Seed coat derived from mitotic cells, Consists of five cell layers, Cell layers die (apoptosis) when seed matures, Pigmentation intensifies as cell layers die.
Genetic: Dominant ‘Ground factor’ P allele is required for pigmentation, Several pigment biosynthesis genes, Several modifying/ intensifying genes, Patterning On/off switch genes.
Biochemical: Colour genes encode enzymes for biosynthesis of flavonoids, Pattern gene(s) are probably transcription factors |
| WRR: White blister rust | 1st infection: WRR4 (stomata)
2nd infection: WRR5/6 (inside)
3rd infection: WRR7/8
* Both WRR5/6 needed for resistance NOT separate* |
| GWAM fits in | Recombinant Inbreds. Natural variation |
| GWAM limiting factors | Sample size (as large as possible), genetic shuffling, number of generations, marker resolution, phenotyping. |
| Haplotype block | A physical group of mutations (unique sequence) that segregates as a unit in a natural population |
| Tag SNP | A Single Nucleotide Polymorphism that can be used as a genetic marker to detect inheritance of a haplotype block by an individual from a natural population |
| Linkage disequilibrium (LD) | A physical region observed as a non-random association of mutations amongst individuals in a population. The average size of LD in a population is influenced by rate of new mutations, number of generations, randomness of mating, natural selection, genetic drift, and population structure. |
