HAU16008-05-1 - Plant Genomics Lecture 5 Friday The...

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Unformatted text preview: Plant Genomics Lecture 5 Friday, October 31, 2008 The Relationship between Genes , Genomes and Phenotypic Traits Gregor Mendel 1822-1884 Charles Darwin 1809-1882 Max Delbruck 1906-1981 1990-20?? ? Genetics Evolution Molecular Biology Genomics Disease Pest Productivity Sugar-Acid Aroma Seedless Peel rots Skin disorders Storage Life The Power of Genetics Seed Color Green and yellow seeds Seed Shape Wrinkled and Round seeds An Infinite Germplasm for Plant Improvement Core Concepts : Genome mapping Genome sequencing Gene distribution Lessons from Mapping projects Recombination and linkage Molecular markers (RFLP, SSR, AFLP etc) Synteny Linkage disequilibrium Allele and Haplotype Ortholog and paralog Allele: Alternative form of a gene. One of the different forms of a gene that can exist at a single locus. Haplotype: A set of closely linked genetic markers present on one chromosome which tend to be inherited together (not easily separable by recombination). Some haplotypes may be in linkage disequilibrium (When the observed frequencies of haplotypes in a population does not agree with haplotype frequencies predicted by multiplying together the frequency of individual genetic markers in each haplotype). Orthologs are genes that are evolutionarily related, share a common ancestor but diverged by speciation. Paralogs , have a common ancestor but have diverged by gene duplication and no longer have a common functional role. So orthologs have the same function but occur in different species, while paralogs exist in the same genome but have different functions. The Problem: How do you make sense from a sea of nonsense? Apple Genome=~800 Mb or 800,000,000 bp Approx number of genes= ~40,000 Approx coding region=1,000 bp 5% of the genome has coding information Genes Nonsense Sense Apple Breeding or Marker Assisted Selection Apple Genome Sequence Genes “Separating the genes from junk” “Markers are typically the spaces between genes but not the genes” Phenotype Forward Genetics Reverse Genetics (Mapping) (Functional Genomics) AG32-3 17.6 PLG39 23.0 CPM30 8.2 CPM35-1 0.0 CPM38 3.3 CPM121-2 3.3 CPM12 3.0 RGA400d3 1.5 CPM178 4.5 CPM18 2.4 CPM121-1 2.4 CPM75 0.1 AG22 3.1 CPM60-2 1.1 CPM68-3 7.6 RGA400C1 28.0 LFCLR 31.5 Pgm2 22.4 AG32-1 16.6 CPM70 6.1 Gpi2 13.4 CPM11 5.0 CPM65 5.0 Lap-2 10.5 CPM46 14.3 CPM205 12.1 RGA51d1 3.5 PLG26 2.4 CPM85 0.4 RGA52d1 0.4 CPM62 4.1 AG11 GROUP 1 Mdh-1 Y Mdh-1 CPM155 17.2 PLG39 17.9 AG32-3 19.5 RGA100 7.4 CPM90 8.0 AG35 5.2 PLG86 8.8 PCHGMS1 8.5 CPM159 6.2 CPM71 13.3 GA-34 13.8 CPM59 6.1 Pgm1 GROUP 2 Icd-2 5.0 CPM68-2 1.6 CPM19-1 1.6 CPM83 4.1 CPM19-2 4.9 CPM6 4.1 CPM207 7.6 CPM35-2 14.4 CPM40 14.9 PLG5 13.0 AG7 14.0 CPM154 16.0 CPM165 1.8 Aat-1 4.9 OPD752 13.4 O6CAP1 0.0 CPM69 4.3 CPM66-1 5.1 AG3 1.3 AG2-2 3.5 CPM3 6.9 AG32-2 13.7 Pgd2 10.2 CPM57 0.0 CPM107 18.0 CPM109 21.5 CPM119 10.4 AG2-1 11.5 CPM60-1 2.4 AG37 3.3 CPM188 GROUP 3 Pcp CPM66-2 8.1 CPM58 1.0 CPM34 8.7 CPM202 2.8 PLG17 8.8 CPM41 3.8 CPM206 5.0 CPM53 13.4 PLG10 6.76....
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HAU16008-05-1 - Plant Genomics Lecture 5 Friday The...

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