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Biol161 07 Bw


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  • Biological complexity revealed by ENCODE. (A) Representation of a typical genomic region portraying the complexity of transcripts in the genome. (Top) DNA sequence with annotated exons of genes (black rectangles) and novel TARs (hollow rectangles). (Bottom) The various transcripts that arise from the region from both the forward and reverse strands. (Dashed lines) Spliced-out introns. Conventional gene annotation would account for only a portion of the transcripts coming from the four genes in the region (indicated). Data from the ENCODE project reveal that many transcripts are present that span across multiple gene loci, some using distal 5′ transcription start sites. (B) Representation of the various regulatory sequences identified for a target gene. For Gene 1 we show all the component transcripts, including many novel isoforms, in addition to all the sequences identified to regulate Gene 1 (gray circles). We observe that some of the enhancer sequences are actually promoters for novel splice isoforms. Additionally, some of the regulatory sequences for Gene 1 might actually be closer to another gene, and the target would be misidentified if chosen purely based on proximity.
  • (A) Seed-shattering habits of rice panicles. Photos taken after grabbing rice panicles. (Left) Nonshattering-type cultivar, Nipponbare. (Right) Shattering-type cultivar, Kasalath, in which the seed has shattered. (B) Chromosomal locations of QTLs for seed-shattering degree, based on an F2 population from a cross between Nipponbare and Kasalath. Positions of circles indicate positions of QTLs, and circle size indicates the relative contribution of each QTL. Red circles, Nipponbare alleles contributing to nonshattering habit; blue circles, Kasalath alleles contributing to nonshattering. qSH1 is marked on chromosome 1 with the nearest DNA marker (C434). (C) NonÐseed-shattering habits of Nipponbare, Kasalath, and NIL(qSH1). Breaking tensile strength upon detachment of seeds from the pedicels by bending and pulling was measured (10). Increase in value indicates loss of shattering. NIL(qSH1), a nearly isogenic line carrying a Kasalath fragment at the qSH1 locus in the Nipponbare background, as shown in fig. S1A. (D) Photo of a rice grain. White box indicates position of abscission layer formation. (E to G) Nipponbare. (H to K) Kasalath. (L to N) NIL(qSH1). (E), (H), and (L) Longitudinal sections of positions corresponding to white box in (D). Arrows point to the partial abscission layer of Kasalath in (H), the complete abscission layer of NIL(qSH1) in (L), and the corresponding region of Nipponbare in (E). (F), (I), and (M) Scanning electron microscope (SEM) photos of pedicel junctions after detachment of seeds. (G), (J), (K), and (N) Close-up SEM photos corresponding to white boxes in (F), (I), and (M). (G) Broken and rough surface of Nipponbare when forcedly detached. (N) Peeled-off and smooth surface of NIL(qSH1) upon spontaneous detachment. In Kasalath, rough center surface (K) and smooth outer surface (J) are observed. Scale bars: 500 µm in (E), (H), and (L); 100 µm in (F), (I), and (M); 10 µm in (G), (J), (K), and (N).
  • Modern examples of dehiscent wild einkorn wheat ear (A) and spikelet (B). Detail of spikelet with smooth wild abscission scar (C), indehiscent domestic ear (D), and detail of spikelet with jagged break (E) are shown. The bar chart (F) gives relative frequencies of subfossil finds with the absolute figures. Records from Aswad and Ramad (6) are of barley; the other four sites are of wheat.
  • Transcript

    • 1. Ocean County College BIOL 161 Lectures Genetics ... The grand synthesis … BIOL161_07
    • 2. An incomplete history
      • Domestication of plants and animals
      • 3. Frances Galton and Karl Pearson
        • late 19th and early 20th centuries
        • 4. human variation in morphometry and behavior
      • Charles Darwin (1861)
      • 5. What happened to Mendel? *** February 8, 1865 ***
        • Rediscovery by Tschermak (Austria), Correns (Germany) and DeVries (Holland) (1903, 1904)
    • 6. Qualitative Inheritance P 1 P 2 F 2 Number Frequency
    • 7. Comb types in chickens
      • Buttercup (V-Shaped)
        • Duplex
      • Strawberry
      • 11. V-shaped
      • 12. Silkie
      There are eight basic comb-types in chickens. In addition, there are several modifying genes (like ‘self-dubbing’, ‘spike’, making comb-typing an adventure!
    • 13. Comb types – what they really look like!
    • 16. Two genes; One Phenotype (P)
      • Single, pea, rose, walnut
        • Comb-type in chickens
    • 17. Two genes; one phenotype (G)
      • Single, pea, rose, walnut
        • Comb-type in chickens
    • 18. The Pea-Comb Phenotype
      • These are individuals carrying the pea-comb allele
      • 19. All in the genetic background of a cross of Chinese Hua-Tung and Russian Orlov breeds
      • 20. Note male/female differences!
      From Wright et al., PLoS Genet. 2009 June; 5(6): e1000512.
    • 21. The resolution
      • Identification of the pea-comb mutation
      • 22. Note the duplication in the repeated sequence
      • 23. Variation in copy number of the 1 st intron in SOX5 causes the phenotype!!!
    • 24. Biological Complexity Revealed Gerstein M B et al. Genome Res. 2007;17:669-681 ©2007 by Cold Spring Harbor Laboratory Press
    • 25. Quantitative Inheritance P 1 P 2 F 2 Frequency Height
    • 26. Mendel vs. the Biometricians
      • Bateson and DeVries
        • traits having continuous variation could only be produced by environmental variation and NOT inherited
      • Only large discontinuous differences or variation could be caused by ‘genes’.
      • 27. These were considered to be measurable, or metrical, traits.
    • 28. The Resolution
      • Johannsen (1909)
        • Seed weight in beans was influenced by both genes and environment
      • Nilsson-Ehle (1910-1914)
        • Multiple genes control grain color in wheat
      • R. A. Fisher (1918)
        • The additive model was proposed!
    • 29. Phenotypic Distribution of a Quantitative Trait
    • 30. The Stars
      • Sir Kenneth Mather
        • 1949 -- Biometrical Genetics
      • The players
        • R. A. Fisher & J. B. S. Haldane (UK)
        • 31. Sewell Wright & Jay Lush (US)
      • The places
        • Iowa State & Edinburgh
          • hogs, poultry, cattle, sheep
        • NC State & Birmingham
          • maize and tobacco (NC), inbred plants (B)
    • 32. The Additive Model of Inheritance
      • P = G + E
        • Phenotype, Genotype, Environment
      • What about G*E ?
        • Genotype by Environment Interaction
      • and, How about G ~ E ?
        • Genotype-Environment Correlation
      • Simplifying assumptions
    • 33. The world and plants
    • 34. The 7 Neolithic Founder Crops
    • 35. Wait a minute … What’s domestication?
      • Economic Use such as meat, fur, eggs, milk, labor companionship!!
      • The breeding, care and feeding of the animal are under the continuous control of man
      • Any situation where artificial selection has replaced, in part, natural selection
    • 36.  
    • 37.  
    • 38. The world, plants and animals
    • 39. Trait changes associated with domestication
      • SIZE:
        • Early domestic animals were smaller than their wild counterparts. Now they are larger, due to artificial selection.
      • COLOR:
        • Many more colors in domestic varieties than observed in the wild.
      • SKULL
        • Facial features shortened relative to cranial size. This is especially evident in swine and sheep. The teeth get smaller and horns decrease in size.
      • SKELETON:
        • Domestic cattle have weak muscle ridges and poorly defined facets of the joints. In domestic pigs, the epiphyses of the limb bones do not fuse with the diaphyses until long after maturity.