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). http://www.sciencemag.org/cgi/content/full/312/5778/1392?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&volume=312&firstpage=1392&resourcetype=HWCIT
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. http://www.sciencemag.org/cgi/content/full/311/5769/1886
Ocean County College BIOL 161 Lectures Genetics ... The grand synthesis … BIOL161_07