QTL Analysis - CREDIT SEMINAR ON QTL MAPPING FOR GENETIC...

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QTL MAPPING FOR GENETIC ANALYSIS& ITS APPLICATIONS CREDIT SEMINAR ON
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Quantitative traits ....... ? Many genes - quantitative traits Characters whose phenotypic variation is continuous & determined by the segregation of multiple loci - Quantitative traits QTL ...... ? The regions within genomes-contain genes associated with a particular quantitative trait - quantitative trait loci (QTLs). The term QTL coined by Gelderman (1975)
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History of QTL mapping Sax, 1923 Association of seed size in beans with seed-coat pigmentation avg sw of 10 beans (gm) of 3 seed col class Thoday, 1961 single gene markers to map individual polygenes / QTLs
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Why QTL analysis………????? What is number of QTLs for a quantitative character? Are these QTLs same or different for each character? Are these character randomly distributed in the genome or there some hot spots in the genome? Causes of heterosis i.e. gene dispersion, over dominance or epistasis. Identify molecular markers for marker assisted selection. Map based gene cloning.
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Requirement for QTL mapping
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Available in very large numbers Not affected by the environment Can be scored at any stage of development Usually neutral No interlocus interactions
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Molecular markers – what information they pr Identify the fragments (genes) associated with the trait To develop linkage map and locate the DNA fragments (genes) on a linkage map Clone the gene (s) associated with the trait To assess genetic diversity
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Population type Co-dominant markers Dominant markers F2 1: 2:1 (AA:Aa:aa) 3:1 (B - : bb) Backcross 1:1 (Cc : cc) 1:1 (Dd : dd) RILs / DHL 1:1 (EE : ee) 1:1 (FF : ff)
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Computer programs are required for this purpose. Commonly used software programs are: JoinMap : (http://www.cpro.dlo.nl.cbw/) : analyzes all types of mapping populations; can combine maps of different mapping populations provided there are common markers. © CPRO-DLO; cost per license dependent on number of licenses. Mapmaker/EXP : (ftp://genome.wi.mit.edu/pub/mapmaker3/): freely distributed, analyzes F 2 and BC mapping populations. Gmendel: (http://gnome.agrenv.mcgill.ca/info/gmendel.htm): freely distributed, analyzes all types of mapping populations; can combine maps of different mapping populations provided there are common markers. MapManager QTX :
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LOD score Is a statistical tool - to test the significance of the presence of linkage LOD threshold values >3 are typically used to construct linkage maps. A LOD value of 3 between two markers indicates that linkage is 1000 times more likely (i.e. 1000:1) than no linkage (null hypothesis). less no. of markers - higher LOD score More no. of markers - lower LOD score
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(P 1 ): ‘A’ (P 2 ): ‘B’ Coding of marker data varies depending on the type of population used.
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