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QTL mapping and analysis

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QTL mapping and analysis

  1. 1. QTL Mapping MSc ag (2) year Agriculture Genetics and Plant Breeding Deen Dayal Upadhyaya Gorakhpur University Gorakhpur Submitted by. Shweta Kumari Submitted to Department of Genetics and plant breeding
  2. 2. Introduction ✩ QTL mapping ✩ QTL mapping is the process to identify the genomic region associated with desirable quantitative trait with the help of DNA marker ✩ In this process DNA markers are tested throughout the genome which are associated with QTLs.
  3. 3. Quantitative Traits Loci ✩ The loci controlling quantitative traits are called quantitative traits Ioci ( QTL) ✩ the term quantitative traits coined by Genderman. ✩ QTL is the region of genome which control quantitative trait ✩ QTL characteristics ✩ The QTLs are controlled by multiple genes ,each segregating according to Mendel's Law. ✩ These traits also a ected by environment to varying degrees ✩ QTL can show dominant or co-dominant
  4. 4. Objective of QTL mapping ✩ The basic objective is to detect QTL ✩ To identify the region of genome that a ects the trait of interest ✩ To analyse the e ect of the QTL on the trait ✩ How much variation for the trait is caused by a specific region ✩ What is the gene action associated with the QTL? ✩ Which allele is associated with the favourable e ect.
  5. 5. Procedure for QTL mapping ✩ Selection of diverse parental lines ✩ Creation of mapping population ✩ Phenotyping of the progeny ✩ Genotyping of the progeny ✩ Construction of linkage map.
  6. 6. Types of mapping population ✩ Recombinant Inbred line(RIL) ✩ Backcross ✩ F2 population ✩ Double haploid ✩ Near isogenic line(NIL)
  7. 7. Backcross mapping population ✩ Advantages: It is easier to identify QTL as there are less epistatic and linkage drag e ects; especially useful for crosses with wild species. ✩ Disadvantages: Di cult or impossible in species that are highly heterozygous and outcrossing. ✩ Use: best when inbred lines are available
  8. 8. F2 mapping Population ✩ Advantage: Fast and easy to construct. ✩ Disadvantage: F3 families are still very heterozygous; so the precision of the estimates can be low (because of the high standard error); can't be replicated
  9. 9. Recombinant Inbred Line ✩ RILs are produced by continuous selfing progeny of individual member of an F2 population until complete homozygous is achieved ✩ Advantages: fixed lines so can be replicated across many locations and/or years; can eliminate problem of background heterozygosity. ✩ Disadvantages: Can take a long time to produce. (Some species are not amenable)
  10. 10. Near Isogenic Line ✩ Advantage: Very precise and statistically strong, as background is constant; especially useful for validation experiments. ✩ Disadvantage: Can take time to construct; only useful for specific target QTL
  11. 11. Doubled Haploid Line ✩ Advantages: 1)Spontaneous chromosome doubling of ✩ Haploid microspores in in vitro culture ✩ 2)Homozygosity achieved in a single step Plants. ✩ Disadvantages: Less recombination between linked markers Not all systems are amenable to in vitro culture
  12. 12. Methods of QTL Detection ✩ Studying single markers one at a time. ✩ The simplest method for QTL analysis. ✩ Can be done by t-tests or ANOVA. ✩ Does not require a complete linkage map.
  13. 13. Simple Interval mapping ✩ Two markers at a time (flanking markers). ✩ Based on linkage mapping of markers. ✩ More accurate than single-marker analysis.
  14. 14. Composite interval mapping ✩ For detection of a QTL more than two markers are used ✩ It is based on linkage mapping of the marker.
  15. 15. Thank you
  16. 16. Zoho Show To create beautiful presentations, download Zoho Show from Play Store https://zoho.to/cy7 QTL mapping.pdf (This PDF has been generated using Zoho Show)

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