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| Author(s): |
João Ricardo Bachega Feijó Rosa
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | Piracicaba. |
| Institution: | Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC) |
| Defense date: | 2012-02-01 |
| Examining board members: |
Antonio Augusto Franco Garcia;
Monalisa Sampaio Carneiro;
Giancarlo Conde Xavier Oliveira
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| Advisor: | Antonio Augusto Franco Garcia |
| Abstract | |
Sugarcane (Saccharum spp.) is a very important crop for sugar and alcohol production in Brazil. A great progress on its genome has emerged through molecular markers, which have been widely used for several purposes, such as QTL mapping based on bi-parental crosses. However, the use of populations derived from designed crosses tend to limit the genetic recombination events, resulting in a lower mapping resolution. In this sense, association mapping has emerged as a promising tool for QTL detection, since may be used natural populations, germplasm collections, elite set of materials, and others, allowing to detect recombination events in a historical and evolutionary context. To define the best strategies of association mapping, it is fundamental to account linkage disequilibrium (LD) and genetic structure existing in a certain population, so to verify the number of molecular markers and to promote the control of false positives. Here we measured LD and population structure across the genome of commercial varieties and clones of interest for sugarcane improvement in Brazil, based on 135 individuals from the Brazilian collection of sugarcane varieties (BCSV). This collection, which was mainly developed for association mapping, brings together important ancestral species, most planted varieties, promising clones, most used varieties as progenitors and varieties from the genetic mapping programs. A total of 1,474 polymorphic markers was scored, considering 86 EST-SSRs and 14 SSRs primers. A previous genetic map was used to verify distances between mapped BCSV markers. Fisher exact test was performed for all pairs of markers and used as a LD measure. Population structure was assessed by the probabilistic model implemented in STRUCTURE and the Neighbor-Joining method, based on simple matching dissimilarity between all pairs of individuals. Strong LD was observed up to 15 cM, mainly within the first 5 cM. Four subpopulations were detected in the BCSV with both methods, which is in agreement with pedigree informations. These results can provide important directions for future studies of genetic mapping, which would certainly need to consider high ploidy level of sugarcane. (AU) | |
| FAPESP's process: | 10/06702-9 - Analysis of linkage disequilibrium in sugarcane |
| Grantee: | João Ricardo Bachega Feijó Rosa |
| Support Opportunities: | Scholarships in Brazil - Master |