The University of Southampton
University of Southampton Institutional Repository

Linking transcript, QTL and association mapping to understand the genetic control of leaf size and shape in Populus

Linking transcript, QTL and association mapping to understand the genetic control of leaf size and shape in Populus
Linking transcript, QTL and association mapping to understand the genetic control of leaf size and shape in Populus
Leaf size in Populus is an adaptive trait and early indicator of biomass yield. In order to investigate the genetic variance contributing to this variation in leaf size a collection of Populus nigra L. were made from across Europe and were planted at a single site in Belgium, in a fully randomized and replicated trial, with leaf traits measured in three consecutive years and biomass estimated at one point in time. Results indicate that leaf traits vary with latitude of sample origin, with significant differences observed in leaf area, epidermal cell number and biomass, but not in leaf shape (leaf ratio), epidermal cell area, stomatal density and stomatal index. Overall a significant positive relationship between latitude of origin and leaf traits was observed with small-leaved genotypes containing fewer epidermal cells observed in the south west (Spain), and large-leaved genotypes occurring in the north and east (the Netherlands, Germany and Italy). A sequence-based genetic study was conducted to identify Single Nucleotide Polymorphisms (SNPs) associated with leaf phenotype. Given that linkage disequilibrium (LD), decays rapidly (r2 = 0.09) in P.nigra, a candidate gene approach for association is valid. Candidate genes were selected from Quantitative Trait Loci (QTL), from a microarray experiment and from bioinformatics and literature searches, identifying sixty robust genes. From this list eight candidate genes were selected for further analysis; ASYMMETRIC LEAVES 1 (AS1), ASYMMETRIC LEAVES 2 (AS2), ACC OXIDASE ( ACO), ERECTA (ER), PHABULOSA (PHAB), ANGUSTOFOLIA (AN), E2Fc and LEAFY. Genetic association was conducted using a General Linear Model (GLM) both with and without population structure. The strongest genetic association was found in AS1, a gene involved in leaf initiation that acts by repressing KNOX genes to increase cell differentiation. Gene expression of the eight candidate genes were examined across extreme leaf genotypes using real time qPCR (RT-qPCR), at three growth stages. Extreme leaf genotypes consisted of five „small? and five „big? leaf genotypes selected from the association population. Significant differences in gene expression was seen between „small? and „big? genotypes in AN, AS2 and AS1. These results suggest that AS1 is a strong candidate gene for leaf size.
Trewin, Harriet
ca9a9ee7-dd07-4c57-8aa1-5fb4ec3cbbdc
Trewin, Harriet
ca9a9ee7-dd07-4c57-8aa1-5fb4ec3cbbdc
Taylor, Gail

Trewin, Harriet (2008) Linking transcript, QTL and association mapping to understand the genetic control of leaf size and shape in Populus. University of Southampton, School of Biological Sciences, Doctoral Thesis, 236pp.

Record type: Thesis (Doctoral)

Abstract

Leaf size in Populus is an adaptive trait and early indicator of biomass yield. In order to investigate the genetic variance contributing to this variation in leaf size a collection of Populus nigra L. were made from across Europe and were planted at a single site in Belgium, in a fully randomized and replicated trial, with leaf traits measured in three consecutive years and biomass estimated at one point in time. Results indicate that leaf traits vary with latitude of sample origin, with significant differences observed in leaf area, epidermal cell number and biomass, but not in leaf shape (leaf ratio), epidermal cell area, stomatal density and stomatal index. Overall a significant positive relationship between latitude of origin and leaf traits was observed with small-leaved genotypes containing fewer epidermal cells observed in the south west (Spain), and large-leaved genotypes occurring in the north and east (the Netherlands, Germany and Italy). A sequence-based genetic study was conducted to identify Single Nucleotide Polymorphisms (SNPs) associated with leaf phenotype. Given that linkage disequilibrium (LD), decays rapidly (r2 = 0.09) in P.nigra, a candidate gene approach for association is valid. Candidate genes were selected from Quantitative Trait Loci (QTL), from a microarray experiment and from bioinformatics and literature searches, identifying sixty robust genes. From this list eight candidate genes were selected for further analysis; ASYMMETRIC LEAVES 1 (AS1), ASYMMETRIC LEAVES 2 (AS2), ACC OXIDASE ( ACO), ERECTA (ER), PHABULOSA (PHAB), ANGUSTOFOLIA (AN), E2Fc and LEAFY. Genetic association was conducted using a General Linear Model (GLM) both with and without population structure. The strongest genetic association was found in AS1, a gene involved in leaf initiation that acts by repressing KNOX genes to increase cell differentiation. Gene expression of the eight candidate genes were examined across extreme leaf genotypes using real time qPCR (RT-qPCR), at three growth stages. Extreme leaf genotypes consisted of five „small? and five „big? leaf genotypes selected from the association population. Significant differences in gene expression was seen between „small? and „big? genotypes in AN, AS2 and AS1. These results suggest that AS1 is a strong candidate gene for leaf size.

Text
Harriet_Trewin_PhD_thesis.pdf - Other
Download (3MB)

More information

Published date: October 2008
Organisations: University of Southampton

Identifiers

Local EPrints ID: 66717
URI: http://eprints.soton.ac.uk/id/eprint/66717
PURE UUID: 09c3aea4-f42e-4ee4-89dd-8bf7967e062d

Catalogue record

Date deposited: 13 Jul 2009
Last modified: 13 Mar 2024 18:35

Export record

Contributors

Author: Harriet Trewin
Thesis advisor: Gail Taylor

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×