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Improving short rotation coppice through breeding and genomics - NF0424

Description
The UK Government is committed to increase renewable energy supplies up to 2010 and beyond. In order to generate significant amounts of energy from biomass, energy crops need to be grown specifically for this purpose. The Government’s target for a circa 10% contribution by 2010 presents a considerable challenge. Of primary importance in meeting this challenge, is that sustainable high yields are obtained from the crop. The overall aim of this project is to deliver the breeding programme and plant materials that will allow further improvement of the willow crop, focussing on the generation of high yielding, pest and disease–resistant elite genotypes that are optimal for UK environmental conditions. A targeted breeding programme underpinned with molecular marker and genomic research will be developed to achieve this goal. In Work Package 1, the aims are to develop a breeding programme that draws from previous molecular marker and genetic mapping research and from the new genomics activities planned in Work packages 2 and 3 to produce elite genotypes with high yields and resistances. Genetic diversity for yield and resistances will be enhanced by a crossing program that makes intelligent use of the germplasm within the National Willow Collection. Selection strategies for yield will be improved. Attempts to overcome existing crossing barriers will be investigated through embryo culture, colchicine treatment and/or mentor pollen techniques and the potential for breeding high yielding willow varieties that use water more efficiently and/or are drought tolerant will be explored. The cost-effectiveness of marker-assisted selection (MAS), using previously established marker-linkages to reduce the number of individuals handled by the breeder, will be evaluated and molecular markers will be used to identify variation in key traits in breeding lines. In Work Package 2, we will physically map the genes with major effects on key agronomic traits. This will be achieved through a genomics-based approach which exploits recent developments in genome sequencing and genomics in poplar. Through previous efforts in willow genetic mapping, we have identified markers for QTLs conferring rust resistance, susceptibility to invertebrate pests and major components of yield. Here, we will confirm the robustness of these QTLs by comparative assessments of the K8 mapping population at the Long Ashton and Rothamsted sites. We will also focus on the major physiological components of yield identified from previous work and map these onto K8. Markers tightly linked to putative QTL will be identified by Bulked Segregant Analysis (BSA) in order to increase the map resolution around these regions. We will exploit poplar genomics, to identify candidate genes for development of EST-based markers in willow and map the candidates on the existing K8 willow map to identify those showing co-location with QTL. Publicly available poplar microsatellites will be mapped on K8 to investigate syntenic relationships between willow and poplar. We will also undertake comparative mapping of the key yield traits identified in both willow and poplar. A BAC library (not yet available in willow) will be constructed for characterisation of map regions containing QTL or candidate genes. In Work Package 3, the locations of QTL known to determine yield in poplar will be compared with the positions of QTL identified in willow in the K8 mapping population to determine ‘robust’ SRC yield QTL. Actual yield QTL will be the top priority in this study, using the ‘total basal volume’ as an accurate measure of yield and then linking this to the six key traits underpinning yield, identified from heritability studies. The molecular genetic map of poplar will be improved and comparative mapping with willow conducted in conjunction with Work package 2. From the available ESTs, and from on-going research on gene expression using microarrays, candidates for yield traits will be identified and mapped using a SNPs-based approach in poplar family 331. The physical sequence of poplar, (available in 2004/5) will be used, with focus on ESTs of interest from microarrays, to detect candidate genes from blast searches and their physical locality on the poplar genome map will be determined. A large and diverse collection of Populus nigra will be used in a linkage disequilibrium study to confirm candidate-QTL associations for yield. This generic programme of work will ensure that the supply of genetically diverse high yielding resistant varieties suitable for UK growing conditions continues for the benefit of the industry. It is anticipated that the breeding chain be supported up to the point where clones could be exploited by industry. Fundamentally, this will benefit growers by improving the economic sustainability of biomass crops. By supporting the proposed work, DEFRA will also secure the internationally competitive position that the UK currently holds on genetic improvement of SRC crops.
Objective
Overall aim

The overall aim of this project is to deliver the breeding programme and plant materials that will allow further improvement of the willow crop, focussing on the generation of high yielding, pest and disease–resistant elite genotypes that are optimal for UK environmental conditions. A targeted breeding programme underpinned with molecular marker and genomic research will be developed to achieve this goal. Poplar will be exploited because of the outstanding progress that has been made in poplar genomics in recent years, the availability of the complete physical sequence in 2004 and because of it’s genetic relatedness to willow.

The primary aim can be broken down into discrete objectives and pursued within three experimental packages focused on:
(i) molecular breeding;
(ii) willow genomics;
(iii) poplar genomics

1. Molecular breeding of improved SRC willow
Objective 1.01 To continue selection of improved genotypes from existing breeding material
Objective 1.02 To enhance genetic diversity within the gene pool for yield and resistance by a crossing program that makes intelligent use of the germplasm within the National Willow Collection and establish improved selection strategies for yield
Objective 1.03 To improve the efficiency of selection of resistance and yield though deployment of molecular markers
Objective 1.04 To screen breeding lines for variation in key traits and key candidate genes
Objective 1.05 To overcome existing barriers in the breeding process through deployment of additional technologies
Objective 1.06 To explore the potential of breeding high yielding willow varieties that use water more efficiently and/or are drought tolerant
Objective 1.07 Identify new sources of disease resistance in willow Objective 1.08 To assess resistances in breeding stocks to newly identified rust pathotypes
Objective 1.09 To investigate the cause of leaf scab/shoot dieback of willows

2. Willow genomics to underpin biomass yield improvement of willow
Objective 2.01 To confirm the location of QTLs already identified by comparative assessments of the K8 mapping population at the Long Ashton and Rothamsted sites
Objective 2.02 To map genes (or QTL) for key yield components
Objective 2.03 To exploit poplar to identify candidate genes for development of EST-based markers in willow by mapping to QTLs on the existing K8 willow map
Objective 2.04 To map publicly available poplar microsatellites on to the existing willow map to investigate syntenic relationships between the poplar and willow genomes.
Objective 2.05 To identify markers tightly linked to phenotypes or putative QTL by Bulked Segregant Analysis (BSA) using AFLP markers. Target AFLPs will then be converted to sequence-tagged site (STS) markers for mapping, assessment in marker-assisted selections, and BAC library screening in 2.06
Objective 2.06 To construct a BAC library for characterisation of map regions containing QTL or candidate genes
Objective 2.07 To develop simple, high throughput marker-screening tools for use in molecular breeding of improved willow varieties
Objective 2.08 To determine the genetic basis of new sources of rust resistance
Objective 2.09 To refine the rust QTLs and produce markers for different resistance loci

3. Poplar genomics to underpin yield improvement in willow and poplar
Objective 3.01 To compare the locations of robust yield QTL in poplar with the QTL identified in willow K8 mapping population .
Objective 3.02 To improve the molecular genetic map of poplar
Objective 3.03 To identify available ESTs as candidates for yield traits and to map these using a SNPs based approach in poplar, family 331.
Objective 3.04 To utilise the physical sequence of poplar, as available in 2004/5 to detect candidate genes from blast searches and to determine their physical locality on the poplar genome map.
Objective 3.05 To use a large and diverse collection of Populus nigra in a linkage disequilibrium study to confirm candidate-QTL associations
Project Documents
• Final Report : Improving short rotation coppice through breeding and genomics   (875k)
• Interim Report : BEGIN extension - Annex   (653k)
• Interim Report : BEGIN extension report   (166k)
Time-Scale and Cost
From: 2003

To: 2010

Cost: £3,511,415
Contractor / Funded Organisations
Rothamsted Research (BBSRC), University - Southampton
Keywords
Agro-Forestry              
Biodiversity              
Breeding              
Genetics              
Genomics              
Integrated Farming Systems              
Microarray              
Molecular Biology              
Sustainable Farming and Food Science              
Sustainable Farming Systems