Developing a physical map of the Lolium perenne genome based on high-information content BAC fingerprinting and BAC-end sequencing

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

Grassland is a predominant crop in the UK and Lolium perenne (perennial ryegrass) is the single, most significant component of the majority of this grassland. In total, UK grasslands account for more than 50% of the land area and 70% of all agricultural land use and the market value of UK agricultural grassland in 2006, measured in terms of meat and milk production, is estimated to have been c. £4.8 billion. In addition to conventional agricultural use, grass and grasslands are of fundamental importance in amenity situations, including sports fields and landscaping, and there is also increasing interest in the development of alternative grassland uses, such as for biofuel and platform chemical production. IBERS is the major centre for ryegrass breeding/germplasm resources within the UK as well as being the focus of bioenergy grass improvement. It has an established infrastructure allowing the interplay of research in plant genetics, genomics, physiology, biochemistry and environmental analysis with breeding and sustainability objectives, thus, it is in a unique position to exploit new genome technologies. A major aim of grass scientists is to be able to define genomic regions that play an important role in determining target traits in these crops, as our ability to influence these traits (eg., drought/heat tolerance, nitrogen use efficiency, flowering, bioenergy traits) is fundamental to maintaining sustainable grasslands. A major step in comprehensive genome analysis is the establishment of a physical map. This involves a number of sequential processes: A) Develop extensive large-insert (BAC) genomic DNA libraries which, effectively, fragment and partition the genome into smaller pieces which can be catalogued. B) Generate distinctive 'fingerprints' of each of these BACs. C) Define the physical order of BACs within the genome by identifying overlapping fingerprint patterns (contiguous clones, or contigs). D) Relate the identified contigs to existing genetic or chromosome maps. Extra information can be obtained by sequencing the ends of each of the BACs. This information can be used in confirming overlapping fingerprint patterns and in helping to define the genome structure. The outcome is that the genome is broken down into an ordered series of manageable fragments. These can be used for targeted DNA sequencing of particular regions of the genome / or for large scale whole genome sequencing. The aim of this research is to develop this resource for grass and other monocot researchers to enable a greater understanding of the genome structure and function. In order to make this information widely available, an open-access web-interface will be developed which will display progress in the project and allow for the raw data to be downloaded, so that other researchers can use it in their own analyses.

Technical Summary

IBERS is the major centre for ryegrass (Lolium spp.) breeding/germplasm resources within the UK. It has an established infrastructure allowing the interplay of plant genetics, genomics, physiology, biochemistry and environmental analysis with breeding and sustainability objectives. Thus, it is in a unique position to exploit new genome technologies in defining genomic regions with important roles in determining target traits. The principle aim of this proposal is to develop a physical map of the L. perenne genome using high information content fingerprinting (HICF) of a c. 10x L. perenne BAC library (241920 clones, estimated genome size 2 - 2.8 Gb) assembled using FingerPrint Contig (FPC) software alignments. Projecting from physical mapping projects in other plant species it is expected that this will produce 5000-10000 unordered contigs. Refinement of this physical map will be done by manual editing of the automated assembly and incorporation of BAC-end sequencing (BES) data from all 241920 clones. This process will identify: a) chimaeric contigs, b) conflicts between fingerprint and BES data and c) new contigs, by detailed analysis of fingerprint patterns of terminal clones of existing contigs. Manual editing may reduce the number of contigs by 50%. As part of this programme, BAC DNA pools will be developed from the 10x library suitable for PCR screening. Screening these pools with cross-species markers of known genetic and/or physical position in the Lolium and other monocot genomes, will align the physical contigs with existing genetic and cytological maps. Further comparative genomic information will be obtained using BLAST searches of the BES against other monocot resources, including a L. perenne GeneThresher (methylation filtered) sequence library. The developing physical map will be displayed using the WebAGCoL software via an open-access web-site. BES data will be submitted to EMBL/GenBank as well as being available via the project web-site.

Publications

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Byrne SL (2015) A synteny-based draft genome sequence of the forage grass Lolium perenne. in The Plant journal : for cell and molecular biology

 
Description We have constructed 3 versions of a BAC-based physical map for an inbred Lolium perenne genotype from 212923 high-information-content fingerprints. These consist of between 2851 and 4050 contigs and identify minimum-tiling-paths of between 19372 and 39250 BACs. The physical map versions have been produced using 2 different softwares (Fingerprint Contig and Linear Topology Contig) and using either all 212923 fingerprints or a subset of 154836 low-repeat-content fingerprints. This allows for validation of contig structure through comparison between methods.
The construction of PCR-screenable BAC library pools has allowed us to screen >1500 mapped markers and associate >800 contigs with genetic map positions. This was achieved using standard PCR and adapting KASPar technology. An additional 198 BAC-ends have been assigned genetic map positions using HindIII RAD sequencing.
Through collaboration with Aarhus University, Denmark, we are integrating the physical map with an NGS-based sequence assembly developed from the same L. perenne genotype.

The physical map has now been published and used to identify genomic regions associated with important traits in a large perennial ryegrass genome wide association study.
Exploitation Route As part of an overall programme to develop a reference genome for Lolium perenne this work contributes to the understanding of the genome structure and assaying the genome variability of this forage grass species. This, in turn, is contributing to the development of molecular breeding approaches.

All details of the physical map have now been published and are available via the public archive at Aberystwyth University
Sectors Agriculture

Food and Drink

 
Description Further time will be required to assess this.
Sector Agriculture, Food and Drink
 
Title BAC library screening pools 
Description BAC library screening pools (superpool and matrix pool) have been prepared from 241920 Lolium perenne BAC library clones. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Lolium perenne physical map development 
 
Title Lolium perenne BAC libraries 
Description 2 BAC Lolium perenne BAC libraries have been produced both consisting of 120960 clones. Restriction enzymes used were HindIII and BstY1 
Type Of Material Cell line 
Year Produced 2011 
Provided To Others? Yes  
Impact Basis of physical map development 
 
Title BAC end sequences from Lolium perenne BAC libraries 
Description 391224 BAC end sequences have been produced from a total of 241920 clones. Average read length c. 525bp 
Type Of Material Database/Collection of data 
Year Produced 2011 
Provided To Others? Yes  
Impact Lolium perenne physical map development and genome sequence 
 
Title BAC library screening pools 
Description BAC library screening pools (superpool and matrix pool) have been prepared from 241920 Lolium perenne BAC library clones. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Lolium perenne physical map development 
 
Title HICF of 2 Lolium perenne BAC libraries 
Description High information content fingerprints (HICF) have been obtained from c.212000 BACs. These are being used in the construction of a L. perenne physical map 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact Lolium perenne physical map development 
 
Title Lolium perenne BAC end sequences 
Description 391224 BAC end sequences produced from HindIII and BstY1 BAC libraries 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact No actual impacts realised to date 
 
Title Lolium perenne BAC libraries 
Description 2 BAC Lolium perenne BAC libraries have been produced both consisting of 120960 clones. Restriction enzymes used were HindIII and BstY1 
Type Of Material Database/Collection of data 
Year Produced 2011 
Provided To Others? Yes  
Impact Lolium perenne physical map development 
 
Description Lolium perenne genomics 
Organisation Aarhus University
Country Denmark 
Sector Academic/University 
PI Contribution As part of this grant we have developed a close collaboratioin with the Univ. Aarhus, Denmark. This has allowed us to closely align this BBSRC funded physical mapping with de novo genome sequencing and assembly - funded by the Danish research council. Joint publications are planned
Collaborator Contribution Univ. Aarhus have developed a Lolium perenne genome assembly using the same genotype studied by Aberystwyth in this grant
Impact In preparation
Start Year 2010
 
Description BBC Radio Wales Science Cafe 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interview concerning the Lolium perenne physical mapping project.
Year(s) Of Engagement Activity 2009
 
Description Cambrian News 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Interview and photographs concerning the Lolium physical mapping project
Year(s) Of Engagement Activity 2009
 
Description ERA-CAPS planning San Diego 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Led to consortium formation for EU FP7 ERA-CAPS application

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Year(s) Of Engagement Activity 2013
 
Description PAG2017 conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Poster presentation within the Plant and Animal Genome conference 2017 (Jan14-18 2017) entitle "Assembly and annotation of a physical map-based draft genome of the forage grass Lolium perenne (P0920)". This is largest international conference devoted to Plants and Animals genomes research.
Year(s) Of Engagement Activity 2017
URL https://app.core-apps.com/pag_2017/abstract/3d5eba754526e3e7211a636665f80a47