Selection of Symbiota by Screening Multiple Host-Symbiont Associations

Abstract

The present invention relates to new methods of selecting and breeding organisms, in particular organisms which exhibit symbiotic behaviour with symbionts, and to new organisms and symbiota developed thereby, such as plant or grass and endophyte symbiota. Multiple symbionts are deployed in multiple organsims and selected for improved symbiotic compatibility and performance early in the breeding process. Methods include producing improved organisms from germplasm, by inoculating host organism germplasm libraries with symbionts seleced from symbiont libraries and selecting improved host organisms exhibiting desired symbiota characteristics, and selection of organism-symbiont associations with a desired genetic and metabolic profile by metagenomic analysis of nucleic acid libraries from an organism or organism-symbiont.

What is claimed is: 
     
         1 . A method of genomic selection of organism-symbiont associations, said method including:
 (i) providing a library of nucleic acid samples from said organism or said organism-symbiont association;   (ii) analysing said samples using metagenomics to obtain a genetic profile for each sample;   (iii) selecting organism-symbiont associations with a desired genetic and metabolic profile.   
     
     
         2 . The method according to  claim 1  including the preliminary steps of:
 (i) providing an organism-symbiont association; 
 (ii) subjecting said organism-symbiont association to one or more environmental conditions; and 
 (iii) preparing a library of nucleic acid samples from each of the environmentally treated organism-symbiont associations. 
 
     
     
         3 . The method according to  claim 1 , wherein said organism is a plant. 
     
     
         4 . The method according to  claim 3 , wherein the plant is a grass. 
     
     
         5 . The method according to  claim 3 , wherein the symbiont is selected from the group consisting of a fungal or bacterial endophyte, a fungal or bacterial epiphyte or a bacterial microbiome. 
     
     
         6 . The method according to  claim 5 , wherein the symbiont is a bacterial microbiome. 
     
     
         7 . The method according to  claim 1 , wherein the step of analysing said samples using metagenomics involves detecting the presence or absence of polymorphic markers. 
     
     
         8 . The method according to  claim 7 , wherein the polymorphic markers are selected from the group consisting of simple sequence repeats and mating-type gene markers. 
     
     
         9 . The method according to  claim 1 , wherein the step of analysing said samples using metagenomics involves sequencing nucleic acid molecules selected from the group consisting of genomic DNA, mitochondrial DNA and ribosomal RNA, and performing sequence comparisons to databases of known nucleic acid sequences which are indicative of bacterial genes. 
     
     
         10 . The method according to  claim 9 , wherein the known nucleic acid sequences are 16S ribosomal RNA sequences. 
     
     
         11 . The method according to  claim 2 , wherein the environmental conditions are selected from the group consisting of nutrient stress, low light, cold stress and water stress.