A method of identifying an organism of a predefined species carrying one or more predetermined mutation(s) in nucleotide(s) of interest [NOI(s)], in a target sequence, said method comprising the steps of: a) Providing a pool of organisms of said species, or reproductive parts thereof, representing a plurality of genotypes; b) Dividing said pool into one or more sub-pools of organisms, or reproductive parts thereof; c) Preparing gDNA samples, each comprising genomic DNA (gDNA), from each genotype within a sub-pool, while maintaining the potential for multiplication of organisms of each genotype within said sub-pool; d) Performing a plurality of PCR amplifications, each comprising the gDNA sample from one sub-pool, wherein each PCR amplification comprises a plurality of compartmentalised PCR amplifications, each comprising part of said gDNA sample, one or more set(s) of primers each set flanking a target sequence and PCR reagents, thereby amplifying the target sequence(s); e) Detecting PCR amplification product(s) comprising one or more target sequence(s) comprising the mutation(s) in the NOI(s), thereby identifying sub-pool(s) comprising said mutation(s); f) Dividing the organisms, or reproductive parts thereof, of said identified sub-pool(s) into secondary sub-pools, such as at least 10, preferably at least 90 secondary sub-pools; g) Preparing gDNA samples, each comprising gDNA from each genotype within a secondary sub-pool, while maintaining the potential for multiplication of organisms of each genotype within said secondary sub-pool; h) Performing a plurality of PCR amplifications, each comprising the gDNA sample from one secondary sub-pool;, one or more set(s) of primers each set flanking a target sequence and PCR reagents, thereby amplifying the target sequence(s); i) Detecting PCR amplification products comprising one or more target sequence(s) comprising the predetermined mutation(s) in the NOI(s), thereby identifying secondary sub-pools under step i) comprising said mutation(s); j) Identifying an organism or reproductive part thereof within said secondary sub-pool carrying said mutation(s) with the proviso that when the species is a plant or an animal, the method does not comprise a step of sexual reproduction. a) Providing a pool of organisms of said species, or reproductive parts thereof, representing a plurality of genotypes; b) Dividing said pool into one or more sub-pools of organisms, or reproductive parts thereof; c) Preparing gDNA samples, each comprising genomic DNA (gDNA), from each genotype within a sub-pool, while maintaining the potential for multiplication of organisms of each genotype within said sub-pool; d) Performing a plurality of PCR amplifications, each comprising the gDNA sample from one sub-pool, wherein each PCR amplification comprises a plurality of compartmentalised PCR amplifications, each comprising part of said gDNA sample, one or more set(s) of primers each set flanking a target sequence and PCR reagents, thereby amplifying the target sequence(s); e) Detecting PCR amplification product(s) comprising one or more target sequence(s) comprising the mutation(s) in the NOI(s), thereby identifying sub-pool(s) comprising said mutation(s); f) Dividing the organisms, or reproductive parts thereof, of said identified sub-pool(s) into secondary sub-pools, such as at least 10, preferably at least 90 secondary sub-pools; g) Preparing gDNA samples, each comprising gDNA from each genotype within a secondary sub-pool, while maintaining the potential for multiplication of organisms of each genotype within said secondary sub-pool; h) Performing a plurality of PCR amplifications, each comprising the gDNA sample from one secondary sub-pool;, one or more set(s) of primers each set flanking a target sequence and PCR reagents, thereby amplifying the target sequence(s); i) Detecting PCR amplification products comprising one or more target sequence(s) comprising the predetermined mutation(s) in the NOI(s), thereby identifying secondary sub-pools under step i) comprising said mutation(s); j) Identifying an organism or reproductive part thereof within said secondary sub-pool carrying said mutation(s)