From ICISWiki

Contents 1 Fingerprinting: Molecular characterization of genetic resources or breeding lines 2 Marker assisted backcrossing (MABC): Introgression of one or more marked segments for a donor to a recipient germplasm using backcrossing and marker selection 3 MAS: Construction of germplasm with target genotypes by gene pyramiding through complimentary recombination 4 MARS: Exploiting allele diversity within populations by using MAB to increase frequency of beneficial alleles for quantitative traits

Fingerprinting: Molecular characterization of genetic resources or breeding lines

Activity	Logistical Tools	Analytic Tools
Eco-geographic analysis using passport data, pedigree information and GIS		Existing tools available from the genetic resources community. Eg: DIVA-GIS, FIGS www.figstraitmine.org (some integrated into the GCP platform)
Selection of accessions	SETGEN: List management INTRACK: Inventory management
Planting	WORKBOOK: Field lay-out
Molecular characterization	SETGEN: Sample tracking, bar coding and LIMS. Data loading to breeding databases
Agro-morphological characterization	WORKBOOK: Field book, electronic data capture. Data loading to breeding databases
Diversity and association analysis and deployment of germplasm for breeding or adoption	INTRACK: inventory system for available characterized germplasm	Existing tools for diversity and association analysis. Eg. STRUCTURE, TASSEL, DARWIN (some integrated into the GCP platform)

Marker assisted backcrossing (MABC): Introgression of one or more marked segments for a donor to a recipient germplasm using backcrossing and marker selection

Activity	Logistical Tools	Analytic Tools
Assuming identified and validated trait markers (usually qualitative traits) select donor and recipient material. Plan crosses.		MBDT: analysis based on target genotype, genetic distance to recipient germplasm, adaptation and potential adoption.
Planting hybridization block, make crosses	SETGEN: Sample tracking and pedigree management INTRACK: Seed inventory management
Make first backcross, genotype BC1F1s	SETGEN: Sample tracking, bar coding and LIMS. Data loading to breeding databases. INTRACK: Seed inventory management.	MOSEL: select plants heterozygous for donor alleles at target loci, minimize size of introgression and select lines homozygous recipient or heterozygous at background loci.
Backcross selected plants to recipient, repeat genotyping and selection	SETGEN: Sample tracking, pedigree management, bar coding and LIMS. Data loading to breeding databases.	MOSEL
Possibly self selected plants to increase homozygosity	SETGEN: Sample tracking and pedigree management. INTRACK: Seed inventory management.	MOSEL: minimize introgression size and fix critical markers
Repeat previous two steps until selected lines are sufficiently homozygous for background and can be easily made homozygous for target loci.	SETGEN: Sample tracking, pedigree management, bar coding and LIMS. Data loading to breeding databases. INTRACK: Seed inventory management.	MOSEL

MAS: Construction of germplasm with target genotypes by gene pyramiding through complimentary recombination

Activity	Logistical Tools	Analytic Tools
Assuming identified and validated trait markers, select parents and plan crosses.	CROPFINDER: Extraction of relevant trait by genotype information form breeding databases for analysis	MBDT: analysis based on complimentary genotypes at target loci, genetic proximity at background loci, and adaptation to target environments. QuLine: Use simulation tools to estimate population sizes and select breeding strategy.
Planting hybridization block, make crosses	SETGEN: Sample tracking and pedigree management. INTRACK: Seed inventory management.
Enter conventional pedigree breeding cycles with phenotypic selection	SETGEN: Sample tracking, pedigree management. WORKBOOK: Field lay-out, phenotyping. Data loading to breeding databases. INTRACK: Seed inventory management.
At an appropriate generation genotype single plants and select based on proximity to target genotype	SETGEN: Sample tracking, pedigree management, bar coding and LIMS. Data loading to breeding databases. INTRACK: Seed inventory management.	MOSEL: Analysis of genotyped lines for phenotypic acceptability and proximity to target genotypes
Continue phenotypic selection until advanced inbreeding.	SETGEN: Sample tracking, pedigree management. WORKBOOK: Field lay-out, phenotyping. Data loading to breeding databases. INTRACK: Seed inventory management.
Verify genotypes and enter selected lines for evaluation, distribution or re-use in hybridization	SETGEN: Sample tracking, bar coding and LIMS. WORKBOOK: Experimental design, field lay-out, multi-site evaluation. Data loading to breeding databases. INTRACK: Seed inventory management.	EDDA: Analysis of multi-location evaluation trials to verify trait expression and adaptation

MARS: Exploiting allele diversity within populations by using MAB to increase frequency of beneficial alleles for quantitative traits

Activity	Logistical Tools	Analytic Tools
In the absence of large identified, stable and validated trait markers (usually quantitative traits) select parents	CROPFINDER: Extraction of relevant trait by genotype information form breeding databases for analysis.	MBDT: Analysis based on genetic distance, complimentary associations, combining ability, phenotype and adaptation
Make crosses	SETGEN: Sample tracking, pedigree management. Data loading to breeding databases. INTRACK: Seed inventory management.	Simulation tools to select breeding tactics – number of crosses, population sizes etc.
Accurately phenotype and extensively genotype early generation lines	SETGEN: Sample tracking, pedigree management. WORKBOOK: Experimental design, field lay-out and randomization, electronic data capture. Sample tracking, bar coding, LIMS. Data loading to breeding databases.	Compute QTL effects within each population, identify significant QTL. MOSEL: Use index selection to select the best lines based on phenotype and QTL content
Inter-mate selected lines	INTRACK: Seed inventory management.	MOSEL, QuMARS
Genotype progeny at selected QTL loci	SETGEN: Sample tracking, bar coding, LIMS. Data loading to breeding databases	MOSEL: select lines based on positive QTL allele content, inter-mate complimentary lines
Inter-mate selected lines	NTRACK: Seed inventory management.	MOSEL, QuMARS
Repeat previous two steps for 2 to 3 cycles to enrich positive QTL allele frequency
Extract fixed lines in conventional breeding for evaluation and advanced testing.	SETGEN: List management. WORKBOOK: Experimental design, field lay-out and randomization, electronic data capture. Data loading to breeding databases. INTRACK: Seed inventory management.	EDDA: Analysis of multi-location evaluation data. Validation of adaptation through GxE QTLxE analysis.