Science-Based Breeding Advice
Breeding recommendations in Kora provide systematic breeding guidance. Based on genetic data, pedigrees, and population goals. Suggest optimal breeding pairs. Identify priority breeding. Recommend contraception when appropriate. Document breeding timeframes. Recommendations transform complex genetic data into actionable breeding decisions. Support conservation goals, genetic improvement, and population sustainability.
This chapter explains how breeding recommendations work. What information they provide. How breeding advice supports program management.
What are Breeding Recommendations?
Breeding recommendations are documented breeding advice based on:
- Pedigree relationships: Avoiding closely related breeding pairs
- Genetic profiles: Considering inbreeding risk and genetic diversity
- Population goals: Supporting conservation targets or breed improvement objectives
- Practical factors: Breeding timing, methods, animal health and readiness
Why breeding recommendations matter:
- Prevent genetic problems: Avoid inbreeding and genetic health issues before breeding occurs
- Maximise genetic diversity: Prioritise breeding that contributes most to population genetic health
- Support conservation: Enable endangered species programs to make optimal breeding decisions
- Coordinate breeding: Provide clear guidance for multi-institutional breeding programs
- Document reasoning: Create permanent record explaining breeding decisions
Example breeding recommendation:
Breeding Recommendation - Conservation Parrot Program:
Recommended Pairing:
Male: "Azure" (Studbook ID: PCP-2024-M-007)
Female: "Jade" (Studbook ID: PCP-2023-F-012)
Recommendation Type: High Priority
Priority Level: HIGH
Genetic Assessment:
Predicted Offspring Inbreeding: 0.028 (very low - excellent)
Genetic Value Score: 0.892 (high contribution to population diversity)
Genetic Compatibility: Excellent
Timeframe: Spring 2025 breeding season
Method: Natural breeding (pair bonded birds)
Target Offspring: 2-3 chicks
Justification:
"Azure carries unique genetics underrepresented in captive population.
Jade has low inbreeding and excellent genetic diversity. This pairing
combines Azure's rare genetics with Jade's genetic health producing
offspring that significantly improve population genetic diversity while
maintaining low inbreeding risk. High priority for upcoming breeding season."
Status: Active recommendation
Valid Until: 2025-12-31
Created By: Dr Sarah Johnson (Program Coordinator)
Created: 2024-10-15
Recommendations provide clear, justified breeding guidance. Transform genetic data into decisions.
Recommendation Types and Priorities
Breeding recommendations categorise breeding advice:
Recommendation Classifications
Recommended: Breeding pair approved based on genetic and population factors. Positive breeding recommendation.
Conditionally Recommended: Breeding acceptable under specific conditions. Timing, health verification, institutional cooperation.
Not Recommended: Breeding discouraged or prohibited. Too closely related, genetic concerns, population over-representation.
High Priority: Critical breeding for population sustainability or genetic preservation. Priority implementation.
Medium Priority: Important breeding contributing positively but not urgently required.
Low Priority: Optional breeding providing modest benefit. Without detracting from priorities.
Contraception: Active recommendation to prevent breeding. Animal genetically over-represented, health concerns, population surplus.
Priority Examples
High Priority Recommendation:
Pairing: Male "Rare-001" × Female "Unique-045"
Reason: Male carries critically underrepresented founder genetics. Only
opportunity to preserve these genetics in next generation. Female
has excellent genetic diversity and low inbreeding.
Action: Priority breeding approval, dedicated resources, close monitoring
Medium Priority Recommendation:
Pairing: Male "Standard-089" × Female "Good-156"
Reason: Genetically appropriate pairing contributing positively to population
diversity without critical urgency. Good breeding pair when high
priority pairings complete.
Action: Approve if resources available after high-priority breeding
Low Priority Recommendation:
Pairing: Male "Common-234" × Female "Typical-178"
Reason: Genetically acceptable but both animals' genetics well-represented
in population. Breeding provides minimal new genetic contribution.
Action: Optional breeding, defer if higher priorities exist
Not Recommended:
Pairing: Male "Father-001" × Female "Daughter-042"
Reason: Parent-offspring relationship creates extremely high inbreeding
(coefficient 0.25). Unacceptable genetic risk.
Action: Breeding prohibited, contraception implemented if necessary
Contraception Recommendation:
Animal: Female "Over-Rep-089"
Reason: Female's genetics extremely over-represented (15 offspring already,
multiple siblings also breeding). Further breeding reduces overall
population genetic diversity.
Action: Implement contraception preventing additional breeding
Priority classifications help breeding programs allocate effort. Resources effectively.
Genetic Value Assessment
Breeding recommendations include genetic value scores. Indicate breeding pair contribution to population:
What genetic value represents:
- Population genetic improvement: How much breeding improves overall genetic health
- Diversity contribution: Genetic variation added to next generation
- Inbreeding risk: Predicted offspring inbreeding (lower is better)
- Genetic complementarity: How well partners' genetics complement each other
Genetic value range: 0.0 (poor genetic contribution) to 1.0 (excellent contribution)
Example genetic value assessment:
Breeding Pair Assessment:
Pair A: Male "Azure" × Female "Jade"
Genetic Value: 0.892 (high)
Interpretation: Excellent breeding pair, significant genetic contribution
Predicted Offspring Inbreeding: 0.028 (very low)
Recommendation: HIGH PRIORITY
Pair B: Male "Common-1" × Female "Common-2"
Genetic Value: 0.512 (moderate)
Interpretation: Acceptable breeding, modest genetic contribution
Predicted Offspring Inbreeding: 0.045 (acceptable)
Recommendation: MEDIUM PRIORITY
Pair C: Male "Sibling-A" × Female "Sibling-B"
Genetic Value: 0.187 (poor)
Interpretation: Poor breeding choice, high inbreeding risk
Predicted Offspring Inbreeding: 0.156 (unacceptably high)
Recommendation: NOT RECOMMENDED
Genetic value quantifies breeding pair quality. Enables objective comparisons.
Breeding Methods and Timeframes
Recommendations include practical breeding guidance:
Breeding Methods
Natural Breeding: Animals allowed to breed naturally. Through normal social and reproductive behaviours.
Assisted Breeding: Artificial insemination or other assisted reproductive techniques.
Passive Breeding: Animals together without active breeding management. Opportunistic breeding.
Example method recommendations:
Natural Breeding Recommendation:
Animals: Pair-bonded parrots (established relationship)
Method: Natural breeding (birds breed naturally when bonded)
Notes: "Birds already pair-bonded, natural breeding appropriate and
successful historically"
Assisted Breeding Recommendation:
Animals: Endangered elephant bull × female at distant zoo
Method: Artificial insemination (animals at different institutions)
Notes: "Bull at Zoo A, female at Zoo B. AI enables breeding without
animal transfer. Semen collection and shipping coordinated
with reproductive specialists."
Timeframe Recommendations
Breeding timeframes suggest when breeding should occur:
Seasonal considerations:
- Species-specific breeding seasons
- Optimal environmental conditions
- Institutional capacity and resources
Example timeframe guidance:
Timeframe Recommendation 1:
"Spring 2025 breeding season (March-May). Aligns with natural breeding
behaviour and ensures chicks fledge during summer abundance."
Timeframe Recommendation 2:
"Next breeding cycle after female's current offspring weaned (estimated
January 2025). Allows proper recovery between breeding attempts."
Timeframe Recommendation 3:
"Delay breeding until genetic testing results available (expected Q1 2025).
Verify genetic compatibility before proceeding with breeding attempt."
Timeframe guidance ensures breeding occurs at appropriate times. Maximises success probability.
Target Offspring Counts
Recommendations may specify desired offspring numbers:
Purpose of target counts:
- Conservation programs: Specific population growth targets
- Genetic preservation: Multiple offspring ensuring genetic representation
- Sustainable management: Avoiding population over-production
Example offspring targets:
High Value Breeding:
Target Offspring: 3-4 chicks
Reason: "Rare genetics justify multiple offspring preserving genetic
diversity. Hand-rearing capacity available if needed."
Standard Breeding:
Target Offspring: 1-2 offspring
Reason: "Normal reproduction maintaining population stability without
over-production."
Conservation Surplus:
Target Offspring: Limit to 1 offspring
Reason: "Population approaching capacity. Single offspring maintains
genetic representation without excess population growth."
Target counts align breeding outcomes with population management goals.
Justification and Reasoning Documentation
Every recommendation includes justification explaining the reasoning:
Justification components:
- Why this pairing: Genetic factors making pairing beneficial
- Population context: How breeding serves program goals
- Risk assessment: Acknowledged risks and mitigation strategies
- Alternative considerations: Why this pairing chosen over alternatives
Example detailed justifications:
High Priority Breeding Justification:
"Azure represents critically underrepresented founder lineage #7, with only
2 individuals in captive population carrying these genetics. Genetic testing
confirms Azure's uniqueness score 0.923 (highly unique). Jade selected as
breeding partner due to:
1. Genetic Compatibility: Predicted offspring inbreeding only 0.028 (excellent)
2. Genetic Diversity: Jade's diversity score 0.801 complements Azure's genetics
3. Proven Breeding: Jade successfully raised 2 previous clutches (good parent)
4. Institutional Capacity: Both birds at Facility A enabling natural breeding
5. Population Impact: Offspring will diversify founder representation critical
for long-term population sustainability
Alternative pairings considered but rejected:
- Azure × Sky: Higher predicted inbreeding (0.047) due to shared ancestry
- Azure × Storm: Female Sky unsuitable breeding age (too young)
Recommendation: Proceed with Azure × Jade pairing Spring 2025, target 2-3 chicks,
natural breeding with nest monitoring."
Thorough justification documents decision-making process. Creates transparent, science-based recommendations.
Recommendation Validity and Expiration
Recommendations include validity periods:
Why expiration dates:
- Changing circumstances: Animals age, health changes, program goals evolve
- Updated genetic data: New testing provides refined genetic information
- Population dynamics: Birth/death of other animals affects recommendations
Example recommendation lifecycle:
Recommendation Created: 2024-10-15
Valid Until: 2025-12-31
Status During Validity:
2024-10-15 to 2025-08-30: Active recommendation
2025-09-01: Breeding attempt successful, 2 chicks hatched
2025-09-01: Recommendation marked completed (breeding occurred)
2025-12-31: Recommendation expires
New Season (2026):
- Population re-analysed with new genetic data including 2024-2025 offspring
- Updated recommendations generated for 2026 season
- Azure may receive different recommendation based on changed circumstances
(previous offspring now contributing to population genetics)
Regular recommendation updates ensure breeding advice reflects current population status.
Managing and Tracking Recommendations
Breeding program coordinators manage recommendations:
Coordinator workflow:
- Review generated recommendations: System produces breeding suggestions based on genetic data and pedigrees
- Evaluate practical factors: Consider institutional capacity, animal health, logistics
- Approve/modify recommendations: Confirm recommendations or adjust based on program knowledge
- Communicate to participants: Distribute breeding assignments to institutions or farms
- Track outcomes: Monitor breeding attempts and document results
- Update following season: Generate new recommendations incorporating breeding outcomes
Example coordination cycle:
Annual Breeding Season Coordination:
November 2024: Annual population analysis and genetic assessment
December 2024: System generates breeding recommendations for 2025 season
January 2025: Coordinator reviews recommendations, approves 8 high-priority pairings
February 2025: Breeding assignments communicated to participating institutions
March-August 2025: Breeding season, institutions attempt assigned pairings
September 2025: Outcomes reported (6 successful breeding, 12 offspring produced)
October 2025: Offspring registered, pedigrees updated, genetic data collected
November 2025: New population analysis incorporating 2025 breeding outcomes
December 2025: Updated recommendations for 2026 season generated
Cycle repeats annually with progressively refined genetic management
Systematic coordination turns recommendations into breeding program implementation.
Integration with Pedigrees and Genetics
Recommendations connect to pedigree and genetic data:
Data sources informing recommendations:
- Pedigree relationships: Identifying closely related animals to avoid
- Genetic profiles: Inbreeding coefficients, diversity, uniqueness scores
- Population analysis: Overall population genetic health and demographics
- Breeding history: Past breeding success, offspring quality
Example integrated recommendation:
Breeding Recommendation - Complete Data View:
Recommended Male: "Jabari" (Elephant Bull)
Studbook ID: BRP-2016-M-009
Age: 8 years (prime breeding age)
Pedigree: Son of "Thunder" and "River" (both deceased)
Siblings: 2 half-siblings via mother "River"
Genetic Profile:
- Inbreeding Coefficient: 0.034 (low)
- Genetic Diversity: 0.756 (good)
- Genetic Uniqueness: 0.612 (moderately unique)
Breeding History: 3 previous offspring (all healthy, good survival)
Recommended Female: "Amara" (Elephant Cow)
Studbook ID: BRP-2015-F-018
Age: 9 years (proven breeder)
Pedigree: Daughter of "Sky" and "Earth" (Sky deceased, Earth age 18)
Siblings: 1 full sister "Mali"
Genetic Profile:
- Inbreeding Coefficient: 0.041 (low)
- Genetic Diversity: 0.789 (good)
- Genetic Uniqueness: 0.701 (moderately unique)
Breeding History: 2 previous offspring (successful mother)
Relationship Check: NOT RELATED (no shared ancestors within 4 generations)
Predicted Offspring Genetics:
- Predicted Inbreeding: 0.031 (low - excellent)
- Expected Diversity: 0.772 (good - above population average)
- Genetic Contribution Value: 0.845 (high)
Recommendation: HIGH PRIORITY BREEDING
Justification: "Genetically compatible pair with no close relationship, both
proven breeders, predicted offspring genetics excellent. Both
animals at same institution enabling natural breeding."
Comprehensive data integration produces well-informed breeding recommendations.