Guidelines For Countries Interpreting Mendelian Sampling Validation Test Results

The following is intended to be a guideline of actions a country could apply if some of its traits, for a given breed, are consistently not within the range of acceptance for the Mendelian Sampling (MS) Test.

Please remember that:

• MS test results are not used by Interbull as a requirement for participating in MACE evaluation services, but are considered as a great investigative tool for National Genetic Centers to detect possible areas requiring improvement in their models or data structures.
• MS test should be applied to both males and females but application of the test to females should be limited to medium-high heritability traits (usually production, stature and somatic cell score). Lower heritability traits should be tested on males only.
• MS test should be applied to the same traits for which conventional validation is conducted. This implies that for conformation traits the test should be applied to the following traits only: STA, USU, LOC and BCS.
• For bulls, the same data edits should be applied as outlined in the Interbull Code of Practice, item 5.1.3. No specific data edits are required for females.
• The MS test requires the following information: Animal’s birth year, EBVs for the animals and their parents and the estimates of the EBV reliabilities.
• Only animals with complete information on both parents should be included in the analyses.

Should your results of the MS test not fall within the range of acceptance, then:

1. Carefully review the software’s log output for any warning messages that may have been issued. Warning messages are usually printed out when:
   1. in some birth year classes the number of animals with observations is less than 50% of the average class size in the testing period,
   2. after checking MS reliabilities of animals, the number of records in some birth year classes is below 10 or,

   3. after checking MS reliabilities of animals, the number of records in some birth year classes is below two in which case the program also terminates.
      
      

      For cases from a) to c), the program suggests changing the time window of the analysis or excluding the outermost year(s). The suggested actions should be carried out and the test repeated.
      
      

2. If the time window applied does includes birth years after genomic pre-selection has been applied in your country, MS test results that are not within the range of acceptance may be due to such genomic pre-selection. Genomic pre-selection decreases the variance of the MS-term, but when the assumption of E[MS]=0.0 is not fulfilled, the estimated var(MS) can even increase. Any effect of genomic pre-selection on the MS test results may be identified by examining results for birth years before and after its introduction nationally.

   1. Apply a time window including only years before the start of genomic pre-selection nationally and re-run the MS test.
      
      

3. The test should be applied on purebred animals only. For heavily crossbred populations it is recommended to:
   1. Investigate the population structure for the time window considered.
   2. Apply the MS test only to purebreds.
   3. If point (b) is not possible and a crossbred population is analyzed, a heterosis effect could be added to the model as an effect.
   4. Re-apply the MS test.