Generate a pedigree chart documenting three-generation genotype frequencies for Angus replacement heifers screened for the calpastatin tenderness trait

Foundation Seedstock File *

Individual Filter Criteria * Select cohort criteria Only registered Angus females eligible for replacement (weaned heifers 6-12 months) All genotyped commercial Angus females born in current calving season Angus replacements from registered dams sired by high-accuracy AI bulls Females from embryo transfer with known three-generation pedigree and genotypes Exclude animals with genotype call rates < 95% Include only females with existing progeny data for validation

Allele Notation and Reference * Select allele notation system ARS-UCD1.2 reference, forward strand coding (A=tender, G=tough) UMD3.1 reference, forward strand (A=tender, G=tough) ARS-UCD1.2 reference, reverse strand (T=tender, C=tough) UMD3.1 reference, reverse strand (T=tender, C=tough) Custom mapping provided in seedstock file Use official Beef Improvement Federation (BIF) standard nomenclature

Generation Processing Mode * Select generation-tracing method Forward from foundation dams (F-0) through daughters (F-1) to granddaughters (F-2) Backward from 2024-born heifers to dams (F-1) to grand-dams (F-2) Iterate both directions and reconcile overlapping animals Exclude great-grandsire vault records (reduce computational load) Pad missing grand-dam data with inferred probabilities from sire lineage

Hardiness Sub-population Select production environment filter (optional) Spring-born herd under intensive grazing with creep feeding Fall-born herd on cool-season pasture, no creep feed Confinement-reared heifers in Midwest feedlots Multi-breed composites with ≤25% non-Angus genetics Registered purebred herds participating in National Cattle Evaluation (NCE) Whole-herd commercial operations with ≥300 breeding females

Output Chart Formats * Select primary chart format Static PDF pedigrees with genotype heat-maps per family line Interactive HTML pedigree with expandable nodes and filtering by genotype CSV matrix flagging genotype and phenotype counts for each kinship triplet GraphML for import into livestock management packages Excel workbook with separate sheets for each generation cohort Publication-ready PDF appendix for peer-reviewed submission

Third-Party Consent Flags * Select consent/database policy Include only animals where farm owner granted full data sharing rights Mask individual IDs but retain lineage structure for publication use Exclude shared-sample datasets that require additional permissions Use synthetic IDs for external sharing, retain mapping keys on farm Honor breed-association restrictions on AI sires if present Limited to in-house research team under institutional data policy

Target Hardy-Weinberg Threshold

Phasing Strategy * Select phasing approach Do not phase — use unphased genotype calls for faster processing Use parental genotypes to phase heifers by transmission rules Employ Beagle 5.4 with Angus reference panel for full imputation Use linkage-disequilibrium pruning (r² > 0.8) before phasing Skip phasing if call rate < 98% to avoid spurious haplotypes

Complementary Notes