Integrating Multiple Correspondence Analysis and GWAS to Evaluate Reproductive Potential in Crossbred Heifers

The objective of this study was to evaluate the reproductive potential of crossbred heifers from dual-purpose systems using body conformation traits and to explore their genomic associations.

A total of 522 heifers from the Colombian Caribbean region were phenotyped for structural and morphological traits, including body condition score, thoracic perimeter, height at withers, body length, ischium length, back level, hoof angle, stance width, hock angle, and rump level. Continuous variables were transformed into categorical classes and analyzed using multiple correspondence analysis (MCA) to build a reproductive potential index (RPI) that was used to perform a GWAS analysis to explore genomic regions.

The first two dimensions explained 11.6% and 8.2% of the total variation, respectively, and were used to construct an RPI. Heifers with higher RPI values exhibited greater thoracic perimeter, height, body length, and ischium length and were associated with wider chest and deeper body conformation, whereas lower RPI values were related to narrower and shallower body traits. However, some structurally desirable traits, such as centered stance, optimal hoof angle, and slightly sloped rump, were not clearly associated with high RPI. Genome-wide association analysis of the RPI did not reveal significant loci, although suggestive signals were identified on BTA3 and BTA19, near RSBN1, PHTF1, and WNT9B.

These findings indicate that MCA-derived indices can summarize conformation-related variation in crossbred heifers, while the absence of strong associations suggests a polygenic architecture with small individual genetic effects.