Supplementary Materials for Dissertation Novel Genomic Approaches to Explore Heterosis, Genetic Diversity, Selection, and Introgression in Cattle

Supplementary Materials for the Dissertation

Title: Novel Genomic Approaches to Explore Heterosis, Genetic Diversity, Selection, and Introgression in Cattle
Author: Gabriel Zayas
Institution: Animal Sciences Department, University of Florida

This repository contains supplementary materials that support the analyses and findings presented in the dissertation. The files include supplementary figures, tables, and datasets relevant to different chapters of the dissertation. Some supplementary materials correspond to already published papers, and proper citations are provided.

Supplementary Data Files and Figures

Object 2-1: Supplementary Data File (Chapter 2)

This Excel file contains supplementary figures and tables supporting the findings in Chapter 2 of the dissertation. The materials in this section originate from the published study:

📄 Zayas GA, Mateescu RG (2025). Genomic signatures of selection in Brangus cattle revealing the genetic foundations of adaptability and production traits using a breed of origin approach. Front Anim Sci 5.

Supplementary Figures:

• Figure 1: Scatterplot and correlation analysis between ADMIXTURE and PCA-based breed composition.
• Figure 2: Scatterplot and correlation analysis between ADMIXTURE and BOA-based breed composition.

Supplementary Tables:

• Table 1: QTL enrichment analysis results in the Seminole Brangus population, identifying significant genomic regions associated with production and carcass traits.
• Table 2: QTL enrichment analysis results in the Williamson Brangus population, highlighting significant associations with metabolic body weight, carcass weight, and average daily gain.
• Table 3: Significant genomic regions identified from a Median-based Z-score test on BOA heterozygosity in both the Williamson and Seminole Brangus populations, based on previous studies.

Object 3-1: Supplementary Figures (Chapter 3)

This Word file contains supplementary figures supporting the findings in Chapter 3 of the dissertation. The materials in this section originate from the published study:

📄 Zayas GA, Rodriguez EE, Hernandez AS, Rezende FM, Mateescu RG (2024). Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation. J Appl Genet.

Supplementary Figures:

• Figure 1: Bar plot showing the distribution of ROH across autosomes. The y-axis represents ROH count, while the x-axis represents chromosomes. The percentage of total ROH per chromosome is indicated above each bar.
• Figure 2: Histogram of ROH lengths categorized into four size classes:
  • Class 1: 1–3.9 Mb
  • Class 2: 3.9–7.8 Mb
  • Class 3: 7.8–13 Mb
  • Class 4: >13 Mb
• Figure 3: Scatterplot depicting ROH length distribution across chromosomes. Each point represents an ROH event, with x-axis indicating its genomic position and y-axis showing its length. ROH events are color-coded by size class.

Object 4-1: Supplementary GWAS and BOA Analysis Tables (Chapter 4)

This Excel file contains supplementary tables summarizing the results of variance component estimation, GWAS, and BOA analyses for carcass and marbling traits in Chapter 4 of the dissertation. The materials in this section originate from the published study:

📄 Zayas GA, Rodriguez E, Hernandez A, Rezende FM, Mateescu RG (2024). Breed of origin analysis in genome-wide association studies: enhancing SNP-based insights into production traits in a commercial Brangus population. BMC Genomics 25: 654.

Supplementary Tables:

• Table 1: Variance component estimates for hot carcass weight (HCW) and marbling score (MARB) using AIREML, comparing SNP-based and BOA-based models with and without principal components.
• Table 2: Significant SNP markers associated with HCW based on GWAS (FDR = 0.05).
• Table 3: Significant SNP markers associated with marbling based on GWAS (FDR = 0.15).
• Table 4: Additive and dominance effects of SNP markers explaining >1% of genetic variation in HCW and MARB.
• Table 5: Significant BOA markers associated with HCW based on BOA GWAS (FDR = 0.30).
• Table 6: ANOVA tables and least square means (LSmeans) for BOA markers explaining >1% of genetic variance in HCW.
• Table 7: Significant BOA markers associated with marbling based on BOA GWAS (FDR = 0.175).
• Table 8: ANOVA tables and least square means (LSmeans) for BOA markers explaining >1% of genetic variance in MARB.

Object 5-1: Supplementary Data File (Chapter 5)

This Excel file contains supplementary tables supporting the findings in Chapter 5 of the dissertation. The materials in this section originate from the published study:

📄 Zayas GA, Dikmen S, Mateescu RG, Hansen PJ (2024). Maintaining breed integrity: Successful introgression of the SLICK1 allele into the Holstein breed. J Hered: esae057.

Supplementary Tables:

• Table 1: Grid search results for optimal window size (5-50 SNPs) and hidden states (2-15) for LAMP-LD ancestry analysis. Includes mean breed ancestry estimates and standard deviations for different parameter combinations.
• Table 2: List of genes located within the BTA4:70669213-72382132 genomic region, including Ensembl Gene IDs and gene names.
• Table 3: Gene enrichment analysis for genes within BTA4:70669213-72324871, using g:Profiler’s gost function. Includes significant GO terms and Reactome pathways, with p-values and term descriptions.

Object 6-1: Supplementary GWAS Results for Thermotolerance Traits (Chapter 6)

This Excel file contains supplementary tables supporting the findings presented in Chapter 6 of the dissertation and are part of a manuscript currently under review in Frontiers in Genetics.

Supplementary Tables:

• Table 1: Significant and suggestive markers identified in GWAS for long hair length. Includes chromosome (BTA), marker position (bp), P-values, GWAS model type, effect type (SNP, BOA, or joint), variant information, effect size (effect ± SE), and nearby genes (±250kb).
• Table 2: Significant and suggestive markers identified in GWAS for short hair length. Includes genomic positions, effect types, and key genes such as CCDC47 and PRLR.
• Table 3: Significant and suggestive markers identified in GWAS for sweat gland area, highlighting intergenic regions and key candidate genes such as HMGA2 and MSRB3.
• Table 4: Significant and suggestive markers identified in GWAS for thermal stress response (thermal stress slope), including joint, SNP, and BOA models. Notable candidate genes include COL8A1 and CMSS1.

Citation and Reproducibility

These supplementary materials are provided to enhance transparency, reproducibility, and accessibility of the analyses conducted in the dissertation. For citation and proper attribution, please reference the corresponding published article(s) when using specific datasets or figures. 

Since the dissertation is not yet published, it currently has no DOI. Once it is finalized and available through the University of Florida’s institutional repository, a citation will be provided here.