Identification and use of CNV for genomic selection in Santa Inês sheep

Author(s)

Giovanni Coelho Ladeira

• Document type: Master's Dissertation
• Press: Piracicaba.
• Institution: Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC)
• Defense date: 2021-08-31

Examining board members

Gerson Barreto Mourão; Luís Fernando Batista Pinto

• Advisor: Gerson Barreto Mourão

Abstract

Copy number variations (CNV) are structural variations in DNA of at least 1 kb that differ from the reference genome in copy number. The growing number of studies with CNV report its association with diseases in humans and several quantitative traits in livestock animals. However, CNV-based genome-wide association studies in Santa Inês sheep, one of the most important breeds in Brazil, have not been reported and, furthermore, information on the inclusion of CNV effects in GEBV prediction models is rare. Thus, the aims of the present study were 1) to identify and quantify CNVs in a population of Santa Inês sheep, 2) to verify possible associations between CNVs and characteristics of interest, 3) to identify possible overlapping of CNV segments significantly associated with the characteristics of interest to previously known QTLs and genes, and 4) to evaluate possible gains in accuracy in GEBV predictions by combining SNP and CNV information (GBa + CNV) compared to GEBV predictions using exclusively SNP information (GBa). Thus, genomic information from 491 Santa Inês sheep (OvineSNP50 BeadChip) was used. The identification of CNVs was performed using the PennCNV software. The CNV information was used to build a genomic relationship matrix based on CNVs, which was incorporated into the mixed model used for the prediction of GEBVs in addition to the traditional SNP information. Next, accuracy was estimated by Pearson\'s correlation between predicted GEBVs for training population and phenotype corrected for fixed effects in the validation population. Predicted GEBVs were used in CNV-based genome-wide association analyses, through the CNVRanger program, to identify regions in the genome associated with performance, efficiency and carcass traits. 1,167 CNV segments were identified, including significant segments (p-value<0.05) associated with traits: carcass yield and residual feed intake, in addition, another 5 CNV segments were considered relevant and indicated for future studies. The significant segments overlapped 4 QTLs and 8 genes, including the SPAST, TGFA and ADGRL3 genes with functions related to cell differentiation and energy metabolism. The inclusion of CNV in the genetic analysis allowed capturing greater genetic variance, however the proportion of genetic variance captured by CNVs varies among characteristics and does not necessarily increase the prediction accuracy. Among the models considered, there was no increase in predictive ability when entering CNV information. Therefore, the results reported in the present study indicate that the inclusion of CNV information in models to predict GEBV should not be a priority. (AU)

• FAPESP's process: 19/19213-0 - Identification and use of CNV for genomic selection in Santa Inês sheep
• Grantee: Giovanni Coelho Ladeira
• Support Opportunities: Scholarships in Brazil - Master