Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle

Abstract

Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing ≈6.5% of the genome. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.

Fig 1. Distribution of CNVR length.

Fig 2. Chromosomal distribution of 521 polymorphic CNVRs (>1% of the population).

The regions were categorized into loss or gain of copy number and states for which both events were observed.

Fig 3. Overlap of the detected Nelore CNVRs with known cattle CNVRs.

A) The Venn diagram shows the genomic size in Mb that is overlapped. Known CNVRs listed in S3 Table were reduced to unique and non-overlapping CNVRs. The overlapped fraction of 79 Mb corresponds to 1,387 Nelore CNVRs. (B) For these 1,387 CNVRs, the histogram shows the number of CNVRs (y-axis) overlapping with known CNVRs by the percentage shown on the x-axis. For example, genomic locations of >700 Nelore CNVRs overlap individually >90% with genomic locations of known CNVRs.

Fig 4. QTL-traits that overlap with polymorphic CNVRs in the Nelore population.

Depicted are the most frequently overlapped traits. Red bars correspond to the observed number of polymorphic CNVRs overlapping with the respective trait, and cyan bars indicate the mean overlap when sampling 1000x random regions matching the polymorphic CNVRs in size and chromosomal location. The error bars indicate the standard deviation and permutation p-values are listed on the right.

Fig 5. Genome wide association of CNV state with shear force estimated breeding value (SF-EBV).

Manhattan plot for 447 CNV segments on somatic chromosomes (x-axis) and the corresponding -log₁₀ p-value (y-axis) indicating the association strength with SF-EBV. Multiple testing correction was performed, controlling the false discovery rate (FDR, [64]). Red and blue lines indicate FDR-corrected p-values of 0.05 and 0.1, respectively. The black arrows indicate CNVRs with p-value <0.1 and list the nearest protein-coding genes up- and downstream of the segment (in a genomic window ≤1Mb). Raw signal strength is shown in S3 Fig.

Fig 6. Shear force estimated breeding value (SF-EBV) distribution in each CN state for six significant CNV segments.

Each dot represents an animal in the corresponding CN state (0-3n) on the x-axis and the assigned SF-EBV on the y-axis. The legend on the top right displays the color code for the CN state. See the main text for a detailed description of each segment and S11 Table for additional details.