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Targeted sequencing reveals deleterious mutations affecting dairy bull fertility.

R. Abdollahi-Arpanahi

Abstract:

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Targeted sequencing reveals deleterious mutations affecting dairy bull fertility.
R. Abdollahi-Arpanahi*, H. A. Pacheco, F. Pe�agaricano. University of Florida Gainesville, FL.

Bull fertility is often overlooked as a potential cause of reproductive inefficiency in dairy cattle. However, semen from one bull is used to inseminate hundreds of cows, and hence, one subfertile bull could have a major impact on herd reproductive performance. We previously identified 5 genomic regions, located on BTA8 (72.2 Mb), BTA9 (43.7 Mb), BTA13 (60.2 Mb), BTA17 (63.3 Mb), and BTA27 (34.7 Mb), that show very significant dominance effects on dairy bull fertility. Each of these regions explains about 5—8% of the observed differences in sire conception rate between bulls. Here, we aimed to identify the causal variants responsible for this variation using targeted sequencing (10Mb per region). For each genomic region, 2 DNA pools were constructed from high-fertility and low-fertility Holstein bulls. The DNA Sequencing analysis included reads quality control (using FastQC), genome alignment (using BWA and ARS-UCD1.2), variant calling (using GATK) and variant annotation (using Ensembl). The sequencing depth per pool varied from 39X to 51X. We identified 7,144 SNPs with opposing homozygous genotypes between low- and high-fertility pools. Notably, 74 of these SNPs were annotated as missense mutations, and at least 5 of them were classified as strong candidate causal variants, i.e., missense mutations with deleterious effects located on genes exclusively/highly expressed in testis or actively involved in the fertilization process. These candidate causal mutations are located in genes ADAM28, TTLL9, TCHP, FOXN4 and ADAM2. This work is the foundation for the development of novel genomic tools for improving dairy bull fertility, these causal mutations will allow the early detection and culling of subfertile bull calves or young genomic bulls.

Keywords: causal variants, DNA sequencing, sire conception rate.