Daniel J. A. Santos's research while affiliated with Loyola University Maryland and other places

Publications (7)

Article
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Background: Ketosis is a common metabolic disease during the transition period in dairy cattle, resulting in long-term economic loss to the dairy industry worldwide. While genetic selection of resistance to ketosis has been adopted by many countries, the genetic and biological basis underlying ketosis is poorly understood. Results: We collected...
Article
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Background: Traditional selection in livestock and crops focuses on additive genetic values or breeding values of the individuals. While traditional selection utilizes variation between individuals, differences between gametes within individuals have been less frequently exploited in selection programs. With the successful implementation of genomi...
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Background: Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The obje...
Article
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Background: Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with repr...
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Background: DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Results: Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486 × coverage), w...
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Background: Crossover localization during meiotic recombination is mediated by the fast-evolving zinc-finger (ZnF) domain of gene PRDM9. To study its impact on dairy cattle performance, we compared its genetic variation between the relatively small Israeli (IL) Holsteins and the North American (US) Holsteins that count millions. Results: Initial...
Article
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Background Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the conseque...

Citations

... Membrane bound mucins have been suggested to play a functional role in cell signaling linked to health and disease (Corfield et al., 2001;Linden et al., 2008). A MUC20 -lncRNA has been reported to bind ROCK1 and to be functionally involved in tumor suppression (Dai et al., 2020) indicating trans-regulation. TNK2 encodes a tyrosine kinase that binds to the Rho family member Cdc42Hs and inhibits both the intrinsic and GTPaseactivating protein-stimulated GTPase activity (Manser et al., 1993). ...
... Therefore, ICSI could be a viable option for the efficient use of semen of suboptimal quality (collected from young bulls) or sex-sorted. Although gametes contribute to genetic variation, selection of gametes based on genetic diversity is now possible using genomic selection [16]. Changing genetic selection from a superior animal for breeding to a superior gamete within an individual is not far from reality, as software that can identify gametic variance is already available [16]. ...
... We detected 854 significant gene-trait pairs for 43 agronomic traits (Supplementary Table 10) in cattle via single-tissue TWAS (S-PrediXcan), representing 337 unique genes (Supplementary Table 11). Of 319 fine-mapped genes 18,19 , we validated 54, including linking expression of DGAT1 in liver and mammary gland, and expression of MGST1 in milk cells, as well as expression of CLN3 in liver to milk yield (Fig. 6d). Expression of ZNF613 in the hypothalamus was the most significant association for many reproduction and body conformation traits, including daughter-still-birth and stature (Supplementary Table 11), supporting our previous finding that ZNF613 is significantly associated with gestation length, possibly through its influence on embryonic development 20 . ...
... Employing whole-genome bisulfite sequencing (WGBS) data (486 × coverage) from neighboring CpG sites among 28 distinct bull sperm samples, Liu et al. (155) identified 31,272 methylation haplotype blocks (MHB) based on the correlation analysis of methylation levels. Of these MHBs, they defined highly variably methylated, variably methylated, and conserved methylated regions. ...
... This SNP lies within NLGN4X, a neuronal cell surface protein with links to autism and Asperger syndrome. None of the regions identified in the current study overlap with other AFC GWAS results, although only literature reports for beef (Stegemiller et al., 2021) or Nellore cattle could be found (Oliveira Júnior et al., 2019;Grigoletto et al., 2020). The potential of a genomic marker for AFC is useful, as measuring AFC is time consuming and difficult in a nonresearch capacity. ...
... Yet, both reported hybrids were female [16,17], which is the homogametic sex in minke whales. There are reports of a Bos indicus PRDM9 variant that, when introgressed into Holstein cattle, induced incompatibility of recombination hotspots and infertility in males but at the same time improved fertility of female hybrids [66]. These observations in cattle, and the lack of male minke whale hybrids, do not allow any conclusions as to whether the postzygotic isolation mechanisms related to PRDM9 incompatibility do or do not generally operate in minke whales. ...
... LD between loci decays as a function of genetic distance and aberrantly elevated LD between distantly positioned markers may suggest misassembled DNA or so-called misplaced markers. Efforts have already been made to localize misplaced markers in the UMD3.1 assembly on the basis of LD measures among SNPs of the bovine 50k array (Utsunomiya et al., 2016) and in the ARS-UCD1.2 assembly based on recombination rate analysis (Qanbari & Wittenburg, 2020). ...