About

David Riley, Ph.D., is a professor of animal breeding and genetics in the Department of Animal Science at Texas A&M University. He received his undergraduate degree in agricultural economics, a master's degree in animal breeding, and a doctorate in genetics, all from Texas A&M University. His teaching responsibilities include graduate courses such as Quantitative Genetics, Genetic Prediction, and Advanced Quantitative Genetics. His research focuses on the association of genes, gene combinations, and molecular variants with beef cattle production traits, particularly those related to reproduction and efficiency. He is interested in incorporating genomic information into traditional animal breeding strategies and in predicting breeding values using such data. Additionally, his research includes assessing and quantifying epigenetic variation in livestock traits and examining the expression of heterosis in crossbred animals for important traits. Prior to joining Texas A&M University in 2009, Dr. Riley worked as a Research Geneticist at the USDA, Agricultural Research Service, Subtropical Agricultural Research Station in Florida, and has experience in swine breeding stock production, selection, and service.

Research topics

• Biology
• Animal science
• Ecology
• Medicine
• Genetics
• Veterinary medicine
• Biotechnology
• Business
• Environmental science
• Psychology

Selected publications

• 191 Systematic effects influencing hair shedding in Admixed beef heifers in the Northern Great Plains

  Journal of Animal Science · 2025-06-01

  articleOpen access

  Abstract Cattle hair shedding is vital for thermoregulation during high summer temperatures, reducing heat stress and enabling energy allocation to production characteristics. Research involving coat shedding in the Northern Great Plains climate is lacking. The objective of this study was to characterize and determine systematic effects influencing coat shedding in yearling, admixed beef heifers in the Northern Great Plains region. We hypothesized that apparent high temperatures would significantly affect shedding capability, with breed composition contributing to observed variability. Over a 4-year period, yearling-age heifers (12.73 +/- 0.51 mo) were transported from the Dickinson Research Extension Center near Manning, ND, to the Beef Cattle Research Complex in Fargo, ND, as part of a long-term study. The study population consisted of 289 heifers representing diverse breed compositions, including American Aberdeen, Angus, Red Angus, Gelbvieh, Limousin, Shorthorn, Simmental, and various first-cross hybrid groups. Photographs of the heifers taken in early June (date 1) and early July (date 2) as part of the annually conducted feed trial were used for scoring in this study. Hair shedding was assessed by 3 evaluators using a standardized 1 to 5 scoring system, where 5 represented a complete winter coat, with scores decreasing by 25% increments, and 1 indicating no winter coat remaining. The average score per date (n = 2) and average relative change value, calculated by subtracting the date 2 average score from the date 1 average score divided by the date 1 average score, was used to compare shedding capability among animals. Influential systematic effects investigated for average relative change of shedding included fixed covariates of average apparent high temperature 14 d or 30 d before date 1 and 14 d or 30 d before date 2 as well as fixed class effects of coat color (n = 2; red vs. black), pedigree-based breed group (n = 9), frame score group (n = 4), and heifer’s dam age category (n = 4). Heifer was included as a random effect in all models. A total of 60 models were explored using mixed model procedures and maximum likelihood estimation to assess model fit based on AIC and BIC values when including and excluding fixed effects. The model with the best fit included average apparent high temperature 30 d before date 1 (P = 0.0001), pedigree-based breed group (P = 0.3457), frame score group (P = 0.6285), and heifer’s dam age category (P = 0.1276). The slope estimate of the average apparent high temperature 30 d before indicates a 2.6% decrease in shedding score per degree increase in apparent high temperature. Day length and its potential interaction with apparent high temperature will be explored in subsequent analyses.

  PublisherOA PDFDOI

• Evaluation of Prenatal Transportation Stress on DNA Methylation (DNAm) and Gene Expression in the Hypothalamic–Pituitary–Adrenal (HPA) Axis Tissues of Mature Brahman Cows

  Genes · 2025-02-04 · 1 citations

  articleOpen access

  Background/Objectives: The experience of prenatal stress results in various physiological disorders due to an alteration of an offspring’s methylome and transcriptome. The objective of this study was to determine whether PNS affects DNA methylation (DNAm) and gene expression in the stress axis tissues of mature Brahman cows. Methods: Samples were collected from the paraventricular nucleus (PVN), anterior pituitary (PIT), and adrenal cortex (AC) of 5-year-old Brahman cows that were prenatally exposed to either transportation stress (PNS, n = 6) or were not transported (Control, n = 8). The isolated DNA and RNA samples were, respectively, used for methylation and RNA-Seq analyses. A gene ontology and KEGG pathway enrichment analysis of each data set within each sample tissue was conducted with the DAVID Functional Annotation Tool. Results: The DNAm analysis revealed 3, 64, and 99 hypomethylated and 2, 93, and 90 hypermethylated CpG sites (FDR < 0.15) within the PVN, PIT, and AC, respectively. The RNA-Seq analysis revealed 6, 25, and 5 differentially expressed genes (FDR < 0.15) in the PVN, PIT, and AC, respectively, that were up-regulated in the PNS group relative to the Control group, as well as 24 genes in the PIT that were down-regulated. Based on the enrichment analysis, several developmental and cellular processes, such as maintenance of the actin cytoskeleton, cell motility, signal transduction, neurodevelopment, and synaptic function, were potentially modulated. Conclusions: The methylome and transcriptome were altered in the stress axis tissues of mature cows that had been exposed to prenatal transportation stress. These findings are relevant to understanding how prenatal experiences may affect postnatal neurological functions.

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• Effects of Fermented Soybean Meal Supplementation on Growth, Carcass Quality, and Intestinal Morphology in Ross 308 and Indian River Broilers

  Animals · 2025-09-11 · 3 citations

  articleOpen accessSenior author

  A total of 700 broiler chicks (350 Indian River and 350 Ross 308) were obtained from a local hatchery. Birds were randomly allocated in a completely randomized design by strain into two dietary groups: a control group (corn–soybean meal) and a treatment group in which 7.5% of soybean meal (SBM) was replaced with fermented soybean meal (FSBM). Each group included 175 birds, distributed across seven replicates (pens) with 25 birds per pen. Birds were weighed at the start of the trial and at the end of each rearing phase (starter (1–14 days of age), and grower phases (15–35 days of age)). Mortality was monitored daily throughout the experiment. Weekly feed intake was recorded for each pen. On day 35, 14 birds were randomly selected from each treatment–strain combination for carcass and meat quality evaluation. Data were analyzed with linear models; strain, diet, and their interaction were the investigated effects. No strain–diet interaction was detected for growth performance, carcass and meat quality, and intestinal morphology traits (p > 0.05). Significant interaction effect on crude protein digestibility is found (p < 0.001). The FSBM improved crude protein digestibility for the Indian River broiler strain, while the opposite occurred in the Ross 308 strain. Fermented soybean meal supplementation did not significantly affect body weight gain, feed conversion ratio (FCR), or feed intake during the study period (p > 0.05). The Ross strain exhibited a higher dressing percentage (p = 0.04) and greater cooking loss (p = 0.01), whereas the Indian River strain showed higher abdominal fat percentage (p = 0.04) and shear force (p = 0.003). The dressing percentage, pH, color parameters, cooking loss, water-holding capacity, and breast fillet yield for FSBM and control groups did not differ (p > 0.05). Ileum villus length and width were significantly higher (p < 0.05) in the FSBM group compared to the control group. In conclusion, Fermented soybean meal can enhance intestinal morphology and crude protein digestibility in a strain-specific manner; however, its impact on growth and carcass attributes is limited at this inclusion level.

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• Analysis of nonsynonymous SNPs in candidate genes that influence bovine temperament and evaluation of their effect in Brahman cattle

  Molecular Biology Reports · 2024-02-07 · 3 citations

  articleOpen access

  BACKGROUND: Temperament is an important production trait in cattle and multiple strategies had been developed to generate molecular markers to assist animal selection. As nonsynonymous single nucleotide polymorphisms are markers with the potential to affect gene functions, they could be useful to predict phenotypic effects. Genetic selection of less stress-responsive, temperamental animals is desirable from an economic and welfare point of view. METHODS AND RESULTS: Two nonsynonymous single nucleotide polymorphisms identified in HTR1B and SLC18A2 candidate genes for temperament were analyzed in silico to determine their effects on protein structure. Those nsSNPs allowing changes in proteins were selected for a temperament association analysis in a Brahman population. Transversion effects on protein structure were evaluated in silico for each amino acid change model, revealing structural changes in the proteins of the HTR1B and SLC18A2 genes. The selected nsSNPs were genotyped in a Brahman population (n = 138), and their genotypic effects on three temperament traits were analyzed: exit velocity, pen score, and temperament score. Only the SNP rs209984404-HTR1B (C/A) showed a significant association (P = 0.0144) with pen score. The heterozygous genotype showed a pen score value 1.17 points lower than that of the homozygous CC genotype. CONCLUSION: The results showed that in silico analysis could direct the selection of nsSNPs with the potential to change the protein. Non-synonymous single nucleotide polymorphisms causing structural changes and reduced protein stability were identified. Only rs209984404-HTR1B shows that the allele affecting protein stability was associated with the genotype linked to docility in cattle.

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• A Beet Armyworm (Lepidoptera: Noctuidae) Ryanodine Receptor Mutation Associated with Diamide Resistance is Present in a Chlorantraniliprole-Resistant Population from South Georgia, USA

  Journal of Entomological Science · 2024-11-18 · 2 citations

  articleOpen access

  A population of beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), larvae was collected from cowpeas (Vigna unguiculata [L.] Walpers) from Scooterville, GA (Tift Co.) in the summer of 2022, following a report of control failure after chlorantraniliprole application. The collected larvae were transported to Tifton, GA for study at the Coastal Plains Experiment Station. The 72-h maximum dose leaf-dip bioassays of the field-population determined percent mortality to be 26, 49, and 87% for the insecticide active ingredients chlorantraniliprole, cyantraniliprole, and spinetoram, respectively. In comparison, the percent mortality of a susceptible lab strain exposed to the same insecticides was 76, 88, and 98%, respectively. Previous studies of a ryanodine receptor target site mutation, I4743M, identified in Chinese populations of beet armyworm, demonstrated an association with resistance to diamide insecticides. All screened samples from the diamide-resistant field population were shown to possess this mutation, while samples from the diamide-susceptible lab colony were shown to be wild-type. A second mutation, G4900E, associated with diamide resistance in other lepidopteran species, was not identified in any of the sequenced samples from either population. This is the second report of diamide insecticide resistance in beet armyworm populations from the southeastern United States, and the first report of the I4743M target site mutation in Georgia.

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• Herbal extract dietary supplementation effect on growth performance and meat quality in broiler raised under two stocking densities

  Scientific Reports · 2024-08-11 · 13 citations

  articleOpen access

  The number of birds or their total live weight in relation to a given area is known as stocking density; higher stocking densities will cause more stress to the birds, which may have an impact on their physiological state, productivity, carcass quality, growth performance, immunity, metabolism, and meat quality. The present study aimed to investigate the potential impact of 2 different stocking densities on growth performance, carcass characteristics, meat quality, serum, and expression of Insulin like growth factor-1 (IGF-1), muscle regulatory genes expression and serum biochemical indicators of broilers supplemented with essential oils (EO). In total, 784-day-old chicks of Ross 308 were randomly assigned into 4 different groups with 7 replicates for each: Normal feed (no essential oils [EO] added) and normal stocking as 9 bird/m2, (NSD). Normal feed (no essential oils [EO] added) and high stocking as 14 bird/m2, (HSD). Feed with essential oils (Digestarom DC® 150 g/Ton of feed) and normal stocking as 9 birds/m2, (NSD + EO). Feed with essential oils (Digestarom DC® 150 g/Ton of feed) and high stocking as 14 birds/m2, (HSD + EO) for 35 days. Bodyweight was recorded at the beginning of the trial and then at the end of each week, feed intake was recorded at the end of each week as well. A total of 28 birds (7 birds per treatment) birds were slaughtered at 35 days of age to evaluate each parameter. The HSD group had the lowest (P < 0.05) feed intake. The NSD groups showed the highest (P < 0.05) body weight gain compared to HSD groups. The HSD + EO had lower adjusted FCR (P < 0.05) compared to HSD. The legs % was the highest (P < 0.05) for NSD group, while HSD + EO had the highest (P < 0.05) Fat Pad percentage. Moreover, HSD had the highest CL%, and the lowest WHC and Warner–Bratzler shear force. For biochemical indicators, (IGF-1) was the lowest (P < 0.05) HSD group. Also, Mammalian Target of Rapamycin (mTOR) and Aspartate Aminotransferase (AST) were higher (P < 0.05) in the EO supplemented groups. Regarding gene expression, the results showed that Myogenin (MyoG) and IGF-1 were lower in HSD while MSTN was higher in the same group, (P < 0.05). In brief, essential oil supplement has improved the performance of broilers under high stocking density situation.

  PublisherOA PDFDOI

• Genetic evaluation of crossbred <i>Bos indicus</i> cow temperament at parturition

  Journal of Animal Science · 2024-01-01

  articleOpen accessSenior author

  Cow temperament at parturition may be mostly a measure of aggressiveness. The heritability of cow temperament at parturition in Bos taurus cows has been reported to be low. The objectives of this study were to estimate the heritability of cow temperament at parturition, conduct a genome-wide association analysis of cow temperament at the time of parturition, and estimate the correspondence of cow temperament at the time of parturition with cow productive performance and early-life temperament traits in Bos indicus crossbreds. Cow temperament was assessed from 1 to 5 indicating increasing levels of aggressiveness of cows (937 cows and 4,337 parturitions) from 2005 to 2022. Estimates of heritability and repeatability were 0.12 ± 0.024 and 0.24 ± 0.018. The estimates of proportion of phenotypic variance were 0.13 ± 0.019 and 0.02 ± 0.011 for permanent and maternal permanent environmental components, respectively. Estimates of heritability for maximum lifetime temperament score and proportions of temperament scores >1 were 0.18 ± 0.07 and 0.13 ± 0.072. Within cycles (generations), 2-yr-old cows had lower temperament score means than cows in most other age categories. There were low to moderate positive estimates of unadjusted correlation coefficients (r = 0.22 to 0.29; P < 0.05) of unadjusted temperament score with temperament measured on the same females when they were 8 mo old. There were low to moderate positive estimates of correlation coefficients (r = 0.09 to 0.37; P < 0.05) of unadjusted temperament score with calving rate, weaning rate, weaning weight per cow exposed, and weaning weight per 454 kg cow weight at weaning. Cows with the lowest temperament score had lower (P < 0.05) calving and weaning rate than cows in other temperament categories. Within 3 of 5 cycles, cows with the lowest temperament score (totally docile) had lower (P < 0.05) weaning weight per cow exposed than cows in other temperament categories. There were 2 SNP on BTA 4 associated with maximum lifetime temperament score (FDR < 0.05). The non-genetic influence of a cow's mother was documented in her own temperament measured at the time of calving; this may be a consequence of learned behavior. Less aggressiveness displayed by cows at the time of calving may be accompanied by lower reproductive and maternal performance.

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• Economic-impact variability among F1 Nellore–Angus herd sires reared together and used in multiple-sire mating groups

  Applied Animal Science · 2024-01-30

  articleOpen access

  This study investigated variation of calf number and resulting economic impacts of F1 crossbred sires that were reared together as calves and used in multi- sire, natural-service breeding groups. Birth (n = 540) and weaning (n = 533) calf records were evaluated retrospectively in a crossbred research herd. Sires per annual breeding group varied from 6 to 9; females exposed per bull ranged from 12.5 to 19.5 across years. Bulls born in the same year were reared together, and all bulls were pastured together when not in breeding groups. Calf performance and economic value were determined annually per sire. Mixed model analyses were conducted that included fixed categorical effects of calf birth year, F1 sire type (Angus-sired vs. Nellore-sired), sire nested within type, calf sex, and the interaction of F1 sire type with calf sex. Large differences were observed in calf numbers and performance. Weaned calves produced annually per sire ranged from 0 to 48, when average expectations were 10.5 to 15.2. Average annual calf performance per sire ranged from 29.7 to 49.4 kg for birth weight and 197.4 to 241.4 kg for weaning weight. Annual economic contribution per sire ranged from $0 to $29,582 when considering half of calf value as being attributed to the sire. Commercial cow- calf producers should consider potential sire variability for calf numbers and birth date in combination with traditional calf performance for improved economic assessments in their herds.

  PublisherDOI

• Assessment of Prenatal Transportation Stress and Sex on Gene Expression Within the Amygdala of Brahman Calves

  Biology · 2024-11-11

  articleOpen access

  As the amygdala is associated with fear and anxiety, it is important to determine the potential effects of gestational stressors on behavior and stress responses in offspring. The objective of this study was to investigate the effects of prenatal transportation stress on amygdala gene expression in 25-day-old Brahman calves, focusing on sex-specific differences. Amygdala tissue samples from prenatally stressed (PNS) and control bull and heifer calves were analyzed using RNA sequencing. A thorough outlier detection process, utilizing visual inspection of multidimensional scaling plots, robust principal component analysis, and PCAGrid methods, led to the exclusion of 5 of 32 samples from subsequent analyses. Differential expression analysis revealed no significant treatment differences between the control and PNS groups within either sex. However, sex-specific differences in gene expression were identified in both the control and PNS groups. The control group showed seven differentially expressed genes between sexes, while ten were identified between PNS males and females, with seven located on the X chromosome. Among these was the ubiquitin-specific peptidase 9 X-linked gene, which plays a role in neurodevelopmental pathways. When comparing males to females, regardless of treatment, a total of 58 genes were differentially expressed, with 45 showing increased expression in females. Gene enrichment analysis indicated that many differentially expressed genes are associated with infectious disease-related pathways. Future research should explore amygdala size and functional responses to various postnatal stimuli.

  PublisherDOI

• Prenatal transportation stress and sex influence the metabolomic profile of the liver of 28-day-old Brahman bulls and heifers

  Physiology · 2024-05-01

  article

  Prenatal transportation stress (PNS) reportedly induced differential DNA methylation of genes related to behavior, immune function, stress response, and metabolism in Brahman heifer and bull calves (doi:10.1093/jas/skz368). The objective of the present experiment was to conduct a metabolomics analysis of liver samples of 25-day-old beef calves to identify biochemicals and determine effects of PNS and sex classification. Mature Brahman cows artificially inseminated to the same Brahman sire were assigned to be either Control (n=35; not transported) or PNS (n=37; 2 h of transportation at 60, 80, 100, 120, and 140±5 d of gestation). Livers were obtained from 16 Control (8 bulls and 8 heifers) and 16 PNS (8 bulls and 8 heifers) calves that were humanely euthanized at 25±2 d of age. Liver samples (200 mg) were submitted to Metabolon, Inc. to identify metabolites by ultra-high-performance liquid chromatography/tandem high resolution/accurate mass spectrometry chromatography methods. An estimate of the false discovery rate was calculated and following log transformation, two-way ANOVA was used to identify significant interactions and biochemicals that differed significantly ( p ≤ 0.05). Principal component analysis (PCA) was also used to compare PNS and sex effects. A total of 851 biochemicals were identified and categorized; this report emphasizes energy pathways and lipid mediators of inflammation. PNS increased 45 metabolites and decreased 21 whereas 23 were increased and 30 decreased in bulls versus heifers. Significant interaction of PNS and sex was noted for 33 metabolites. Glucose did not differ due to PNS; however, it was increased in bulls versus heifers. Maltotriose and maltose were higher in PNS, and it was greater in heifers than bulls. Lactate was higher in bulls than heifers. Lipid mediators of inflammation were elevated in PNS calves. to our knowledge this is the first report on the liver metabolome of prenatally stressed calves. These observations suggest an influence of prenatal stress and sex on liver metabolomics within 1 month of age in cattle. USDA NIFA Award No. 2019-67015-29573. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

  PublisherDOI

Frequent coauthors

• John B. Heppner

  University of Florida

  3519 shared

• John L. Capinera

  3225 shared

• Cyrus Abivardi

  1920 shared

• Lawrence E. Hurd

  978 shared

• Menachem J. Berlinger

  978 shared

• Peter H. Adler

  966 shared

• Kenneth W. McCravy

  University of Georgia

  961 shared

• Erik Christiansen

  Mental Health Services

  684 shared

Labs

• Department of Animal SciencePI

Education

• B.S., Agricultural Economics

  Texas A&M University

• M.S., Animal Breeding

  Texas A&M University

• Ph.D., Genetics

  Texas A&M University