SAES-422 Multistate Research Activity Accomplishments Report

Sections

Status: Approved

Basic Information

Participants

Name Institution Email David Riley TAMU david-riley@tamu.edu Rhonda Vann Mississippi State rcv2@msstate.edu Bob Godfrey Univ Virgin Islands rgodfre@uvi.edu Jeremy Powell Univ of Arkansas jerpow@uark.edu Bryan Kutz Univ of Arkansas bkutz@uark.edu Megan Rolf Kansas State megrolf@k-state.edu Brittni Littlejohn Univ of Arkansas bplitt@uark.edu Ann Straiger Auburn University Eas0115@auburn.edu Brian Rude Mississippi State Bjr13@ads.msstate.edu Raluca Mateescu University of Florida raluca@ufl.edu Andy Herring TAMU Andy.herring@tamu.edu Mike Looper University of Arkansas looper@uark.edu Romdhane Rekaya University of Georgia rrekaya@uga.edu

Brief Summary of minutes of annual meeting: Due to the pandemic situation, the meeting was help digitally via zoom. Individual station progress reports were presented and achievements in the different objectives of the project were discussed. Collaboration opportunities including the potential for joint grant applications were explored.

Accomplishments

Objective 1: Estimate genetic variation associated with animal health and structural soundness using classical animal breeding and genomic techniques to facilitate sustainable beef cattle production systems

  • Eye pigmentation

 

  • Digital photographs to determine the proportion of the eyelid pigmentation were collected at multiple locations. Images were collected on Hereford cows (n=435; Texas), Angus-based cows (n=135, Arkansas), purebred Hereford calves (n=??; Mississippi) and Hereford crossbreds (n=??; Mississippi)

 

  • Whole blood samples were collected from the photographed animals and were frozen.

 

  • Additional phenotypes (cow traits related to weaning and calf traits) were collected for potential assessment of their association with eye pigmentation

 

  • Images and whole blood samples collected at Arkansas herd will be transferred to Dr. Riley at TAMU to be added to the eye pigmentation database.

 

  • Around 5,000 animals are already photographed and genotyped

 

  • Images will be used to derive eye pigmentation phenotypes and blood samples will be used for SNP marker genotyping. The resulting data will be used in GWAS analyses

 

  • A grant proposal let by Dr. Hanna (North Dakota University) and the collaboration of the Texas, Mississippi, and Arkansas teams was submitted to USDA-AFRI

 

  • Udder conformation

 

  • Additional udder conformation data was collected at three Texas locations (McGregor, College Station, Menard). More than 800 cows have been scored

 

  • Udder and teat scores were recorded on around 2xx cows (we need # of cows from Trent) and 9 heifers at Arkansas, Mississippi and Virgin Island stations

 

  • Data is being consolidating for preliminary analyses

 

  • Foot structure

 

  • An Angus-based fall calving cowherd (n ≈ 135) was observed and hoof scores were recorded at weaning. Cows were evaluated on a scale from 1 to 9 for foot angle and claw set according to the American Angus Association

 

  • Hoof scores and (hoof angle and claw set) were collect on 24 yearling Senepol bulls (n=13) and heifers (n=11)

 

  • Skull conformation

 

  • Skull conformation images were collected in Bos taurus, Bos indicus, and Bos taurus-Bos indicus crossbred cattle.

 

  • A USDA-AFRI proposal was developed through the collaboration with Dr. Bryan Davis of TAMU College of Veterinary Medicine

 

  • The long-term goal is to identify genomic regions that statistically associate with skull variation.

 

Objective 2: Systems approach to analyzing novel ERTs associated with female production including longevity, fertility and meat quality database creation

  • Fertility data (traits) were collected from fall and spring calving herds (n=??) at the Mississippi station

 

  • A new approach was developed to determine the minimum length of an autozygous track to be declared as a run of homozygosity segment (ROH). The implications of ROH classification on measuring inbreeding depression on growth and fertility traits were assessed using a purebred Hereford cattle population

 

  • The effects on inbreeding on size and reproductive traits across four generations of Nellore-Angus crossbred cattle were assessed using genomic and pedigree information

 

  • A grid search method to classify inbreeding into recent and ancient classes was developed and applied to growth and fertility traits in Herford cattle.

Objective 3: Documentation of genetic components and development of thermotolerance measurements pertaining to heat tolerance adaptive traits in sustainable beef cattle production systems

 

  • Genetic parameters for hair characteristics and core body temperature in a multibreed Brahman-Angus herd were assessed

 

  • Collection of phenotypic data describing thermal tolerance in Bos Indicus influenced populations and characterization of the genetic component underlying these traits.

 

  • Mature cows and replacement heifers (n=135) were evaluated for shedding on a scale from 1 to 5 at the Mississippi station

 

Collection of coat scores on all herds at Texas station (2 to 4 times per year)

Impacts

  1. • Confirmation of differential additive genetic variance for % intramuscular fat corresponding to geographical coordinates offer an alternative for parameterization of regional effects in genetic prediction
  2. • Confirmation that female fertility is reduced with increases in inbreeding as indicated by runs of SNP homozygosity could support alternative genomic strategies for trait management or improvement
  3. • Unsound udders and teats are associated with reduced productive life and inferior calf performance, and poor udder and teat conformation is a major reason why cows are culled from the breeding herd
  4. • Sound feet are important components in cattle production systems and can influence nutritional aspects of cattle. Implementing these scores can aid in selecting for more sound cows
  5. • Hair shedding scores, although subjective, are well within the reach of both commercial and seedstock breeders. By using these scores and understanding their implications in cattle production, producers can utilize them in the match of genetic resource and production resources. This could easily increase current overall production
  6. • The genetic parameters estimated indicate that hair characteristics are highly heritable and core body temperature under various THI conditions is moderately heritable. These values of heritability indicate a large, exploitable genetic variance in body hair length and core body temperature which can be selected upon to improve heat tolerance in cattle. As Brahman breed influence increased both hair length and body temperature decreased, indicating that cattle producers can improve thermotolerance by incorporating Brahman germplasm into their herds
  7. • The beneficial effect of Brahman genetics is dependent on the magnitude of environmental heat stress. When breed groups were exposed to moderate or high heat stress, the Brahman group had a significantly superior resilience to heat stress, but when exposed to severe heat stress even Brahman group could not adequately cope
  8. • Breed groups with 75% and 100% Brahman genes had superior resilience to heat stress, breed groups with 25%, 34.5% and 50% were intermediate between Brahman and Angus group and the purebred Angus group had the lowest heat stress resilience. While this supports the use of Brahman genetics to improve thermotolerance in typical crossbreeding systems, it is also evident that given the random nature of segregation, a high percentage of Brahman genetics is needed to benefit from the increased heat tolerance. This also has a less desirable impact on other production traits like reproduction and carcass quality
  9. • A search algorithm was developed to identify the minimum length of autozygous segments to be declared as ROH. The algorithm approximates the mutation load at the individual level using available phenotypic information. This is of valuable practical importance as direct assessment of mutation load using genetic/genomic information is seldom available for the majority of livestock populations and complex traits
  10. • Selection tends to reduce or even eliminate deleterious alleles. Therefore, more recent inbreeding is likely to have a greater contribution to inbreeding depression. Distinguishing between new and old inbreeding could provide a better assessment of genome-wide inbreeding and facilitate management of the harmful effects of inbreeding depression largely caused by accumulation of deleterious mutations. A new method to classify

Publications

  1. Referred articles

 

Delgadillo Liberona*, J.S., J.M. Langdon, A.D. Herring, H.D. Blackburn, S.E. Speidel, S. Sanders, and D.G. Riley.  2020.  Random regression of Hereford percentage intramuscular fat on geographical coordinates.  J. Anim. Sci.  98:1–10.   doi:10.1093/jas/skz359

Riley, D.G., C. Mantilla-Rojas, R.K. Miller, K.L. Nicholson, C.A. Gill, A.D. Herring, P.K. Riggs, J.E. Sawyer, J.W. Savell, and J.O. Sanders.  2020.  Genome association of carcass and palatability traits from Bos indicus-Bos taurus crossbred steers within electrical stimulation status and correspondence with steer temperament 3. Aroma and flavor attributes of cooked steaks.  Livest. Sci.  233:103943.  https://doi.org/10.1016/j.livsci.2019.103943

Cooke, R.F., R.C. Cardoso, R.L.A. Cerri, G.C. Lamb, K.G. Pohler, D.G. Riley, and J.L.M. Vasconcelos.  2020.  Cattle adapted to tropical and subtropical environments:  genetic and reproductive considerations.  J. Anim. Sci.  98:1–14.  https://doi.org/10.1093/jas/skaa015

Riley, D.G., J.E. Sawyer, and T.M. Craig.  2020.  Shedding and characterization of gastrointestinal nematodes of growing beef heifers in Central Texas.  Vet. Parasitol.: X 3:100024

Rouquette, M. Jr., K.D. Norman, D.G. Riley, and R.D. Randel.  2020.  Body condition of F1 (Hereford × or Angus × Brahman) cows at weaning and effects on cow-calf performance and subsequent postpartum performance.  Appl. Anim. Sci.  36:890–897

Simmons, M.A.*, P.K. Riggs, S. Sanders, A.D. Herring, J.O. Sanders, and D.G. Riley.  2021.  Distributional characterizations and testing for differences of relatedness and inbreeding of a subpopulation of American Hereford bulls.  Transl. Anim. Sci.  5:1–10.  doi: 10.1093/tas/txab008

Dikmen S., K.M. Sarlo Davila, E. Rodriguez, T.L. Scheffler, P.A. Oltenacu and R.G. Mateescu. 2020. Comparison of Tympanic and Tail Temperatures in Angus and Brahman Steers. J Anim Sci Res 4(4). dx.doi.org/10.16966/2576-6457.147

Leal-Gutiérrez J.D., M.A. Elzo, C. Carr, and R.G. Mateescu. 2020. RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef. PLOS One. 15(11): e0240895. doi:10.1371/journal.pone.0240895

Leal-Gutiérrez J.D., F.M.Rezende, J.M Reecy, L.M. Krammer, F. Peñagaricano and R.G. Mateescu. 2020. Whole genome sequence data provides novel insights into the genetic architecture of meat quality traits in beef. Frontiers in Genetics. doi: 10.3389/fgene.2020.538640

Sarlo Davila K.M., A. Howell, A. Nunez, A. Orelien, V. Roe, E. Rodriguez, S. Dikmen, and R.G. Mateescu. 2020. Genome-wide association study identifies variants associated with hair length in Brangus cattle. Animal Genetics. 51:811-814. doi: 10.1111/age.12970

Mateescu R.G., K.M. Sarlo Davila, S. Dikmen, E. Rodriguez, and P.A. Oltenacu. 2020. The effect of Brahman genes on body temperature plasticity of heifers on pasture under heat stress. J. Anim. Sci. 1:98(5):skaa126. DOI: 10.1093/jas/skaa126

Leal J.D., M.A. Elzo, and R.G. Mateescu. 2020. Identification of eQTLs and sQTLs associated with meat quality in beef. BMC Genomics. 21:104. doi.org/10.1186/s12864-020-6520-5

Sumreddee, P., S. Toghiani, E. H. Hay, A. Roberts, S. E. Aggrey, and R. Rekaya. (2020). Runs of homozygosity and analysis of inbreeding depression. J. Anim. Sci., 98(12), 1-11  https://doi.org/10.1093/jas/skaa361

Toghiani, S., Hay, E., Fragomeni, B., Rekaya, R., & Roberts, A. J. (2020). Genotype by environment interaction in response to cold stress in a composite beef cattle breed. Animal, 14(8), 1576-1587 doi:10.1017/S1751731120000531

Toghiani, S., Hay, E. H., Roberts, A., & Rekaya, R. (2020). Impact of cold stress on birth and weaning weight in a composite beef cattle breed. Livestock Science, 236, 6 pages. doi:10.1016/j.livsci.2020.104053

Sumreddee, P., S. Toghiani, E. H. Hay, A. Roberts, S. E. Aggrey, and R. Rekaya. (2021). Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information. BMC Genomics DOI: 10.1186/s12864-021-07872-z

 

  1. Abstracts/Presentations

 

Burnett, R. H., M. A. Duvic, J. G. Powell, D. Riley, and T. Smith. 2020. Evaluation of hair coat shedding ability as an adaptive trait in Angus cattle in the southern U.S. (Abstr) Southern Section Animal Science meeting, Chattanooga, TN

 

Duvic, M. A., R.H. Burnett, C. Glenn, and T. Smith. 2020. Relationship of winter hair growth and performance in Angus dams. (Abstr) Southern Section Animal Science meeting, Chattanooga, TN

 

deCarvalho Balieiro J. C, J. D. Leal Gutierrez, C. Paschoal V.R., Carr, M.A. Elzo, and R.G. Mateescu. Comparative transcriptomic profile for meat tenderness in a multibreed Brahman-Angus Population. 66th International Congress of Meat Science and Technology. (2020)

 

Sarlo Davila K., Howell A., Nunez A., Orelien A., Roe V. Rodriguez E., Dikmen S. and Mateescu R.G. PRLR and PCCA variants associated with hair length in Brangus heifers. American Association of Animal Science Annual Meeting. Virtual meeting (2020)

 

Mateescu R.G., Leal J.D., M.A. Elzo. Expression QTL mapping for meat quality in beef cattle. American Association of Animal Science Annual Meeting. Virtual meeting (2020)

 

Mateescu R.G., Sarlo Davila K., Dikmen S., Nunez A., Rodriguez E., and Oltenacu P.A. Phenotypic plasticity of heat tolerance in beef cattle. American Association of Animal Science Annual Meeting. Virtual meeting (2020)

 

Mateescu R.G., Leal J.D., M.A. Elzo. Integrated -omics approaches for meat quality improvement. Plant and Animal Genome Meeting, San Diego, CA. (2020)

 

Sarlo Davila K., Howell A., Nunez A., Orelien A., Roe V. Rezende F., Dikmen S. and Mateescu R.G. Genome-wide association study for hair length in Brangus heifers. Plant and Animal Genome Meeting, San Diego, CA. (2020)

 

Dodd, Logan T., David P. Anderson, David G. Riley, Barton Johnson, and Andy D. Herring. 2021. Assessing variability of herd sire economic value for commercial operations. J. Anim. Sci. Suppl. Abstract for ASAS meeting in Louisville.

 

Mickey, Dana M., James O. Sanders, David G. Riley, and Andy D. Herring. 2021. Calf performance and sex ratios in second generation reciprocal Nellore-Angus crosses. J. Anim. Sci. Suppl. Abstract for ASAS meeting in Louisville.

 

Noland, R., W. Shaffer, CM Ahlberg, K. Allwardt, A Broocks, K. Bruno, L. McPhillips, A Taylor, CR Krehbiel, CJ Richards, U DeSilva, DL CanOverbeke, RG Mateescu, LA Kuehn, RL Weaber, JM Bormann, and MM Rolf.  2020.  Genome-wide association analysis for respiration rate in beef cattle.  ASI Undergraduate Research Forum.  Manhattan, KS.  December 8.

 

Sumreddee P, S. Toghiani, E. Hay, S. E. Aggrey, and R. Rekaya. Partitioning of Inbreeding Depression using Pedigree and Genomic Approaches. Journal of Animal Science 98 (Supplement_4):247-248 30 Nov 2020 

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