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Genetic characterization of 24 Angus × Hereford cows from the Jornada Experimental Range, Las Cruces, NM, USA

General Information
Data Package:
Local Identifier:knb-lter-jrn.200036001.1
Title:Genetic characterization of 24 Angus × Hereford cows from the Jornada Experimental Range, Las Cruces, NM, USA
Alternate Identifier:DOI PLACE HOLDER
Abstract:

The southwestern US is increasingly facing dry and variable climate conditions, requiring beef operations to adopt novel strategies to meet these emerging challenges. One potential approach is the use of locally adapted cattle breeds or biotypes. A distinctive Angus x Hereford (AH) research herd at the USDA Agricultural Research Service Jornada Experimental Range provides an opportunity to explore the genetic makeup of a desert-adapted cattle herd bred for over four decades under the extreme and harsh conditions of New Mexico’s Chihuahuan Desert. The objective of this study was to analyze the population structure, genetic diversity and signatures of selection of the AH research herd (n = 24). All cows were genotyped using a 64K SNP chip. Principal component and admixture analyses confirmed the mixed genetic background of the AH cows, predominantly of Angus ancestry. The heterozygosity level, effective population size, and inbreeding coefficient indicated that the AH cows maintain moderate genetic diversity and inbreeding levels. Genomic regions under positive selection revealed genes and Quantitative Trait Loci associated with beneficial carcass traits, milk composition, fertility, body homeostasis, antioxidant activity, immune response, and terrain utilization. This research herd could potentially serve as a valuable genetic resource for improving the adaptability and productivity of commercial beef cattle in harsh semi-arid and arid environments, balancing hardiness and performance.

Short Name:Jornada Experimental Range – Angus x Hereford Herd Genetics
Publication Date:2024-12-17
Language:English
For more information:
Visit: https://southwestbeef.org
Visit: DOI PLACE HOLDER

Time Period
Begin:
2023-03-22
End:
2023-03-22

People and Organizations
Contact:Jornada Information Manager (USDA-ARS Jornada Experimental Range) [  email ]
Creator:Spetter, Maximiliano J (New Mexico State University)
Creator:Utsumi, Santiago A (New Mexico State University)
Creator:Armstrong, Eileen M (Universidad de la República, Uruguay)
Creator:Jara, Eugenio (Universidad de la República, Uruguay)
Creator:Ross, Pablo J (Inguran LLC dba STgenetics, USA)
Creator:Macon, Lara (USDA-ARS Jornada Experimental Range)
Creator:Perea, Andrés R (New Mexico State University)
Creator:Funk, Micah P (New Mexico State University)
Creator:Cibils, Andrés F (New Mexico State University)
Creator:Spiegal, Sheri (USDA-ARS Jornada Experimental Range, Research Rangeland Management Specialist)
Creator:Duff, Glenn (New Mexico State University)
Creator:Estell, Rick E (USDA-ARS Jornada Experimental Range)
Associate:Dunlap, Rob (USDA-ARS Jornada Experimental Range, field crew)

Data Entities
Other Name:
JER AH Genetics Data Files
Description:
Zipped file containing a .ped file and a .map file
Detailed Metadata

Data Entities

Non-Categorized Data Resource

Name:JER AH Genetics Data Files
Entity Type:otherEntity
Description:Zipped file containing a .ped file and a .map file
Physical Structure Description:
Object Name:JER_AH_Genetics_Data_Files.zip
Size:1335944 byte
Authentication:db75840f24fe55db0b08b20c6e36bafe Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-jrn/200036001/1/5e71813a8cc0228db3c5b139022cd932

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
nonepositive selection
USDA National Ag Library's Agricultural Thesaurusarid lands, beef cattle, cross breeding, genetic diversity, population structure, single nucleotide polymorphism

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Methods

Animal handling and sampling protocols were approved by the New Mexico State University Institutional Animal Care and Use Committee (protocol #2210000082). Ear tissue punches (Tissue Sampling Unit, Allflex, NJ, USA) were collected from the 24 cows and sent to Genetic Visions-STTM laboratory (Middleton, WI, USA). Genotyping was conducted using the VM2 SNP array (Genetic Visions-STTM), which features 63,683 SNPs. Quality control was performed using PLINK v1.9 software (Purcell et al., 2007) with the following parameters: (i) call rate <0.9; (ii) Minor Allele Frequency <0.05; and (iii) deviation from Hardy-Weinberg equilibrium (HWE) at p-value <10-6. SNPs located on sex chromosomes and those with unknown genomic positions were excluded.

Data Files

This data package includes .zip file, which contains a .map file and a .ped file. JERAH.map contains genotypes information of 24 Angus x Hereford cows in PLINK ped format. Allele strand is in forward format. JERAH.map contains SNP information in PLINK map format. Chromosomes coordinates are according to UMD3.1.1 Bos taurus assembly.

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007 Sep;81(3):559-75. doi: 10.1086/519795. Epub 2007 Jul 25. PMID: 17701901; PMCID: PMC1950838.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Maximiliano J Spetter
Organization:New Mexico State University
Address:
Las Cruces, NMN 88003-8003 U.S.A.
Email Address:
mspetter@nmsu.edu
Id:https://orcid.org/0000-0002-5298-8167
Individual: Santiago A Utsumi
Organization:New Mexico State University
Address:
Las Cruces, NM 88003-8003 U.S.A.
Email Address:
sutsumi@nmsu.edu
Id:https://orcid.org/0000-0001-6553-9902
Individual: Eileen M Armstrong
Organization:Universidad de la República, Uruguay
Address:
Uruguay
Email Address:
eileen.armstrong@gmail.com
Id:https://orcid.org/0000-0002-1769-1368
Individual: Eugenio Jara
Organization:Universidad de la República, Uruguay
Address:
Uruguay
Email Address:
eugeniojara19@gmail.com
Id:https://orcid.org/0000-0002-9750-2642
Individual: Pablo J Ross
Organization:Inguran LLC dba STgenetics, USA
Email Address:
pablo.ross@stgen.com
Id:https://orcid.org/0000-0002-3972-3754
Individual: Lara Macon
Organization:USDA-ARS Jornada Experimental Range
Address:
Las Cruces, NM 88003-8003 U.S.A.
Id:https://orcid.org/0009-0006-3521-4326
Individual: Andrés R Perea
Organization:New Mexico State University
Address:
Las Cruces, NM U.S.A.
Email Address:
arperea@nmsu.edu
Id:https://orcid.org/0000-0003-3603-1960
Individual: Micah P Funk
Organization:New Mexico State University
Email Address:
funkm@nmsu.edu
Id:https://orcid.org/0000-0002-2682-5364
Individual: Andrés F Cibils
Organization:New Mexico State University
Email Address:
acibils@nmsu.edu
Id:https://orcid.org/0000-0002-4733-6463
Individual: Sheri Spiegal
Organization:USDA-ARS Jornada Experimental Range
Position:Research Rangeland Management Specialist
Email Address:
sheri.spiegal@usda.gov
Id:https://orcid.org/0000-0002-5489-9512
Individual: Glenn Duff
Organization:New Mexico State University
Address:
Las Cruces, NM 88003-8003 U.S.A.
Email Address:
glennd@nmsu.edu
Id:https://orcid.org/0000-0002-7494-3920
Individual: Rick E Estell
Organization:USDA-ARS Jornada Experimental Range
Email Address:
rick.estell@usda.gov
Id:https://orcid.org/0000-0002-3469-4712
Contacts:
Organization:USDA-ARS Jornada Experimental Range
Position:Jornada Information Manager
Address:
P.O. Box 30003, MSC 3JER New Mexico State University,
Las Cruces, NM 88003-8003 USA
Phone:
575-646-1739
Email Address:
jornada.data@nmsu.edu
Web Address:
https://jornada.nmsu.edu/ltar/data/documentation
Associated Parties:
Individual: Rob Dunlap
Organization:USDA-ARS Jornada Experimental Range
Address:
Las Cruces, NM 88003-8003 U.S.A.
Email Address:
robby.dunlap@usda.gov
Role:field crew
Metadata Providers:
Organization:Jornada Experimental Range LTAR (USDA-ARS)
Address:
P.O. Box 30003, MSC 3JER New Mexico State University,
Las Cruces, NM 88003-8003 USA
Web Address:
https://jornada.nmsu.edu

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2023-03-22
End:
2023-03-22
Geographic Region:
Description:Jornada Experimental Range: USDA Jornada Experimental Range
Bounding Coordinates:
Northern:  32.778734Southern:  32.473162
Western:  -106.868125Eastern:  -106.592781

Project

Parent Project Information:

Title:Sustainable Southwest Beef Coordinated Agriculture Project (CAP)
Personnel:
Individual:Dr. Sheri Spiegal
Address:
P.O. Box 30003, MSC 3JER,
New Mexico State University,
Las Cruces, NM 88003-8003 United States
Phone:
575-646-7018 (voice)
Email Address:
sheri.spiegal@usda.gov
Role:SW Beef Project Director
Individual:Dr. Glen Duff
Address:
Clayton Livestock Research Center,
15 NMSU Ln,
Clayton, NM 84115 United States
Phone:
575-644-0366 (cell)
Email Address:
glennd@nmsu.edu
Role:SW Beef Project Director
Individual:Dr. Brandon Bestelmeyer
Address:
P.O. Box 30003, MSC 3JER,
New Mexico State University,
Las Cruces, NM 88003-8003 United States
Phone:
575-646-4842 (voice)
Email Address:
brandon.bestelmeyer@usda.gov
Role:Research Leader (USDA LTAR)
Abstract:

The Sustainable Southwest Beef Coordinated Agriculture Project (CAP) is a five year (2019-2024) project that evaluates and promotes ranch and rangeland resilience in the Southwestern US. The project is funded by the USDA’s National Institute of Food and Agriculture (NIFA) and coordinated through New Mexico State University and the Jornada Long-Term Agroecosystems Research program (JER-LTAR). JER-LTAR is part of a national network of long-term agricultural and rangeland ecology research sites funded by the US Department of Agriculture (USDA). The Jornada Experimental Range is administered by the USDA-ARS (USDA Agricultural Research Service).

Funding:

The Sustainable Southwest Beef CAP is supported by the USDA-NIFA (USDA-NIFA-AFRI-Sustainable Agricultural Systems, Grant Number: 2019-69012-29853).

The JER-LTAR program is supported by the USDA Long-Term Agroecosystem Research Network (CRIS# 3050-11210-009-00D).

Maintenance

Maintenance:
Description:complete
Frequency:notPlanned
Other Metadata

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

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