Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle
Abstract Background Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluat...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | deu |
| Published: |
BMC
2023-11-01
|
| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-023-00850-x |
| _version_ | 1827770813881778176 |
|---|---|
| author | Amanda B. Alvarenga Kelli J. Retallick Andre Garcia Stephen P. Miller Andrew Byrne Hinayah R. Oliveira Luiz F. Brito |
| author_facet | Amanda B. Alvarenga Kelli J. Retallick Andre Garcia Stephen P. Miller Andrew Byrne Hinayah R. Oliveira Luiz F. Brito |
| author_sort | Amanda B. Alvarenga |
| collection | DOAJ |
| description | Abstract Background Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~ 1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS. Results There was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22–0.24 and CS: 0.22–0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common significant genomic regions were observed between US and AU for FA and CS. Significant single nucleotide polymorphisms were identified on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair. Conclusions This study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU. |
| first_indexed | 2024-03-11T12:44:50Z |
| format | Article |
| id | doaj.art-8b85cfcf66a9448a95e25959f09221f7 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-03-11T12:44:50Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-8b85cfcf66a9448a95e25959f09221f72023-11-05T12:05:15ZdeuBMCGenetics Selection Evolution1297-96862023-11-0155111910.1186/s12711-023-00850-xAcross-country genetic and genomic analyses of foot score traits in American and Australian Angus cattleAmanda B. Alvarenga0Kelli J. Retallick1Andre Garcia2Stephen P. Miller3Andrew Byrne4Hinayah R. Oliveira5Luiz F. Brito6Department of Animal Sciences, Purdue UniversityAmerican Angus Association, Angus Genetics Inc.American Angus Association, Angus Genetics Inc.American Angus Association, Angus Genetics Inc.Angus AustraliaDepartment of Animal Sciences, Purdue UniversityDepartment of Animal Sciences, Purdue UniversityAbstract Background Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~ 1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS. Results There was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22–0.24 and CS: 0.22–0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common significant genomic regions were observed between US and AU for FA and CS. Significant single nucleotide polymorphisms were identified on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair. Conclusions This study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU.https://doi.org/10.1186/s12711-023-00850-x |
| spellingShingle | Amanda B. Alvarenga Kelli J. Retallick Andre Garcia Stephen P. Miller Andrew Byrne Hinayah R. Oliveira Luiz F. Brito Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle Genetics Selection Evolution |
| title | Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle |
| title_full | Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle |
| title_fullStr | Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle |
| title_full_unstemmed | Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle |
| title_short | Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle |
| title_sort | across country genetic and genomic analyses of foot score traits in american and australian angus cattle |
| url | https://doi.org/10.1186/s12711-023-00850-x |
| work_keys_str_mv | AT amandabalvarenga acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle AT kellijretallick acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle AT andregarcia acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle AT stephenpmiller acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle AT andrewbyrne acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle AT hinayahroliveira acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle AT luizfbrito acrosscountrygeneticandgenomicanalysesoffootscoretraitsinamericanandaustraliananguscattle |