Evaluation of genetic differences between two autochthonous Spanish cattle breeds
Genetic diversity was assessed in five subpopulations (Negra-MORB and Cárdena-MORC for Morucha breed; Jarda-JAR, Bociblanca-BOC, and Avileña-Negra Ibérica breed-ANI for Avileña Negra Ibérica main breed) belonging to two local Spanish cattle breeds (Avileña Negra Ibérica-AVI and Morucha-MOR) by using...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2025-12-01
|
| Series: | Italian Journal of Animal Science |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/1828051X.2024.2449454 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832584710052642816 |
|---|---|
| author | Paola E. Milia Alberto Cesarani Clara Diaz Cristina Meneses Juan Carlos Parejo Laura Falchi Nicolò P. P. Macciotta Corrado Dimauro |
| author_facet | Paola E. Milia Alberto Cesarani Clara Diaz Cristina Meneses Juan Carlos Parejo Laura Falchi Nicolò P. P. Macciotta Corrado Dimauro |
| author_sort | Paola E. Milia |
| collection | DOAJ |
| description | Genetic diversity was assessed in five subpopulations (Negra-MORB and Cárdena-MORC for Morucha breed; Jarda-JAR, Bociblanca-BOC, and Avileña-Negra Ibérica breed-ANI for Avileña Negra Ibérica main breed) belonging to two local Spanish cattle breeds (Avileña Negra Ibérica-AVI and Morucha-MOR) by using univariate and multivariate statistical approaches. A total of 4,137 animals (2,785 ANI, 333 BOC, 127 JAR, 263 MORB and 629 MORC) were genotyped with the Affymetrix Beadchip Microarray HD. After quality control, 30,391 common SNPs were retained. In the univariate approach, the Wright fixation index (FST) was computed between and within breeds. In the multivariate approach, the stepwise discriminant analysis and the canonical discriminant analysis (CDA) were applied. The highest weighted FST value (0.05) was computed between BOC and MORB. Instead, the lowest values were found between ANI and JAR and between ANI and BOC. In the multivariate approach, CDA significantly discriminated the five breeds by using 1,144 markers. Of the four Canonical functions (CAN1, CAN2, CAN3 and CAN4) extracted by CDA, CAN1 fully separated AVI and MOR whereas CAN2 disentangled the two subpopulations of MOR. Considering CAN3 and CAN4, the CDA separated AVI subpopulations. Among markers selected by both FST and CDA, the top 10 discriminant SNPs were mapped to genomic regions harbouring genes involved in coat colour, behaviour, and morphological traits. This study confirmed that the two breeds, different at phenotypic level, are different also at genetic level. Moreover, the results showed that MOR subpopulations are more different from each other than the AVI ones. |
| format | Article |
| id | doaj-art-2627f3f23a824fcab7cdfe5642b3cff3 |
| institution | Kabale University |
| issn | 1594-4077 1828-051X |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Italian Journal of Animal Science |
| spelling | doaj-art-2627f3f23a824fcab7cdfe5642b3cff32025-01-27T11:59:10ZengTaylor & Francis GroupItalian Journal of Animal Science1594-40771828-051X2025-12-0124136137510.1080/1828051X.2024.24494542449454Evaluation of genetic differences between two autochthonous Spanish cattle breedsPaola E. Milia0Alberto Cesarani1Clara Diaz2Cristina Meneses3Juan Carlos Parejo4Laura Falchi5Nicolò P. P. Macciotta6Corrado Dimauro7Dipartimento di Agraria, University of SassariDipartimento di Agraria, University of SassariDepartamento de Mejora Genética Animal, INIA-CSICDepartamento de Mejora Genética Animal, INIA-CSICDepartamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de ExtremaduraDipartimento di Agraria, University of SassariDipartimento di Agraria, University of SassariDipartimento di Agraria, University of SassariGenetic diversity was assessed in five subpopulations (Negra-MORB and Cárdena-MORC for Morucha breed; Jarda-JAR, Bociblanca-BOC, and Avileña-Negra Ibérica breed-ANI for Avileña Negra Ibérica main breed) belonging to two local Spanish cattle breeds (Avileña Negra Ibérica-AVI and Morucha-MOR) by using univariate and multivariate statistical approaches. A total of 4,137 animals (2,785 ANI, 333 BOC, 127 JAR, 263 MORB and 629 MORC) were genotyped with the Affymetrix Beadchip Microarray HD. After quality control, 30,391 common SNPs were retained. In the univariate approach, the Wright fixation index (FST) was computed between and within breeds. In the multivariate approach, the stepwise discriminant analysis and the canonical discriminant analysis (CDA) were applied. The highest weighted FST value (0.05) was computed between BOC and MORB. Instead, the lowest values were found between ANI and JAR and between ANI and BOC. In the multivariate approach, CDA significantly discriminated the five breeds by using 1,144 markers. Of the four Canonical functions (CAN1, CAN2, CAN3 and CAN4) extracted by CDA, CAN1 fully separated AVI and MOR whereas CAN2 disentangled the two subpopulations of MOR. Considering CAN3 and CAN4, the CDA separated AVI subpopulations. Among markers selected by both FST and CDA, the top 10 discriminant SNPs were mapped to genomic regions harbouring genes involved in coat colour, behaviour, and morphological traits. This study confirmed that the two breeds, different at phenotypic level, are different also at genetic level. Moreover, the results showed that MOR subpopulations are more different from each other than the AVI ones.http://dx.doi.org/10.1080/1828051X.2024.2449454genetic diversitymultivariate analysisautochthonous cattlepopulation genetics |
| spellingShingle | Paola E. Milia Alberto Cesarani Clara Diaz Cristina Meneses Juan Carlos Parejo Laura Falchi Nicolò P. P. Macciotta Corrado Dimauro Evaluation of genetic differences between two autochthonous Spanish cattle breeds Italian Journal of Animal Science genetic diversity multivariate analysis autochthonous cattle population genetics |
| title | Evaluation of genetic differences between two autochthonous Spanish cattle breeds |
| title_full | Evaluation of genetic differences between two autochthonous Spanish cattle breeds |
| title_fullStr | Evaluation of genetic differences between two autochthonous Spanish cattle breeds |
| title_full_unstemmed | Evaluation of genetic differences between two autochthonous Spanish cattle breeds |
| title_short | Evaluation of genetic differences between two autochthonous Spanish cattle breeds |
| title_sort | evaluation of genetic differences between two autochthonous spanish cattle breeds |
| topic | genetic diversity multivariate analysis autochthonous cattle population genetics |
| url | http://dx.doi.org/10.1080/1828051X.2024.2449454 |
| work_keys_str_mv | AT paolaemilia evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT albertocesarani evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT claradiaz evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT cristinameneses evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT juancarlosparejo evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT laurafalchi evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT nicoloppmacciotta evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds AT corradodimauro evaluationofgeneticdifferencesbetweentwoautochthonousspanishcattlebreeds |