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Genetic differentiation of Mexican Holstein cattle and its relationship with Canadian and U.S. Holsteins.

García-Ruiz A, Ruiz-López Fde J, Van Tassell CP, Montaldo HH, Huson HJ - Front Genet (2015)

Bottom Line: Admixture analysis differentiated between the genetic composition of the Conv and Lowi systems, and five ancestry groups associated to sire's country of origin were identified.The minimum distance between markers to estimate a useful LD was found to be 54.5 kb for the Mexican HO populations.Mexican HO cattle in Conv and Lowi populations share common ancestry with CAN + USA but have different genetic signatures.

View Article: PubMed Central - PubMed

Affiliation: Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México Ajuchitlán, Mexico.

ABSTRACT
The Mexican Holstein (HO) industry has imported Canadian and US (CAN + USA) HO germplasm for use in two different production systems, the conventional (Conv) and the low income (Lowi) system. The objective of this work was to study the genetic composition and differentiation of the Mexican HO cattle, considering the production system in which they perform and their relationship with the Canadian and US HO populations. The analysis included information from 149, 303, and 173 unrelated or with unknown pedigree HO animals from the Conv, Lowi, and CAN + USA populations, respectively. Canadian and US Jersey (JE) and Brown Swiss (BS) genotypes (162 and 86, respectively) were used to determine if Mexican HOs were hybridized with either of these breeds. After quality control filtering, a total of 6,617 out of 6,836 single nucleotide polymorphism markers were used. To describe the genetic diversity across the populations, principal component (PC), admixture composition, and linkage disequilibrium (LD; r(2) ) analyses were performed. Through the PC analysis, HO × JE and HO × BS crossbreeding was detected in the Lowi system. The Conv system appeared to be in between Lowi and CAN + USA populations. Admixture analysis differentiated between the genetic composition of the Conv and Lowi systems, and five ancestry groups associated to sire's country of origin were identified. The minimum distance between markers to estimate a useful LD was found to be 54.5 kb for the Mexican HO populations. At this average distance, the persistence of phase across autosomes of Conv and Lowi systems was 0.94, for Conv and CAN + USA was 0.92 and for the Lowi and CAN + USA was 0.91. Results supported the flow of germplasm among populations being Conv a source for Lowi, and dependent on migration from CAN + USA. Mexican HO cattle in Conv and Lowi populations share common ancestry with CAN + USA but have different genetic signatures.

No MeSH data available.


Related in: MedlinePlus

Linkage Disequilibrium average for different genetic distances between SNP pairs in the Mexican Holstein systems [conventional (Conv) and low income (Lowi)] and the North American Holstein population (CAN + USA).
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Figure 5: Linkage Disequilibrium average for different genetic distances between SNP pairs in the Mexican Holstein systems [conventional (Conv) and low income (Lowi)] and the North American Holstein population (CAN + USA).

Mentions: Mean LD, calculated as r2 for different distances (at intervals of 100 Kbp) between SNP were calculated for the Conv, Lowi, and CAN + USA populations (Figure 5). At all distances, average r2 was highest for CAN + USA animals, intermediate for individuals from the Mexican Conv farms, and smallest for cattle representing the Lowi systems. The differences between the CAN + USA and Conv populations r2 were quite small (∼0.01) while differences between Conv and Lowi were larger and consistent, ranging from 0.03 to 0.04. The persistence of LD phase between Conv, Lowi, and CAN + USA populations was calculated at the same interval distances as was LD (Figure 6). As expected, the persistence of LD phase decreased when the distance between markers was increased. At all intervals, the highest correlations were between Conv and Lowi populations, with the lowest correlation being between Lowi and CAN + USA. At a distance of <100 Kb (with an average of 54.5 kb), the correlations ranged from 0.91 to 0.94 and for a distance >500 kb correlations varied from 0.75 to 0.81 between the Conv-Lowi and Lowi-CAN + USA, respectively.


Genetic differentiation of Mexican Holstein cattle and its relationship with Canadian and U.S. Holsteins.

García-Ruiz A, Ruiz-López Fde J, Van Tassell CP, Montaldo HH, Huson HJ - Front Genet (2015)

Linkage Disequilibrium average for different genetic distances between SNP pairs in the Mexican Holstein systems [conventional (Conv) and low income (Lowi)] and the North American Holstein population (CAN + USA).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321612&req=5

Figure 5: Linkage Disequilibrium average for different genetic distances between SNP pairs in the Mexican Holstein systems [conventional (Conv) and low income (Lowi)] and the North American Holstein population (CAN + USA).
Mentions: Mean LD, calculated as r2 for different distances (at intervals of 100 Kbp) between SNP were calculated for the Conv, Lowi, and CAN + USA populations (Figure 5). At all distances, average r2 was highest for CAN + USA animals, intermediate for individuals from the Mexican Conv farms, and smallest for cattle representing the Lowi systems. The differences between the CAN + USA and Conv populations r2 were quite small (∼0.01) while differences between Conv and Lowi were larger and consistent, ranging from 0.03 to 0.04. The persistence of LD phase between Conv, Lowi, and CAN + USA populations was calculated at the same interval distances as was LD (Figure 6). As expected, the persistence of LD phase decreased when the distance between markers was increased. At all intervals, the highest correlations were between Conv and Lowi populations, with the lowest correlation being between Lowi and CAN + USA. At a distance of <100 Kb (with an average of 54.5 kb), the correlations ranged from 0.91 to 0.94 and for a distance >500 kb correlations varied from 0.75 to 0.81 between the Conv-Lowi and Lowi-CAN + USA, respectively.

Bottom Line: Admixture analysis differentiated between the genetic composition of the Conv and Lowi systems, and five ancestry groups associated to sire's country of origin were identified.The minimum distance between markers to estimate a useful LD was found to be 54.5 kb for the Mexican HO populations.Mexican HO cattle in Conv and Lowi populations share common ancestry with CAN + USA but have different genetic signatures.

View Article: PubMed Central - PubMed

Affiliation: Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México Ajuchitlán, Mexico.

ABSTRACT
The Mexican Holstein (HO) industry has imported Canadian and US (CAN + USA) HO germplasm for use in two different production systems, the conventional (Conv) and the low income (Lowi) system. The objective of this work was to study the genetic composition and differentiation of the Mexican HO cattle, considering the production system in which they perform and their relationship with the Canadian and US HO populations. The analysis included information from 149, 303, and 173 unrelated or with unknown pedigree HO animals from the Conv, Lowi, and CAN + USA populations, respectively. Canadian and US Jersey (JE) and Brown Swiss (BS) genotypes (162 and 86, respectively) were used to determine if Mexican HOs were hybridized with either of these breeds. After quality control filtering, a total of 6,617 out of 6,836 single nucleotide polymorphism markers were used. To describe the genetic diversity across the populations, principal component (PC), admixture composition, and linkage disequilibrium (LD; r(2) ) analyses were performed. Through the PC analysis, HO × JE and HO × BS crossbreeding was detected in the Lowi system. The Conv system appeared to be in between Lowi and CAN + USA populations. Admixture analysis differentiated between the genetic composition of the Conv and Lowi systems, and five ancestry groups associated to sire's country of origin were identified. The minimum distance between markers to estimate a useful LD was found to be 54.5 kb for the Mexican HO populations. At this average distance, the persistence of phase across autosomes of Conv and Lowi systems was 0.94, for Conv and CAN + USA was 0.92 and for the Lowi and CAN + USA was 0.91. Results supported the flow of germplasm among populations being Conv a source for Lowi, and dependent on migration from CAN + USA. Mexican HO cattle in Conv and Lowi populations share common ancestry with CAN + USA but have different genetic signatures.

No MeSH data available.


Related in: MedlinePlus