Index-in-retrospect and breeding objectives characterizing genetic improvement programmes for South African Nguni cattle

Matjuda, L. E.; MacNeil, M. D.; Maiwashe, A.; Leesburg, V R; Malatje, M. M.

doi:10.4314/sajas.v44i2.9

Cited by 11 publications

(6 citation statements)

References 14 publications

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“…In addition, Decker et al ( 2012 ) estimated Ne in North American Angus using molecular inbreeding coefficients and found current Ne to be 94. On the other hand, effective population sizes obtained for Afrikaner, Nguni, and Bonsmara cattle in this study were in agreement with those reported based on pedigree data for the Afrikaner (Pienaar et al, 2014 ), Nguni (Matjuda, 2012 ), and Bonsmara (Santana et al, 2015 ). The low effective population sizes for the Angus and Holstein breeds compared to those for the Nguni, Bonsmara, and Drakensberger at more recent generations, could be due to intense selection and probably widespread use of artificial insemination and the use of relatively few elite sires after 1970 (Hayes et al, 2009 ).…”

Section: Discussionsupporting

confidence: 92%

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

et al. 2015

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Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

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Section: Discussionsupporting

confidence: 92%

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

et al. 2015

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“…It is recognised as an important animal genetic resource possessing valuable adaptive traits resulting in a breed that can survive and reproduce efficiently in marginal production areas (Mapiye et al 2007;Matjuda et al 2014). Nguni cattle are not only able to tolerate harsh environmental conditions but also have natural immunity to tick-borne diseases and parasites that could limit livestock production (Marufu et al 2011;.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Sanarana

Visser

Bosman

et al. 2015

Trop Anim Health Prod

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The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study molecular characterization was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69% (UFH) to 72% PED with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8% of the total genetic variation was due to the genetic differentiation between the populations and 92.2% accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on 2 limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.

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“…Several studies include WW as a selection objective (MacNeil et al, 1994;Wolfová et al, 2005;Bittencourt et al, 2006;Matjuda et al, 2014;Ochsner et al, 2017). The RE weighting is variable, according to the systems adopted and the final product.…”

Section: Discussionmentioning

confidence: 99%

Selection indexes for Nellore production system in the Brazilian Pantanal

Portes¹,

Menezes²,

Silva³

et al. 2021

Revista Brasileira De Zootecnia

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The objective was to develop selection indexes for Nellore cattle raised in full-cycle production system in the Brazilian Pantanal. The resulting offspring are retained as replacements or sold at two years of age. Preliminary analyses explored effects of scale on economic values (EV). However, given the available data, these effects were very small. Presented herein are results from a simulated system consisting of 5,000 cows with all animals maintained on pasture as is typical in Pantanal. The EV were determined by approximating the partial derivatives of the profit function, changing one trait at a time, by one unit, while keeping the other traits constant. Traits in the breeding objective were mature cow weight, direct and maternal weaning weight, postweaning average daily gain, subcutaneous fat depth, longissimus muscle area, and stayability. Economic values were calculated on the basis of number of animals (per head), number of animal units, and arroba of carcasss weight. Regardless of the basis, maternal weaning weight and subcutaneous fat depth made negligible contributions to the breeding objective. Proportions of variation in the breeding objectives (per head, per animal unit, per arroba) explained by cow weight, direct weaning weight, postweaning average daily gain, stayability, and longissimus muscle area were:

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Index-in-retrospect and breeding objectives characterizing genetic improvement programmes for South African Nguni cattle

Cited by 11 publications

References 14 publications

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

Selection indexes for Nellore production system in the Brazilian Pantanal

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