Browsing by Author "Dzomba, Edgar Farai."

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Antimicrobial resistance, plasmid profiles and sequence typing of enterotoxigenic escherichia coli isolates causing colibacillosis in neonatal and weaning piglets of South Africa.
(2016) Ranketse, Mary.; Dzomba, Edgar Farai.; Muchadeyi, Farai Catherine.; Madoroba, Evelyn.
Abstract available in PDF file.
Breed effects on the virulence gene profiles and genetic diversity at FUT1, MUC4, MUC13 and MUC20 candidate genes for controlling diarrhoea-causing Escherichia coli.
(2013) Mohlatlole, Ramadimetja Prescilla.; Dzomba, Edgar Farai.; Chimonyo, Michael.
Escherichia (E) coli infections result in diarrhoea and oedema in growing pigs. Enterotoxigenic (ETEC), shigatoxin producing (STEC) and enteroaggregative (EAEC) E. coli have been identified as the principal causes of colibacillosis in most pig production systems. These E. coli use fimbrial and non-fimbrial adhesins to adhere to the intestines and cause infection. Absence or presence of the receptors on the intestinal walls determines the resistance or susceptibility of the host to the E. coli. In other populations, candidate genes linked to the receptors have been found to be associated with resistance/susceptibility to infection and are used in marker-assisted selection programs. This study investigated the presence and prevalence of ETEC, STEC and EAEC and the associated virulence genes in 263 E. coli isolates sampled from Landrace, Large White, Duroc and Indigenous piglets from the Animal Production Institute of the Agricultural Research Council (ARC) in Irene and Middledrift farm in Eastern Cape Province. The study also investigated polymorphisms at six candidate genes associated with two E. coli receptors in the same pig populations. Over 39 % of the isolates tested positive for the E. coli virulent genes investigated. None of the samples had fimbrial adhesins. The mode of attachment of the investigated E. coli was through non-fimbrial adhesins which were found in 49.06% of the isolates. The 106 E. coli isolates were categorized into 25 pathotypes carrying definable and unique combinations of E. coli virulence factors. The resistant allele for Alfa (1) fucosyltransferase 1 (FUT1) M307, a candidate gene for FI8R, was present in less than 1 % of the population. Various mutations of mucin genes MUC4 g.8227, MUC20 c1600 and g.191 were found in the population. Their respective alleles for controlling F4ab/ac E. coli adhesion in pigs were predominant in both breeds. Three loci (FUT1, MUC20 g.191 and MUC20 c.1600) deviated from Hardy Weinberg equilibrium (HWE) in the Indigenous and the Large White breeds. Heterozygotes deficiency and high levels of within breed diversity was observed in these two breeds at the mentioned loci. Overall, the study observed a wide range of toxin and colonisation factors (CFs) giving rise to diverse pathotypes in South African pigs. The absence of fimbrial adhesins suggests a different colibacillosis control program from that previously used. The presence of the resistant alleles in most of the loci investigated was low, however their presence suggest it is possible to use them to generate a resistant population using marker assisted selection. This study serves as a foundation for future pig colibacillosis control and immunity studies in the South African pig herds.
Breed susceptibility to enterotoxigenic and enteroaggragative Escherichia coli strains in South African pigs.
(2013) Chaora, Nyaradzo Stella.; Chimonyo, Michael.; Dzomba, Edgar Farai.
Escherichia coli diarrhoea is the most important source of mortality in piglets. The most frequently isolated strain in enterotoxigenic E. coli diarrhoea is F4ab/ac. Recent studies in South Africa reported non-fimbrial strains such as PAA and EAST-1 to be prevalent. The objective of the study was to determine whether there are breed differences among pigs with respect to E. coli adhesion phenotypes and correlate them to polymorphisms at selected candidate genes in the South African population. A total of 225 pigs aged 3-12 weeks of the imported (Large White, Landrace and Duroc), local and crossbreds, were sampled from the Eastern Cape and Limpopo provinces of South Africa and genotyped for PCR-RFLP polymorphisms at four candidate genes associated with E. coli F4ab/ac resistance/susceptibility. These genes were Mucin 4 (MUC4), Mucin 13, (MUC13), Mucin 20 (MUC20) and Transferrin Receptor (TFRC). The TFRC and MUC13 genes were less polymorphic, the C allele was close to fixation and the homozygous CC genotype was the most frequent in all three pig populations. There was a significant difference (P <0.05) in allelic and genotypic distribution amongst breeds for the TFRC locus. The g.8227G>C polymorphism in MUC4 segregated in all three breeds and the marker was moderately polymorphic. There was a significant difference (P <0.05) in genotypic distribution amongst breeds for MUC4.The g.191C>T polymorphism in MUC20 segregated in the local and crossbred pigs and was close to fixation in the imported pigs. There was a significant difference (P <0.05) in allelic and genotypic distribution amongst breeds for MUC20, which was moderately polymorphic. There was a reduction in heterozygosity in both the TFRC and MUC13 loci, although MUC4 and MUC20 genes had higher heterozygosity levels. The MUC4 gene had a negative FIS value, indicating outbreeding at this locus. The MUC20, MUC13 and TFRC genes had a positive FIS value, indicating inbreeding at these loci. Overall, the studied population was outbred. Imported pigs in TFRC and MUC20 deviated from Hardy-Weinberg equilibrium (HWE). All breeds were in HWE at the MUC4 and MUC13 genes. There was no linkage disequilibrium observed amongst the analysed loci. iv A total of 109 piglets of three breeds (Large White, indigenous and crossbred) aged 3-5 weeks, were investigated for the susceptibility to E. coli F4, PAA strains and EAST-1 toxin. Adhesion tests were conducted on pig intestinal cells, which were viewed under a phase contrast microscope. Three phenotypes were identified as, adhesive, weakly adhesive and non-adhesive. There was a significant association (P <0.05) between breed and level of adherence of the F4 and PAA strains. Highest frequencies of adhesion phenotypes were observed in the indigenous pigs for both F4 and PAA E. coli strains. Large White pigs had the lowest frequency of non-adhesion in F4 and PAA E. coli strains. The F4 strain had a higher (P <0.05) level of adherence compared to PAA and EAST-1 in Large White pigs. Age of pigs had a significant effect on the level of E. coli adherence in indigenous and crossbred pigs (P <0.05). Adhesion of F4 and EAST-1 was higher in weaned indigenous and crossbred pigs, respectively, than in suckling piglets. There was no significant difference between F4 adhesion and the genotypes at all four candidate genes genotypes. The study showed that both imported and local pig populations carry receptors and are susceptible to F4, PAA and EAST-1 E. coli infections. Indigenous pigs were less susceptible than Large White to E. coli infection. Although polymorphic and segregating in the populations, the MUC4 g.8227G>C and MUC20 g.191C>T mutations were not associated with the adhesion phenotypes and cannot be used in the selection of susceptible animals.
Characterisation of the divergence of the Elsenburg Merino resource flock.
(2012) Naidoo, Pavarni.; Dzomba, Edgar Farai.; Cloete, Schalk Willem P.
The Elsenburg Merino flock has been divergently selected for the ability of ewes to rear multiple offspring since 1986. Updated genetic trends for reproduction are reported for the Elsenburg Merino resource flock. The objective was to determine whether genetic trends estimated previously for the Elsenburg Merino Resource flock changed significantly with the introduction of genetic material from the industry to the high (H) line. All analyses included the full pedigree file, consisting of 6547 individuals. Heritability estimates were 0.08 ± 0.02 for number of lambs weaned and 0.11 ± 0.02 for corrected weight of lamb weaned. The ewe permanent environment variance was estimated at 0.09 ± 0.02 and 0.11 ± 0.02 for number of lambs weaned and for corrected weight of lamb weaned, respectively. Genetic trends for the H and low (L) lines were divergent (P < 0.05) for all reproduction traits during the period prior to the observed breakpoints. Progress for number of lambs weaned in the H line stabilised after 1999 while a decline in response for weight of lamb weaned in the H line occurred after 2003. The change points may result from reduced selection intensity during the formation of reciprocal crossbred lines, or the introduction of unrelated industry sires in the H line. The pedigree was analysed and inbreeding trends computed for the H and L lines with the aim to test the significance of inbreeding within the lines. The software packages used for the statistical analyses were ENDOG v4.8 and POPREP web analysis software. The average inbreeding coefficients (F) were 1.47% and 0.73% for the divergently selected H and L lines. The rate of inbreeding (ΔF) per generation was 0.5% for the H line and 0.6% in the L line. The overall rates of inbreeding per generation were different in the H and L lines but within acceptable levels. The L line, however, showed an unwanted recent increase in inbreeding that will need to be considered in future. Since 2003, part of the Elsenburg Merino breeding flock was subjected to structured reciprocal within-breed crossing. Lamb survival traits and ewe reproductive performance of purebred (H and L) and reciprocal crosses (HxL and LxH) were evaluated using least squares analyses. Levels of heterosis were also assessed. The mean survival of the two crossbred lines was notably superior to the midparent value in absolute terms, although the contrast did not reach statistical significance (P = 0.098). Further research is required to establish whether this within breed heterosis for lamb survival can be exploited to decrease lamb losses. Reproduction, number of lambs born (NLB) and number of lambs weaned (NLW) in the H line was higher than in the L line (P < 0.05) while the two crossbred lines were intermediate and different from both the H line and the L line (P < 0.05) from the analyses of annual reproduction and overall “lifetime” reproduction across three lambing opportunities. Individual heterosis for annual reproduction was estimated at 2.2% for NLB, 13.8% for NLW and 8.5% for corrected weight of lamb weaned (TWW), with the estimate for NLW reaching significance (P < 0.05). Corresponding estimates for total production over three lambing opportunities were 8.7% for TNLB, 19.1% for TNLW and 13.8% for TTWW, with the estimate for NLW reaching significance (P < 0.05). Ten RAPD markers were used to study molecular divergence between the H and L lines. Phenotypic data on the lifetime reproduction of ewes born in 1999 and 2000 indicated that reproduction in the H line ewes was markedly higher than that of L line contemporaries (P < 0.01). The RAPD assay, conducted on 15 ewes from each line, used eight primers and produced 87% polymorphic loci. The mean coefficient of genetic differentiation between lines (Gst) was estimated to be 0.25. In conclusion, the H and L lines were shown to be divergent for genetic trends and levels of inbreeding. The derived estimates of heterosis may also be used to infer divergence between the lines and significant molecular divergence proven using RAPD assays.
Effects of within-litter birth weight variation of piglets on performance at three weeks of age and at weaning.
(2011) Zindove, Titus Jairus.; Chimonyo, Michael.; Dzomba, Edgar Farai.
The impact of within-litter weight variation on the productivity of pig enterprises is poorly understood. The objective of the study was to determine the effect of within-litter birth weight variation on litter performance at three weeks of age and at weaning. The study was conducted using records from 1 788 litters, collected between January 1998 and September 2010, from a pig herd at the Agricultural Research Council (ARC), Irene. The records consisted of piglet identity, breed of sow, breed of boar, parity number, date of farrowing, number of piglets born alive (NBA), individual piglet weight at birth, three weeks and at weaning. From these records, mean birth weight (MBWT), litter weight at birth (TBWT), within-litter birth weight coefficient of variation (CVB), minimum birth weight (MinB) and maximum birth weight (MaxB) were calculated. Mean weight at three weeks (MWTT), litter weight at three weeks (LWTT), within-litter weight coefficient of variation at three weeks (CVT), percent survival to three weeks (SURVT), mean litter weaning weight (MWWT), litter weight at weaning (LWWT), within-litter weaning weight coefficient of variation (CVW) and percent survival at weaning (SURVW) were computed as derivatives. The factors affecting CVB were analysed using the General Linear Model procedures (SAS, 2008). For the relationships between CVB and litter performance at three weeks and weaning, PROC STEPWISE was used. The PROC REG (SAS, 2008) was then used to test whether the relationships between CVB and CVT, SURVT, MWTT, LWTT, CVW, SURVW, MWWT, LWWT and LWWT. Multiparous sows farrowed litters with higher (P<0.05) CVB than gilts. The litter weight (TBWT) and NBA, fitted as covariates, also affected (P<0.05) CVB. The correlation between CVB and NBA was 0.30. The CVB had a linear relationship (P<0.05) with SURVT (SURVT = 83.21 - 0.20 CVB), CVT (CVT = 16.71 + 0.50 CVB), SURV (SURW = 87.9 – 0.04CVB) and CVW (CVW= 15.8 + 0.5CVB). An increase of CVT with CVB depended on parity (P<0.05). The rate of increase of CVT with CVB was highest in Parity 1 (b=0.41) followed by Parity 2 (b=0.36) then middle aged (Parity 3-5) sows (b=0.32). The CVB had no effect on MWTT, LWTT, MWWT and LWWT (P>0.05). The CVB was shown to be an important determinant of SURVT and SURVW. A uniform litter at birth is likely to lead to a homogenous litter at three weeks and weaning, thereby reducing costs of production. Pig producers should, therefore aim at producing homogenous litters at birth.
Estimation of genetic and demographic parameters of extensively raised chicken populations using genome-wide single nucleotides polymorphism (SNP) data.
(2015) Khanyile, Khulekani Sedwell.; Dzomba, Edgar Farai.
Village chicken populations are raised under a farming system that faces a number of challenges such as small flock size, lack of animal performance and pedigree records, lack of proper husbandry and poorly defined and structured mating systems all of which can negatively influence the genetic structure of the populations. Understanding of the evolutionary history, demographic structure, inbreeding levels and risk of a population to extinction is important in facilitating genetic improvement programs while maintaining biodiversity of extensively raised chicken populations. Linkage disequilibrium (LD) is an important source of information about historical events of recombination in a population and together with an understanding of the haplotype structure can provide valuable guidelines for breed improvement. This study was undertaken to investigate the existing LD level, inbreeding levels, effective population size and haplotype structure of extensively raised chicken populations from Southern Africa. A total of 312 village chickens from Malawi (n = 30, from one ecotype), South Africa, (n = 146, from three different ecotypes) and Zimbabwe (n = 135, from three different ecotypes) were genotyped using the Illumina chicken iSelect SNP60K bead chip. LD was calculated for each population from a total of 43,175 SNP after pruning for minor allele frequency (MAF) <0.05, genotyping call rate of <0.95, and deviation from Hardy Weinberg Equilibrium (HWE) p <0.001 and missing genotypes of more than 5%. Linkage disequilibrium averaged 0.41±0.006 and was observed to extend up to a marker distance of 100 kb. From the LD, effective population size was estimated that indicated reduced size of the breeding population over the past 40 generations to less than 20 individuals. Haplo-block structure analysis resulted in a total of 649, 2104 and 2442 blocks from Malawi, South Africa and Zimbabwe, respectively. Most of the observed blocks were less than 20 kb with a few that were more than 500 kb. Haplo-block genome coverage was 39 Mbp, 64.4 Mbp and 54.5 Mbp for Malawi, South Africa, and Zimbabwe, respectively. Large haplo-blocks on chromosome 8 spanned QTL regions associated mostly with body composition traits. The LD pattern was consistent with low effective population sizes and loss of heterozygosity in the village chicken populations. Potentially useful haplo-blocks spanning regions of known QTLs should be targeted for further analysis and identification of genes conferring optimal production performance of village chickens under harsh and marginalized production systems. Overall, the study provides baseline information on the utility of genome wide SNP data in studying extensively raised village chicken populations.
Gene expression profiling of South African indigenous goat breeds using RNA-seq technologies in search of genes associated with growth and carcass quality traits.
(2020) Ncube, Keabetswe Tebogo.; Muchadeyi, Farai Catherine.; Dzomba, Edgar Farai.
Abstract available in pdf.
Genetic diversity and differentiation of pelt, mutton and wool sheep breeds of South Africa using genome-wide single nucleotide polymorphisms.
(2021) Dzomba, Edgar Farai.; Chimonyo, Michael.
Sheep, Ovis aries, are a versatile species that has, over hundreds of years, been adapted to South African environmental conditions resulting in more than 40 breeds that are raised for various objectives and production systems and constituting a population of close to 30 million animals. The South African sheep genetic resource presents unique and distinct phenotypes and genotypes that, put together, contribute to the global biodiversity observed in sheep that ought to be conserved and used for improved human livelihoods and economies. South Africa shares its sheep genetics with the global world, through both exportation and importation of germplasm. The broad objective of the study was to profile the genomic architecture of South African sheep populations to provide information for optimal utilization, conservation and improvement. Four hundred South African sheep belonging to 13 breeds of mutton, wool, dual purpose (mutton and wool), pelt and uncharacterised non-descript indigenous sheep were sampled and genotyped. In addition, 623 genotypes from the International Sheep Genomics Consortium representing European, Asian, African sheep breeds were subsampled. A series of statistical genomic analyses were pursued. In Chapter 3, genetic diversity, population genetic structure and divergence between South African sheep breeds was investigated using the OvineSNP50 Beadchip. A total of 400 sheep belonging to 13 breeds representing mutton, pelt and mutton and wool dual-purpose breeds and Nguni sheep as a representative of indigenous non-descript genotypes were genotyped. To gain a clearer understanding of the genetic diversity of South African breeds relative to other breeds, 623 genotypes from six African, two Asian and eight European breeds were included in the analyses. The study demonstrated low genetic diversity (HO ≤ 0.27) in small and geographically restricted populations of Namaqua Afrikaner; Nguni, and Blackhead Persian relative to moderate to high diversity (HO ≥ 0.38) in Merino and Merino-derived commercial breeds (i.e. Dohne Merino, Australian Merino and Chinese Merino). Overall, the African and Asian populations were the most inbred populations with FIS ranging from 0.17 ± 0.05 in Grey Swakara and Ronderib Afrikaner sheep to 0.34 ± 0.07 in the Namaqua Afrikaner. Principal component analysis separated the fat-tailed sheep (i.e. Swakaras, Nguni, Black Head Persian, Ethiopian Menzi, Meatmaster) from the rump-tailed sheep of Merino and Dorset Horn etc., as well as according to breed history and production systems. Similarly, ADMIXTUREbased clustering revealed various sources of within- and amongst-breed genomic variation associated with production purpose, adaptation and history of the breeds. An analysis of FSTv based breed differentiating SNPs suggested selection and population divergence on genomic regions associated with growth, adaptation and reproduction. Overall, the analysis gave insight into the current status of the sheep genetic resources of South Africa relative to the global sheep population highlighting both genetic similarities as well as divergence associated with production system and geographical distribution and local adaptation. The second set of analyses (Chapter 4) focused on assessing the genetic diversity, population structure and breed divergence in 279 animals including the three Merino-derived breeds and five presumed ancestral populations of Merinos and non-Merino founding breeds of Damara, Ronderib Afrikaner and Nguni. Highest genetic diversity values were observed in Dohne Merino with Ho = 0.39 ± 0.01 followed by Meatmaster and South African Merino with Ho = 0.37 ± 0.03. The level of inbreeding ranged from 0.0 ± 0.02 (Dohne Merino) to 0.27 ± 0.05 (Nguni). Analysis of Molecular Variance (AMOVA) showed high within population variance (>80 %) across all population categories. The first Principal Component (PC1) separated the Merino, South African Mutton Merino (SAMM), Dohne Merino and Afrino from the Meatmaster, Damara, Nguni and Ronderib Afrikaner. PC2 aligned each Merino derived breed with its presumed ancestors and separated the SAMM from the Merino and SA Merino. Within population selection based on |iHS| indices yielded selection sweeps across the AFR (12 sweeps), Meatmaster (4 sweeps) and Dohne Merino (29 sweeps). Genes associated with hair/wool traits such as FGF12, metabolic genes of ICA1, NXPH1 and GPR171 and immune response genes of IL22 IL26, IFNAR1 and IL10RB were reported. Other genes included HMGA which was observed as a selection signature in other populations, WNT5A important in the development of the skeleton and mammary glands, ANTXR2 associated with adaptation to variation in climatic conditions and BMP2 which has been reported as strongly selected in both fat-tailed and thin-tailed sheep. Using the Rsb analysis for selection sweeps, the Dohne Merino vs SAMM shared all six sweeps regions on chromosomes 1, 10 and 11 with the comparison for Afrino vs SAMM. Genes such as FGF12 on OAR 1:191,3-194,7Mb and MAP2K4 on OAR11:28,6-31,3Mb were observed. The selection sweep on chromosome 10 region 28,6-30,3 Mb, harbouring the RXFP2 for polledness, was shared between Dohne Merino vs Merino, Meatmaster vs Merino and Meatmaster vs Nguni. The Dohne Merino vs Merino and the Meatmaster vs Merino also shared an Rsb-based selection sweep on chromosome 1 region 268,5 - 269,9 Mb associated with the Calpain gene, CAPN7. The study demonstrated some genetic similarities between the Merino and Merino-derived breeds emanating from common founding populations as well as some divergence driven by breed-specific selection goals. Chapter 5 tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The ROH were screened and their distribution within chromosomes and between breeds were analysed to assess breed history and associated selected pressures. ROH were computed at cut-offs of 1-6 Mb, 6-12 Mb, 12-24 Mb, 24-48 Mb and >48 Mb. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1- 6 Mb) category (88 %). Most animals had no ROH >48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common ROH per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH islands ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were predominantly associated with metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. In line with observations in Chapter 3, the frequency and patterns of distribution of ROH observed in this study corresponded to the breed history and implied selection pressures exposed to the sheep populations under study. Chapter 6 investigated (i) LD between adjacent SNPs, (ii) LD decay with increased marker distance, (iii) trends in effective population size over time and (iv) consistency of gametic phase in 13 South African sheep breeds South African Merino (n = 56), Merino (n =10); Mutton Merino (n = 10), Dohne Merino (n = 50), Meatmaster (n = 48), Blackhead Persian (n =14) and Namaqua Afrikaner (n = 12), the four pelt-colour based Swakara subpopulations of Grey (n = 22); Black (n = 16); White-vital (n = 41) and White-subvital (n =17) Dorper (n = 23); Afrino (n = 51) and unimproved Nguni sheep (n = 30). Linkage disequilibrium (r2) averaged 0.16 ± 0.021and ranged from 0.09 ± 0.14 and 0.09 ± 0.13 observed in the SA Merino and Dohne Merino respectively to 0.28 ± 0.29 observed in the Blackhead Persian sheep. Chromosome 10 had the highest LD with r2 values ranging from 0.10 ± 0.15 (SA Merino) and 0.12 ± 0.18 (Dohne Merino) to 0.28 ± 0.30 in Blackhead Persian and 0.29 ± 0.30 (SA Mutton Merino). Across the 14 breeds, LD decayed from 0.27 ± 0.30 at 0-10Kb window to 0.02 ± 0.03 at 1000- 2000 Kb window. A progressive decrease in Ne across generations across all populations was observed with effective population size of <500 for all the populations 66 generations ago decreasing to <250, 23 generations ago and well below 100, 13 generations ago. Highest correlations in gametic phase were observed within the 0-10kb window between pairs of Merino and Merino-derived breeds. The highest correlation observed with Nguni sheep was with Dorper sheep (0.33) within the 0-10kb window, which was similar to that observed with Blackhead Persian sheep and Dorper (0.32) again within the same window. The study reported considerable LD persistent over short distance in the South African sheep breeds. The implications of the observed LD, LD decay and consistency in gamete phase on applications such as GWAS, QTL mapping and GS were discussed. It was concluded that the South African sheep population is highly diverse with that diversity found both within and between populations. Genetic differences between fat tailed sheep population, Merino type breeds and the English Dorset were demonstrated as well as low levels of genetic diversity in small and indigenous breeds such as the Nguni, Namaqua Afrikaner and Blackhead Persian. The frequency and patterns of distribution of ROH observed in this study corresponded to the breed history and implied selection pressures exposed to the sheep populations under study. The utility of the OvineSNP50 Beadchip as a genomic tool for the South African Sheep population was also demonstrated. Keywords: Ovis aries; SNP data; genomic structure; production system; selection signatures; ROH
Investigation into the relationship between leptin genotypes, body condition and carcass traits of Nguni and Hereford cattle.
(2010) Etsebeth, Kerry-Lee.; Dzomba, Edgar Farai.
Leptin, a 16 (kilo Dalton) kDa hormone secreted predominantly by white adipocytes, regulates reproduction, energy intake and expenditure, and is involved in immune system function. Previous studies have identified associations between polymorphism E2FB in the leptin gene (lep) of cattle and milk quality and quantity, feed intake, and fat deposition in dairy and beef cattle though further studies have shown inconclusive results. Furthermore, indigenous South African cattle have not been involved in lep investigations or the applicability of the marker in South African beef grading systems. An investigation was conducted into the association of an SNP of a cytosine (C) to thymine (T) SNP (single nucleotide polymorphism) mutation in exon 2 of the bovine lep (leptin) gene with weight gain, body condition, carcass fat content and quality in a population of indigenous Nguni cattle (n = 70) as well as a population of exotic British Hereford cattle (n = 54). The Hereford population had higher T-allele frequencies and a lower P-value (P = 0.172) for the E2FB genotypes than the Nguni population (P = 0.958). The resulting E2FB lep genotypes CC, CT and TT did not show an association with the pre- and post-slaughter traits initial live weight (ILW), body condition score (BCS), slaughter live weight (SLW), carcass fat content (FAT), carcass conformation (CFN) or warm carcass mass (WCM) for either population though t-tests revealed an association with the CT genotype with increased ILW than TT and a significantly higher WG in the TT genotypes than the CT (P<0.05). Subsequently, differences in pre- and post-slaughter traits in both populations were largely attributable to breed differences. The Hereford population exhibited significantly higher WG, CFN, SLW, WCM and CCM (P<0.05) than the Nguni population. The Nguni displayed significantly higher ILW and BCS values when graded in terms of the commercial South African AAA feedlot system.
Landscape genomic approach to investigate genetic adaptation in South African indigenous goat populations.
(2016) Mdladla, Khanyisile.; Dzomba, Edgar Farai.; Muchadeyi, Farai Catherine.
Abstract available in PDF file.
Population genetics of Swakara sheep inferred using genome-wide SNP genotyping.
(2015) Malesa, Masoko Tshenakaho.; Dzomba, Edgar Farai.; Muchadeyi, Farai Catherine.
The pelts of Swakara sheep breed of Namibia are famous for their lustrous features and are unmatched in quality across the globe. These pelts occur in four subpopulations of white, grey, black and brown. The white pelt is the most preferred pelt colour. However, there is a challenge in producing white pelts due to the sub-vital factor that affects homozygous white lambs, thought to be a result of the negative impact of years of inbreeding and selection pressures. Sub-vital performance is a genetic disorder that causes digestive complications in lambs resulting in their death within days of birth. The ability to identify carriers or affected individuals of sub-vital performance at an early stage will save the Swakara industry production costs and reduce mortality rates in the white subpopulation. In this study, high-throughput SNP genotyping was used to perform a population genetics study, which investigates the genetic structure of Swakara with the aim of identifying structural differences between sub-vital individuals and the other coat colours, and by using GWAS to determine the variants contributing to sub-vitality in subtle effects and their associated genes in Swakara. This study will also look at selection pressures in Swakara, the genetic differentiation between subpopulations, level of inbreeding and the presence of ROH segments in Swakara and their associated genes that relate to sub-vital performance. Genetic statistical tools such as PLINK, ARLEQUIN and SVS were used to perform the analyses required for this population study. Ninety Swakara sheep were collected from Namibia and South Africa. These were sub-divided into four colour subpopulations of black (n = 16), grey (n = 22), vital white (n = 35) and sub-vital white (n = 17). The DNA from each of these was then genotyped using the OvineSNP50 beadchip. The genotyping success rate was > 93% across all the colour subpopulations. The quality control (QC) post genotyping was done by removing SNPs that departed from HWE > 0.0001, had low allele frequencies MAF < 0.01, SNP markers that had missing/low call rates (GENO) > 0.01 and individuals that had missing genotypes (MIND) > 0.1. This QC was done for every subpopulation described in this study prior to all other succeeding analyses. The inbreeding coefficient F was high in the black subpopulation (0.04798±0.069) and lowest in the grey (0.01074±0.079) Swakara sheep. The genetic diversity for the Swakara subpopulations showed a consensus in the results and showed the most diversity between the black and white subpopulations. The PCA results also showed the genetically similar subpopulations, as identified by pairwise FST values, clustered together. Forty-two unique ROH were observed across 10 chromosomes in 33 (out of 90) individuals and spanned between 5198.93-7126.85 KB in length in the four colour subpopulations. The white sub-vital group had the highest number of ROHs (18). Seven overlapping/consensus regions of homozygosity were observed on chromosome 2, 7, 9, 10, and 20. There was no correlation between the frequency of ROHs in an individual and the level of inbreeding, however the black subpopulation had the highest level of inbreeding and had the highest average of ROH length among the other subpopulations but this was not a consistent trend with the other subpopulations. The GWAS revealed at least five SNPs associated to sub-vitality located on chromosome 3, 5, and 8. Chromosome 3 had three different SNPs associated to sub-vitality. The most prominent SNPs was located on chromosome 3, which is associated to a gene, IGF1, responsible for insulin-like growth factor and contributes to the development of foetal organs. The genes identified by GWAS and cROH pointed to the cause of sub-vitality due to the contributing effects of biological functions related to metabolic activities. A targeted gene sequencing study would be required to assess the differences in the sequences of the identified significant SNPs, the IGF1 genetic region, in order to examine the possible causal mutations of sub-vitality. A study focussed more on the white and sub-vital subpopulation, with an increased sample size and a targeted gene sequencing approach would assess the differences in the targeted sequences of both case and control individuals.
Prevalence and antibiotic sensitivity of enterotoxigenic Escherichia coli isolates in South African pig population.
(2015) Sikhosana, Zizile Emelda Lilly.; Dzomba, Edgar Farai.; Madoroba, Evelyn.; Muchadeyi, Farai Catherine.
Escherichia coli (E. coli) are among the leading bacterial causes of diarrhoea and edema in newborn and weaned pigs. Pathogenic strains of E. coli are classified into enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteroaggreagative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC) and diffusely adherent E. coli (DAEC) based on virulence factors. Infection with E. coli is achieved by adherence of fimbrial and/or non-fimbrial adhesins to the intestines and the release of toxins thereafter. The increasing rates of antimicrobial resistance are posing a threat in the treatment of porcine E. coli infections. The aim of this study was to determine the prevalence of pathogenic Escherichia coli virulence genes and antibiotic sensitivity of enterotoxigenic Escherichia coli isolates from neonatal and post-weaning pigs in Limpopo and Eastern Cape provinces of South Africa. For this purpose, 325 rectal swabs were collected from pigs from the Eastern Cape and Limpopo provinces of South Africa to investigate the prevalence of ETEC relative to other E. coli strains. Classical microbiological tests were conducted for confirmation of E. coli and PCR was used for the detection of fimbrial, non-fimbrial adhesins and toxin genes. In addition, antimicrobial susceptibility of ETEC positive isolates was determined by the Kirby-Bauer disk diffusion method. Of the 325 swabs collected, 303 isolates were identified as E. coli with 67% (205/303) harboring at least one of the tested virulence genes (LT, STa, STb, EAST-1, Stx1, Stx2, Stx2e, VT1, VT2, hlyA, F4, F5, F6, F18, F41, AIDA-1, EAE and PAA) and categorized into 48 pathotypes. A total of 36 (11.9%) isolates was classified as ETEC, having heat-labile (LT) enterotoxin as the most prevalent. Only a single isolate (2.8%) carried fimbriae (F4/F5). Instead, non-fimbrial adhesins PAA, AIDA-1 and EAE were detected. The ETEC positive isolates displayed 47.2%, 38.9% and 36.1% resistance to oxytetracycline, ampicillin and trimetroprim respectively. Most of the ETEC isolates were sensitive to florphenicol (100%), cefotaxime (97.2%) and enrofloxacin (77.8%). Multi-drug resistance was detected in 50% of the isolates. The study demonstrated that there are various E. coli pathotypes in South Africa. The detection of non-fimbrial adhesins reinforces existing knowledge that fimbriae are not the only colonization factors associated with ETEC. Based on the antimicrobial susceptibility patterns observed, florphenicol, cefotaxime and enrofloxacin could be used for the treatment of ETEC infections in South African pigs.