ARC Biotechnology Platform

South Africa

ARC Biotechnology Platform

South Africa
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Mtileni B.J.,ARC Animal Production Institute | Mtileni B.J.,Stellenbosch University | Muchadeyi F.C.,ARC Biotechnology Platform | Maiwashe A.,ARC Animal Production Institute | And 3 more authors.
Tropical Animal Health and Production | Year: 2012

Individual interviews were conducted in 137 households using semi-structured questionnaires to determine the influence of socioeconomic factors on production constraints faced by indigenous chicken producers in the rural areas of South Africa. The major constraints to village chicken production were mortality (95 % of the households) followed by feed shortage (85 %) and low chicken sales (72 %). The logistic regression model showed that households that owned imported/crossbred chickens practiced extensive production system without housing structures and did not have vaccines were more likely to experience high levels of chicken mortality. Poor and youth-headed households with no supplements and vaccines had high probability of Newcastle disease. The probability of a household to experience chicken feed shortage was lower in households that owned indigenous chickens than those that owned imported/crossbred chickens (odds ratio, 11.68; 95 % confidence interval, 1.19-27.44). Youth-headed households that had small flocks and no access to veterinary services were not likely to sell chickens. It was concluded that gender, age, wealth status, production system, chicken flock size, type of chicken breed owned, accessibility of veterinary services, availability of supplements, vaccines and shelter influence village chicken farmer's production constraints such as feed availability, chicken mortality, prevalence of diseases and chicken sales. © 2012 Springer Science+Business Media B.V.

Severn-Ellis A.,ARC Institute for Tropical and Subtropical Crops | Schoeman M.H.,ARC Institute for Tropical and Subtropical Crops | Willemse S.,ARC Institute for Tropical and Subtropical Crops | Sippel A.,ARC Institute for Tropical and Subtropical Crops | And 2 more authors.
Acta Horticulturae | Year: 2012

Soil-borne vascular wilt pathogens cause among the most devastating plant diseases worldwide. Guava wilt disease (GWD) caused by Nalanthamala psidii, resulted in the loss of more than half the guava production area in the Limpopo and Mpumalanga provinces of South Africa during the 1980s. Resistant guava selections were developed but renewed outbreaks of guava wilt disease in 2009, now also affecting the tolerant ARC-ITSC developed cultivar 'TS-G2', is placing the guava industry under threat once again. Alternative control measures are currently not available and host resistance remains the most logical choice for control. However, the lack of known sources of plant resistance and the emergence of additional pathogen races pose as major obstacles. Accurate identification and knowledge about the genetic variation within the pathogen population are therefore key aspects in the development of resistant guava cultivars. The aim of this study was firstly to determine the identity of 18 new fungal isolates obtained from infected 'TS-G2' trees. The internal transcribed spacer of the ribosomal RNA gene cluster (ITS), nuclear large ribosomal sub-unit (LSU), as well as the partial second largest subunit of the RNA polymerase II (rpb2) and the larger subunit of ATP citrate lyase (acl1) gene exons and introns of the new fungal isolates and reference isolates were sequenced and compared. Sequence analysis established the identity of the new isolates to be identical to N. psidii reference strain (CBS 439.89) previously isolated in South Africa, but differed from N. psidii stains from Malaysia and Taiwan. Although species diagnosis was possible, it was not possible to show geographic distribution- or determine pathogenicity relationships between isolates. The development of microsatellites or Simple Sequence Repeat (SSR) markers using high throughput sequencing was therefore investigated. A total of 15 645 SSRs were identified consisting mostly of tri- and tertra- nucleotide motifs. Selected SSRs will be used to facilitate further fungal population studies. © ISHS.

Abolnik C.,Onderstepoort Veterinary Institute | Abolnik C.,University of Pretoria | De Castro M.,ARC Biotechnology Platform | Rees J.,ARC Biotechnology Platform
Virus Genes | Year: 2012

A random amplification/deep sequencing approach was applied to determine the complete genomic sequence of an Avian Paramyxovirus Type 4 (APMV-4) strain isolated from a wild duck in South Africa in 2010. This sequence represents the fourth full genome of APMV-4 in public sequence databases and the first for the African continent. A total of 87,402,081 Illumina paired-end reads were obtained of which 47,338,867 (54.16 %) mapped to the reference genome EU877976. The entire genomic sequence of 15,054 nt, including the intact termini, was recovered at a high redundancy (coverage per base: average = 198,861.06, minimum = 52 and maximum = 1,790,889). Pairwise comparison of full genomic nucleotide sequences indicated that APMV-4/Egyptian goose/South Africa/N1468/10 shared 97.3 % sequence identity with APMV-4/KR/YJ/06, 96.4 % sequence identity with APMV-4/mallard/Belgium/15129/07 and 90.8 % nucleotide sequence identity with APMV-4/duck/HK/D3/75. Genomic features were consistent with previously sequenced viruses including predicted open reading frames for the NP, P, F and L genes, but variations in coding regions for the M and HN genes were identified. The sequencing approach adopted in this study could successfully indicate quasispecies in the viral stock. © 2012 Springer Science+Business Media, LLC.

Fernandez-Fernandez F.,East Malling Research EMR | Antanaviciute L.,East Malling Research EMR | van Dyk M.M.,University of Pretoria | Tobutt K.R.,East Malling Research EMR | And 5 more authors.
Tree Genetics and Genomes | Year: 2012

An apple rootstock progeny raised from the cross between the very dwarfing 'M. 27' and the more vigorous 'M. 116' ('M. M. 106' × 'M. 27') was used for the construction of a linkage map comprising a total of 324 loci: 252 previously mapped SSRs, 71 newly characterised or previously unmapped SSR loci (including 36 amplified by 33 out of the 35 novel markers reported here), and the self-incompatibility locus. The map spanned the 17 linkage groups (LG) expected for apple covering a genetic distance of 1,229.5 cM, an estimated 91% of the Malus genome. Linkage groups were well populated and, although marker density ranged from 2.3 to 6.2 cM/SSR, just 15 gaps of more than 15 cM were observed. Moreover, only 17.5% of markers displayed segregation distortion and, unsurprisingly in a semi-compatible backcross, distortion was particularly pronounced surrounding the self-incompatibility locus (S) at the bottom of LG17. DNA sequences of 273 SSR markers and the S locus, representing a total of 314 loci in this investigation, were used to anchor to the 'Golden Delicious' genome sequence. More than 260 of these loci were located on the expected pseudo-chromosome on the 'Golden Delicious' genome or on its homeologous pseudo-chromosome. In total, 282.4 Mbp of sequence from 142 genome sequence scaffolds of the Malus genome were anchored to the 'M. 27' × 'M. 116' map, providing an interface between the marker data and the underlying genome sequence. This will be exploited for the identification of genes responsible for traits of agronomic importance such as dwarfing and water use efficiency. © 2012 Springer-Verlag.

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