Molecular characterisation of ARC pome fruit collections in South Africa

Mhelembe, Khethani Give (2015-03)

Thesis (MSc)--Stellenbosch University, 2015.


ENGLISH ABSTRACT: Apple (Malus pumila Mill.) and pear (Pyrus communis L.), commonly known as pome fruits, are important deciduous fruit crops in South Africa. The challenges of climate change, disease incidence, distant markets and fluctuating consumer preferences necessitate new cultivars. The Agricultural Research Council (ARC) Infruitec-Nietvoorbij conducts a breeding programme aimed at developing new cultivars that are well adapted, resistant to pests and diseases and good storage potential. A recent review of the pome fruit gene banks, the breeders’ raw material, revealed misidentification and poor characterisation limitating the efficiency of its utilisation. To address these problems, the current study used microsatellite markers to investigate the trueness to type of accessions in the ARC gene banks. In addition, accessions of apple identified as true to type, were genotyped for the ACS1 gene involved with ethylene production and fruit ripening. Two sets of 12 microsatellite markers recommended by a European working group on Pyrus/Malus, one for apple and one for pear, were utilised to fingerprint 540 apple and 197 pear accessions. Eleven and eight of 12 markers, were used respectively to successfully discriminate across the apple and pear accessions, with the exception of clones and sports of particular cultivars. Where possible, fingerprints were compared with those of their reported parents. The use of recommended markers facilitated the comparison of ARC pear accessions with those of the collection in Brogdale (UK). Trueness to type of accessions were established and misidentified accessions were also detected. A similar comparison will be conducted for apple when the Brogdale apple accessions fingerprints become available. Several accessions were found to be false, 78 apple and 22 pear, and removal from the collection was recommended. For ACS1 genotyping of 292 apple accessions, customised fluorescently labelled ACS1-Pr were used rather than the published ACS1-5 primers. Of the 292 apple accessions, 29 were homozygous for the b allele associated with low ethylene and good storage potential. Novel size variation in one allele of the ACS1 gene, was detected in some Malus species and ornamental hybrids. Successful amplification in a multiplex reaction was achieved and proves to be a cost effective method for simultaneous molecular fingerprinting and ACS1 genotyping. True to type material will facilitate confident use of genetic resources in the breeding programmes, and the ACS1 genotypes will identify candidate parents for developing good storage performing cultivars for distant markets.

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