Doctoral Degrees (Genetics)

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Browsing Doctoral Degrees (Genetics) by Subject "Apple (Malus pumila Mill.) -- Breeding"

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    Mapping of dwarf growth habit traits in apple (Malus pumila Mill.) using molecular markers and transcriptomics approaches
    (Stellenbosch : Stellenbosch University, 2020-03) Mbulawa, Zama Thandekile Laureen; Bester-van der Merwe, Aletta Elizabeth; Kriel, Johan; Tobutt, Kenneth R.; Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: Apple (Malus pumila Mill.) is one of the most important deciduous fruit crops worldwide. Apples are traditionally valued as an important dietary source of fibre and are high in antioxidants, contributing to human nutrition. In South Africa, the apple industry plays a vital role in the country's agricultural economy due to global exports. In recent years, more emphasis has been directed to dwarf trees, as they are well suited for profitable high-density orchards and sustainability of fruit production. However, dwarfism cannot always be linked to increased yield. At Bien Donné Research Farm of the Agricultural Research Council (ARC) Infruitec-Nietvoorbij’, several dwarf growth habits exist, which is related to a form of hybrid incompatibility, hybrid necrosis. One of them is associated with undesirable characteristics such as crinkled leaves and poor growth. Expression of hybrid necrosis in plants can lead to a significant reduction in productivity, due to the deleterious epistatic interactions between alleles that arose from divergent genetic backgrounds. Few, if any, genetic studies have thus far investigated crinkle dwarf growth traits in apple. This study aimed to examine the genetic basis underlying the crinkle dwarf phenotype by employing multidisciplinary approaches that included segregation pattern studies, assessment of self-incompatibility (hybrid incompatibility), molecular mapping and transcriptomic profiling of pooled samples of apical buds and young leaves from normal and from crinkle dwarf phenotypes. The genetics behind the crinkle dwarf trait was undertaken by studying the segregation patterns of the first filial generation (F1) apple progenies, where parental combinations were heterozygous. Segregation ratios of 9:7 and 3:1 were observed, for which crinkled dwarf phenotypes is expressed when one of the two genes is homozygous recessive (D-ee or ddE-). Additionally, the involvement of self-incompatibility (S) was investigated by identifying the parental S-genotypes using PCR based consensus and allele-specific primers of the apple S-RNAse gene. Eight parental S-genotypes were determined. Herein, the S-genotypes of Malling 1 (‘M.1’) (S3S9) and TSR1T187 (S7S24) were deduced for the first time. High-density SNP-based parental genetic linkage maps of ‘McIntosh’ and ‘M.1’ were constructed using the apple 20K Infinium SNP array. The crinkle dwarf trait was mapped on linkage group (LG) 8 in ‘McIntosh’ and on LG2 in ‘M.1’. In the consensus genetic map, crinkle dwarf trait also mapped on LG8. Additionally, the crinkle dwarf trait obtained for the parental genetic maps were validated using Kruskal-Wallis (KW) analysis. To gain deeper insights into the genes regulating crinkle dwarf phenotype, transcriptome profiles of pooled meristematic tissues of normal and crinkle dwarf phenotypes were generated using RNA-sequencing technology. A total of 921 significantly differentially expressed genes (DEGs), with 763 up-regulated and 158 down-regulated transcripts, were identified. Gene expression analyses revealed that defense signaling and stress-related genes were up-regulated during the expression of crinkle dwarf phenotype along with the activation of several antioxidant proteins/enzymes. The high expression of lactoperoxidase (Class III peroxidase) together with glutathione S-transferase suggests the involvement of reactive oxygen species (ROS). Genes typically encoding for pathogenesis-related proteins (chitinase and pectin), antioxidant enzymes, receptor-like protein (protein serine/threonine phosphatase), as well as alpha-linolenic acid, a precursor of the phytohormone jasmonic acid were all up-regulated during expression of crinkle dwarf phenotype. These findings support the notion that crinkle dwarf phenotype does indeed exhibit hybrid necrosis symptoms. Consequently, an autoimmune response might have been triggered by the allele incompatibilities, in this case between ‘McIntosh’ and ‘M.1’. Overall, the information generated in this study will aid in designing an in-house screening system for eliminating seedlings carrying crinkle dwarf genes from the ARC breeding material. In future, these findings will also aid in the design of crosses with predictable outcomes and in broadening a sustainable genetic base of the apple cultivars for high productivity orchards, while avoiding raising seedlings with dwarf growth habit associated with crinkled leaves.