Browsing Doctoral Degrees (Genetics) by Author "Bierman, Anandi"
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- ItemMapping and survey sequencing of Dn resistance genes in Triticum aestivum L.(Stellenbosch : Stellenbosch University, 2015-03) Bierman, Anandi; Oberholster, A-M.; Stellenbosch University. Faculty of AgriScience. Department of Genetics.ENGLISH ABSTRACT : Diuraphis noxia Kurdjumov (Russian Wheat Aphid; RWA) is a pest of wheat and barley that has spread from its home range in the fertile crescent to most wheat producing countries except Australia. Since its first introduction to South Africa and the USA in the late 20th century, breeding programs for wheat phenotypes resistant to the aphid were put in place. Conventional breeding practices rely on phenotypic screening to verify traits carried by offspring and genetic tools such as marker assisted selection (MAS) have greatly aided this process in speed and accuracy. The size and complexity of the wheat genome, its allopolyploid nature and repetitive elements have, however, posed a challenge to studies on the genetics of this cereal crop. Many studies have focused on chromosome 3B which is the largest of the wheat chromosomes and easily separated from the redundant genomic background by techniques such as flow cytometry. The similarity in size of the remaining chromosomes however, limits the application of flow cytometry to their isolation. Databases such as Grain-Genes (http://wheat.pw.usda.gov/GG2/index.shtml) house marker data from various mapping studies for all wheat chromosomes and in 2014 the International Wheat Genome Sequencing Consortium (IWGSC) completed the draft genome sequence of wheat categorized by chromosome. Sources of resistance (Dn resistance genes) against RWA are located on chromosome 7D. but despite the marker and sequence data available currently, mapping studies specific for the Dn resistance genes are few. Additionally, sequence data available is derived from cultivars susceptible to RWA and is not comprehensively annotated and assembled in many cases. In this study, we demonstrate a novel, combined approach to isolate and characterize the Dn resistance genes through the use of a genetic map constructed from Amplified Fragment Length Polymorphism (AFLP), Expressed Sequence Tag (EST) and microsatellite markers and a physical map constructed from Next Generation Sequencing (NGS) data of ditelosomic chromosomes (7DS and 7DL) isolated by microdissection on the PALM microbeam system. A 122.8 cM genetic map was produced from 38 polymorphic AFLP markers and two ESTs with the microsatellite Xgwm111 as anchor to related genetic maps. Through comparison to maps available on GrainGenes the location of the Dn1 resistance gene was narrowed down to a deletion bin (7DS5-0.36-0.62) on the short arm of chromosome 7D with an AFLP marker (E-ACT/M-CTG_0270.84) mapping closely at 3.5 cM and two ESTs mapping at 15.3 cM and 15.9 cM from Dn1. Isolation of individual chromosome arms 7DS and 7DL using the PALM Microbeam system allowed sequencing of the chromosome without the redundancy of the remainder of the hexaploid genome. Through isolating the chromosome arms in this way, a >80-fold reduction in genome size was achieved as well as a major reduction in repetitive elements. Analysis of the sequencing data confirmed that 7DL is the physically shorter arm of the chromosome though it contains the majority of protein coding sequences.