Spatial Assessment of Saccharum Species Hybrids and Wild Relatives in Eastern South Africa

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Spatial Assessment of Saccharum Species Hybrids and Wild Relatives in Eastern South Africa Spatial assessment of Saccharum species hybrids and wild relatives in eastern South Africa DM Komape orcid.org 0000-0003-3705-5438 Dissertation submitted in fulfilment of the requirements for the degree Masters in Environmental Sciences at the North-West University Supervisor: Prof SJ Siebert Co-supervisor: Dr DP Cilliers Co-supervisor: Prof J Van den Berg Graduation May 2019 24676748 ABSTRACT Sugarcane (Saccharum hybrids) belongs to the Andropogoneae in the Poaceae. The grass family is known to have provided the world’s most economically important crops. In assessing the risk of cultivating genetically modified (GM) grass crops in South Africa, gene flow studies have to be conducted prior to the approval or release of such crops into the environment as hybridisation may occur between crop plants and wild relatives if certain barriers to gene flow are crossed. The aim of the study was to conduct a spatial assessment of Saccharum and its relatives in eastern South Africa and to assess potential gene flow, which in turn will inform the way forward for risk assessments. Eleven Saccharum wild relative species were selected for analyses based on their presence in the sugar producing region of South Africa: four species in the Saccharinae and seven in the Sorghinae. Spatial, temporal and gene flow assessments of wild relatives were conducted: prevalence, spatial overlap, proximity, dispersal potential, flowering times, hybridisation potential and relatedness. Field surveys, herbarium distribution records and literature were used to assess these factors and to determine the gene flow likelihood. A total of 815 herbarium specimens were sourced from 11 suitable herbaria and they were supplemented by 34 observations during field visits to sugarcane cultivation areas. The presence of all target species was confirmed in sugarcane areas. Imperata cylindrica (L.) Raeusch., Sorghum arundinaceum (Desv.) Stapf and Miscanthidium capense (Nees) Mabb. scored the highest likelihood for prevalence, flowering time and spatial overlap with sugarcane. Although I. cylindrica and S. arundinaceum generally ranked the highest for spatial and temporal assessments, they were not important candidates for gene flow potential from sugarcane, since they were not considered as reproductively compatible due to their low scoring on the relatedness assessment. Cleistachne sorghoides Benth., Miscanthidium capense, Miscanthidium junceum (Stapf) Pilg.and Sarga versicolor (Andersson) Spangler scored higher as close relatives of sugarcane in the study area. Miscanthidium species ranked highest for gene flow potential and were the only target species that were flagged by this study as having a high likelihood for gene flow with sugarcane. This is supported by the more recent divergent age from sugarcane that falls within the period considered to be optimal for hybridisation within Saccharinae species. When considering the likelihood scores of all species, the regions with the highest likelihood for gene flow were associated with coastal and southern-inland KwaZulu-Natal. These areas should be avoided when cultivating GM sugarcane should it be approved in the future, or in-depth risk assessments should be conducted before release. This study recommends that future studies be done to assess pollen compatibility and viability for sugarcane and related species (Miscanthidium capense and M. junceum) as part of a risk assessment, as some gene flow barriers, such as proximity and flowering time, was shown to be crossed in this study. Keywords: Eastern South Africa; Gene flow likelihood; Genetically Modified (GM); Spatial assessment; Sugarcane; Taxonomy; Wild and weedy crop relatives i Acknowledgements I would firstly like to thank, Almighty God for blessing me with the opportunity, strength and wisdom to carry out this study. I would secondly like to thank the following people and institutions for their valuable contributions to my dissertation: ➢ My supervisors, Prof Stefan John Siebert, Prof Johnnie Van den Berg and Dr Dirk Petrus Cilliers for their continued support, guidance and efforts invested in this study. It has indeed been a great blessing to work with them and I learned a lot from them. ➢ My family for their continuous love, support and believing in me. ➢ Special appreciations to my beloved younger sister, Miss Mmaphuti Edith Komape for her hospitality, love and encouragements throughout this study. ➢ Mr Perfection Chauke and Miss Hlobby Khanyi for accompanying me to the study sites and assisting with data collection. ➢ Dr Dyfed Lloyd Evans and Miss Hlobby Khanyi for sharing their relatedness data. ➢ Dr Sandy Snyman for assisting with coordinating the project. ➢ Dr Benny Bytebier (NU), Dr Reeny Reddy (J), Dr Lize Joubert (BLFU), Mrs Magda Nel (PRU), Mrs Annemarie van Heerden (KMG), Mr Erich van Wyk and Mrs Aluoneswi Caroline Mashau (PRE) for allowing me to collect data in their herbaria. ➢ Ms Barbara Turpin (BNRH), Dr Mervyn Lötter (LYD) and Dr Madeleen Struwig (NH) for sending herbarium specimen electronically. ➢ Mrs Aluoneswi Caroline Mashau (PRE), for assistang me with identifications of grasses. ➢ South African Biosafety and South African Sugarcane Research Institute (SASRI) for the financial support. ➢ FK Norway project and Unit of Environmental Sciences and Management, North-West University for providing additional financial support. ➢ A.P Goossens herbarium (PUC) for logistics. ➢ North-West University botany writing group for the effective writing sessions. SOLI DEO GLORIA Behold, I will do a new thing; now it shall spring forth; shall you not know it? I will even make a way in the wilderness, and rivers in the desert. Isaiah 43:19 ii TABLE OF CONTENTS PAGE NUMBER Abstract……………………………………………………………………………………..……….….….....i Acknowledgements………………………………………………………………………….……..….….....ii Table of Contents………………………………………………………….……………………….….….....iii List of Figures………..………………………………………………………………………………………vi List of Tables…………...………………………………………………………………………………….…ix Chapter 1: Introduction………………….……………………….…………………………….………....1 1.1 Background………………………………………………………….…………………..……………….1 1.2 Motivation…………………………………………………………....……………………..…………….2 1.3 Aim and Objectives……………………………………………….…………………….……………….3 1.4 Dissertation Outline……………………………………………….………………………….….…….3 1.5 References……………………………………………………………………………..………….……..5 Chapter 2: Literature Study……………………………………………………………………...……….8 2.1 Biodiversity and its benefits.……………………………...…………………………………...……….8 2.2 Threats to biodiversity…………….…………………………………………………………………….8 2.2.1 Biological invasions…………………………………………………………………………..……..8 2.2.2 Urbanization………………………………………………………………………………….……...9 2.2.3 Agriculture………………………………………………………………………………….…..…….9 2.3 Saccharum taxonomy and origin……………………………………………………………………..10 2.4 Importance of Saccharum species…………………………………………………………………...11 2.5 Genetically Modified Crops……………………………………………………….…………………..11 2.6 Genetically Modified Saccharum……………………………………………………………………..12 2.7 Risk Assessment……………………………………………………………………………………….13 2.8 Risks to biodiversity…………….……………………………………………………………………...13 2.9 Risk analysis………………………………………………………………………………………...….14 2.10 References………………………………………..……………………………………………….….15 Chapter 3: Materials and Methods…………………………………………………………………..…23 3.1 Criteria used to select target species……………………………………………….……………..…23 iii 3.2 General methodologies applied for assessing taxonomy, distribution and conducting spatial and gene flow assessments……………………………………………………………………………….23 3.2.1 Sourced herbarium specimens and field collections for herbarium voucher specimens of Saccharum wild relatives…………………………………………………………………….……….…...23 3.2.2 Phytogeography assessment of Saccharum wild relatives……………………….…….…….25 3.3 Analytical approaches applied for assessing the taxonomy and distribution of sugarcane and their wild relatives……………………………………………………………………………….…….……26 3.3.1 Scientific names and synonyms of Saccharum wild relatives……………………….….….…26 3.3.2 Morphologies of Saccharum wild relatives compared with Saccharum hybrids……..……..27 3.3.3 Distribution of Saccharum wild relatives in eastern South Africa……………………….……27 3.3.4 Habitats of Saccharum wild relatives in eastern South Africa…………………………...……27 3.4 Analytical approaches for assessing spatial and potential gene flow from Saccharum hybrids to their wild relatives…………………………………………………………………………………..…....…27 3.4.1 Relatedness of Saccharum wild relatives to Saccharum hybrids and one another…..…...28 3.4.2 Prevalence Saccharum wild relatives in Saccharum cultivation areas…………………......28 3.4.3 Spatial overlap of Saccharum wild relatives with Saccharum cultivation areas….……..….28 3.4.4 Proximity of Saccharum wild relatives to Saccharum hybrids in Saccharum cultivation areas…………………………………………………………………………………………..………….….29 3.4.5 Potential gene flow from Saccharum hybrids to their wild relatives…………….…….….…..29 3.4.6 Dispersal potential of Saccharum wild relatives across the study area…………...………..30 3.4.7 Flowering times of Saccharum hybrids and their wild relatives……………………...…….…30 3.4.8 Likelihood scores of factors analysed for spatial assessment and potential gene flow from Saccharum hybrids to their wild relatives……………………………………………….………….…....31 3.5 References……………………………………………………………………………….…….……….32 Chapter 4: Study Area…………………………………………………..……………………….……….37 4.1 Agricultural activities………………………………………………………………………….………..37 4.2 Commercial cultivation of sugarcane………………………………………………………………..37 4.3 Biomes, bioregions and conservation areas……………………………………..……….….…..…37 4.3.1. Biomes………………………………………………………………….……….……….………...37
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