Department of Genetics

Honours class 2024 Shines

Genetics Research Explores Conservation, Food Security, and Human Health Challenges

In the prestigious Jan Mouton Building, the honours students in our Genetics Department showcased their final research projects on November 20, 2024, marking the completion of a challenging and transformative year. The modern lecture hall, with its state-of-the-art design and warm ambiance, provided the perfect setting for a day filled with intellectual curiosity and academic achievement.

The day began with a motivating speech by our Head of Department, Mr. Willem Botes, who inspired the students to reflect on their academic journey and the significance of their contributions to genetics research. The presentations that followed reflected the broad scope and impact of the department’s work. Some students focused on population genetics, studying species like sharks and dusky kob to better understand genetic diversity and conservation strategies. Others tackled challenges in agriculture and food security, working on crops such as wheat, beans, citrus, mushrooms, and grapevine to improve yields, resilience, and nutritional value. Meanwhile, human genetics research brought vital insights into health issues, focusing adolescent obsessive-compulsive disorder (OCD) and intervertebral disc degeneration (IDD) in Southern African populations.

Over the past six months, these students immersed themselves in complex research, bridging theoretical knowledge with practical applications. From acquiring bioinformatics skills (Sequence analysis, phylogenetics, AlphaFold, MEGA, etc.) to conducting wet-lab experiments such as PCR, qPCR, RNA, DNA extraction, and gene cloning, they honed a diverse set of technical and analytical skills. This rigorous research phase followed an intense first semester of theoretical training, covering advanced modules such as Molecular Techniques, Human and Animal Genetics, Genetic Data Analysis, Statical analysis, Scientific Writing, Plant Genetics + Crop Improvers, and Genomics.

As the day progressed, the initial nerves and tension in the room gave way to growing confidence and excitement. The professionalism displayed by the students was evident, and their passion for their work shone through with every presentation. By the afternoon, the atmosphere was vibrant and celebratory. While some of these graduates have expressed a strong interest in pursuing Master’s degrees to further their academic careers, others are eager to apply their skills and knowledge in the working world, stepping into industries where their expertise will make a meaningful impact. Both paths are a testament to their dedication and the solid foundation they have built here in the Genetics Department. The day concluded with a speech by our Honours Coordinator, Dr. J. Lashbrook, who commended the students for their hard work. The honours class of 2024 has proven their commitment to excellence, overcoming challenges and growing as a scientist but also as an individual.

Congratulations to the honours class of 2024! Your journey has been a challenging one, but you have emerged stronger, more skilled, and ready to take on the next chapter. The Genetics Department is immensely proud of you and looks forward to seeing all that you will achieve in the future.

Composed by The Department Scribe – M. le Roux

 

Master’s Students Showcase Expertise in Genetics Research

Master’s Students Showcase Expertise in Genetics Research Ahead of December Graduation

On the morning of November 21, 2024, the Genetics Department hosted the defense presentations of MSc students preparing for their December graduation. The atmosphere in the venue was a mix of anticipation and pride, as each candidate confidently stepped forward to present the culmination of two years of dedicated research. Their presentations were a testament to their hard work, expertise, and deep understanding of their respective fields.

The presentations began with M O’Meara, who presented their research on identifying optimal genetic markers for predicting quantitative measures in neuropsychiatric disorders. This research was conducted under the supervision of Dr Nathaniel McGregor, the project showcased indeed contributed to our current understanding complex traits related to mental health. Following this, J Dove took the stage to present their work on developing a CRISPR-based detection system for Candidatus Liberibacter africanus, a critical advancement for tackling diseases affecting the agricultural industry. This research was conducted under the supervision of Professor Johan Burger.  HC van der Westhuizen followed with an impressive presentation on the assembly and annotation of the genome of the sea urchin, Tripneustesgratilla. Supervised by Professor Clint Rhode, their work highlighted the importance of genomic tools in understanding marine biodiversity and its implications for environmental and evolutionary research. Concluding the session, K Haridass presented their study on exploring the abiotic resistance traits of the local wild wheat relative, Thinopyrum distichum–supervised by our head our head department Mr Willem  Botes, this research contributed valuable insights to improving crop resilience in the face of climate challenges.

Throughout the session, the students demonstrated a remarkable command of their research, confidently explaining complex methodologies, findings, and implications. At the end of each presentation, they faced a series of advanced genetic questions from the audience and examination panel, designed to test their depth of understanding and ability to think critically. With poise and precision, they answered these questions, further reinforcing their status as emerging experts in their respective fields.

These defense presentations were not only an academic milestone but also a celebration of the journey each student had undertaken. The Genetics Department is immensely proud of their achievements and looks forward to the impact they will undoubtedly make in their future endeavors.

Composed by The Department Scribe – M. le Roux

 

High Office and Awards for Genetics Staff and Students

Academic staff and students of the Department of Genetics have been attending several scientific meetings and receiving honours and awards, reaffirming the quality and standing of research in the Department.

At the Aquaculture Association of Southern Africa’s conference, hosted at Stellenbosch (9- 13 September 2024), Ms Samantha Joao (PhD candidate in Genetics, Supervisor Prof. Clint Rhode) received the Best Student Oral Presentation Award for her talk, entitled: “Examining growth in dusky kob (argyrosomus japonicus) via differential transcriptomic analysis of gill tissue”.

Doctoral candidate Ms Jessica Winn (Supervisor: Prof. Aletta Bester-van der Merwe) and recent doctoral graduate Dr Kelvin Hull (Supervisor: Prof. Clint Rhode) was awarded the South African Genetics Society’s(SAGS) Postgraduate Award for Best Published Paper in the categories for Population & Evolutionary Genetics, and Functional & Developmental Genetics, respectively.

Ms Winn for her paper, “A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae” published in the journal Genomics this year; and Dr Hull for his work entitled, “Gene expression differentials driven by mass rearing and artificial selection in black soldier fly colonies”, published in the journal Insect Molecular Biology last year.

The awards where formally presented at the gala dinner of the joint conference of the South African Genetics Society and the South African Society for Bioinformatics (SASBi), Bio2024, hosted by the University of Pretoria (23-25 September 2024).

The SAGS Postgraduate Awards entails a cash prize, free conference registrations, and the prestigious Hofmeyr-Van Schaick Medal (Bronze). Prof. Clint Rhode was also re-elected, for a second term in office, as the President of the SAGS at the society’s general meeting, also held during the conference.

The Agrication Programme (Pilot)

The Agrication Programme was piloted in 2023 as a programme exposing learners to agricultural research environments and technologies. Two agricultural research environments hosted 125 learners over four practical demonstrations which linked curriculum topics teachers from participating schools were struggling with (figure 1). A Community of Practice for Agricultural Educators was also initiated as an evaluator platform for relevant learner and teacher development programmes (figure 2).

Figure 1: From left to right: Agricultural Sciences and Agricultural Management Practices learners from Kayamandi High School undergoing a practical demonstration on soil properties and greenhouse production (hosted by the Department of Agronomy, HortiDemo Centre); Kayamandi High School Agricultural Sciences learners exposed to a tissue culture demonstration; Soneike High School participating in a tissue culture demonstration. All tissue culture demonstrations were hosted at the Institute for Plant Biotechnology and facilitated through the Plant Growth Promoting Substances Research Group led by Dr Paul Hills.

Figure 2: The initiated Community of Practice of Agricultural Educators. From left to right SU Collaborative workshop facilitators (Mhlengi Khambule, Dr. Estelle Kempen, Ms. Olianda Zhuwawo) and agricultural sciences educators, Ms. Akhtari Abbas, Ms. Sinako Matshoba, Mr. Sinethemba Mdlambuzi from Soneike , Kwamfundo and Iqhayiya High Schools. Picture by Mr. Cobus Rabe (Longacres
High School).

A. Sustainable Agriculture mini-lecture
Four mini lectures were presented to a total of 120 grade 11 students from Kayamandi High School and Soneike High School. The presentations were used to introduce demonstrations (Objective B and C) hosted by the Institute for Plant Biotechnology (tissue culture programme) and the Department of Agronomy (soil and crop management) respectively. Learners were varyingly engaged in the minilecture, some stating that they had covered some of the topics in class while others were seemingly more interested in engaging with the practical elements to follow. A suggestion was to have the minilecture recorded and shared with the teachers and learners beforehand, in so doing using this as a
preparatory tool as well as allow for more time for the demonstrations.

B. Tissue culture programme
The institute for Plant Biotechnology hosted grade 11s from Kayamandi High School and Soneike High School for tissue culture demonstrations on the 28th July and 25th August 2023 respectively. An article descriptively reported on the demonstrations and can be found here. Two out of the three intended schools were able to attend. We were unable to confirm a date with Somerset College despite numerous attempts. A third school will however be hosted, depending on progress made on the other objectives.

C. Industry exposure sessions
The department of Agronomy hosted two grade 11 cohorts from Kayamandi High School in December 2022 and 26th May 2023 respectively. The HortiDemo Centre was the primary demonstration site following the mini-lecture presented in the AgroHub. An article descriptively reported on the exposure sessions and demonstrations. The article can be found here. The latest demonstration also showcased the DIVAGRI solar desalination greenhouse demo unit. Prospects for on-farm exposure visits to DIVAGRI participating farms around Stellenbosch are currently being discussed.

D. Parent and teacher inquiry workshops
A collaborative workshop was held at the AgroHub in October 2023. Teachers from 7 High Schools in the Western Cape participated in the workshop. The workshop sought to identify challenges faced by the teachers in the delivery of the Agricultural Sciences subject, and how our programme can best support them. The teachers identified several challenges and collaborative support approaches. An
outcome was the initiation of the Community of Practice (CoP) for Agricultural Educators (currently hosted on WhatsApp) which will serve as a useful knowledge and perspective-sharing platform as well as a school-based programme critique. The CoP will also serve as an ideal platform to identify teacher training needs. It was difficult to attain parent perspectives, teachers however recommended using Grade 9 subject selection meetings to interact with parents on this topic.

E. Community of Practice in Sustainable Development Policy
The initiation of the senior and postgraduate student focused Community of Practice (CoP) was challenged by the graduation of the early adopting students. However, students from the Department of Agronomy and Institute for Plant Biotechnology showed interest in getting involved, particularly in the demonstrations and exposure sessions. Developing terms of reference for the different CoP working groups is currently under way, we hope to use these as part of a call to students to join. This way interested students are aware of what to expect beforehand. Progress has also been made with collaborating with the Education Faculty, with two senior staff from different departments and a
student teacher society interested to getting involved.