Abstract

Ivermectin is an anthelmintic drug commonly used in ruminant animals to combat nematode infestations. However, after three decades of intensive use, Ivermectin resistance is now quite widespread. Resistance to anthelmintic drugs is also seen in humans and it has been suggested that Ivermectin may be inducing genetic selection pressure on Onchocerca volvulus, a nematode that causes onchocerciasis; also known as “river blindness” in humans. In this context, the development of new alternatives to control nematode infections is needed. Onobrychis viciifolia, commonly known as sainfoin, is a medicinal leguminous tanniferous forage crop. It has beneficial nutraceutical, anti-bloating and anti-parasitic, activity. It also has indirect environmental benefits by reducing methane emissions from ruminant livestock, when used in their feed, and improving protein uptake due to ‘rumen-escape’ protein metabolism. Sainfoin is therefore a possible alternative to alfalfa or clover in animal nutrition, but since the 1950’s, it has not benefited from genetic or agronomic improvements and farmers are reticent to seriously consider it as an alternative.

This research is focused on targeting the key issues limiting sainfoin cultivation; it is very difficult to establish and farmers often experience poor yields in the first year. In order to develop tools necessary for systematic genetic improvement, we have undertaken an in-depth genetic characterisation of O. viciifolia germplasm. Key molecular markers that will enable Marker Assisted Selection (MAS) have been identified. Agronomic limitations have been addressed by screening potential herbicide treatments to aid its establishment. We have utilised RNA -sequencing to generate a de-novo transcriptome assembly and enable gene discovery, identification, annotation and subsequent development of a suite of markers, which will help selection of germplasm. In this study, we have developed the first comprehensive annotation of sainfoin and so far have identified nearly 3,500 Simple Sequence Repeat (SSR) markers that will be available for further breeding programs. In the herbicide trial, a panel of nine herbicide treatments were tested. Biochemical analyses were also undertaken to assess qualitative differences in the harvested forage crop and suitable herbicides for early establishment were identified.