Resistance to Fusarium basal rot and response to arbuscular mycorrhizal fungi in Allium

Onion (Allium cepa L.) cultivation in low input and organic farming systems is hampered by Fusarium basal rot (FBR) and the limited ability of onion to take up nutrients like phosphorus. The symbiosis with arbuscular mycorrhizal fungi (AMF) contributes to plant acquisition of phosphorus, among other benefits. This PhD research studied the potential contributions from A. fistulosum and A. roylei to breed onion cultivars with resistance to FBR and enhanced benefit from the symbiosis with AMF. The genetic basis of these traits was studied in an A. cepa x (A. roylei x A. fistulosum) population. A collection of Fusarium isolates was analysed using AFLP markers. The most abundant species was F. oxysporum (with isolates clustered in two clades) followed by F. proliferatum. The Allium species were screened for FBR resistance using one F. oxysporum isolate from each clade, and one F. proliferatum isolate. Allium fistulosum showed high levels of resistance to these three isolates and A. roylei intermediate levels of resistance. High level of resistance from A. fistulosum was dominantly expressed in the A. roylei x A. fistulosum hybrid and the tri-hybrid population. A molecular linkage map based on AFLP markers was developed for the A. roylei x A. fistulosum hybrid. A QTL for FBR resistance from A. roylei was mapped on chromosome 2, and a QTL from A. fistulosum on chromosome 8. Each QTL separately had significant effect on FBR but did not confer complete resistance, thus more QTLs from A. fistulosum remain to be discovered. Regarding Allium-AMF relationship, a first step of research studied genetic diversity and colonization levels of naturally occurring AMF, comparing organic and conventional onion farming in the Netherlands. All plants were colonized with 60% average arbuscular colonization. Onion yields were positively correlated with colonization. AMF phylotypes were identified by rDNA sequencing. The number of phylotypes per field ranged from one to six. Two Glomus-A phylotypes were the most abundant, whereas other phylotypes were infrequently found. Organic and conventional fields had similar number of phylotypes and Shannon diversity indices. A few organic and conventional fields had larger number of phylotypes, which suggested that specific environmental conditions or agricultural practices influence AMF diversity. The genetic basis for the response to AMF in the tri-hybrid Allium population was evaluated in two independent greenhouse experiments. The weights of mycorrhizal plants were significantly larger than the non-mycorrhizal plants. Mycorrhizal Responsiveness (MR) was negatively correlated with plant weight in the non-mycorrhizal condition and was therefore considered unsuitable as an index for plant breeding purposes. Two new indices were proposed: mycorrhizal benefit (MB) and mycorrhizal breeding value (MV). Tri-hybrid genotypes showed transgressive segregation for plant weight, MB, and MV. Two QTLs from A. roylei for these traits were detected on chromosomes 2 and 3. A QTL from A. fistulosum for MV (but not MB), plant weight and the number of stem-borne roots was found on linkage group 9. Positive correlations between plant weight, rooting system and benefit from mycorrhiza were observed, which open prospects to combine these traits in the development of more robust onion cultivars.