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Potato onions (Allium cepa var aggregatum G. Don) are multiplying or aggregating onions, very similar to shallots and have been historically cultivated throughout Europe. Currently in Northern Europe they are maintained in home gardens and ex situ field collections. Potato onions are primarily vegetatively propagated, however in Estonia, near Lake Peipsi, this species has been propagated by seed since the seventeenth century. There is increasing interest in Northern Europe in utilizing this germplasm in organic and/or sustainable farming systems. The genetic diversity and relationship between and within European potato onion collections is unclear. From historical records it is known that cultivation, exchange and trade of potato onion has occurred throughout Europe for hundreds of years. This study utilised molecular markers to assess genetic diversity, duplication of genotypes and relationships among and between Nordic, Baltic, Czech and Croatian potato onion collections. Of 264 accessions, 80 catalogued as unique had identical genotypes with one or more other accessions, and are putative duplicates. The genetic diversity within two Estonian sexually propagated accessions was comparable to that found in all of the vegetatively propagated accessions. Accessions from the Nordic countries grouped together genetically, as did Latvian and Lithuanian accessions. Croatian accessions were genetically separated. These genetic relationships suggest historical movement of potato onion germplasm in North-Eastern Europe. The results, in conjunction with other passport and characterization data, can assist in the development of potato onion core collections, facilitating the conservation and utilization of valuable potato onion genetic resources.

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.

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 phyl

Keywords: Allium cepa , Allium roylei , Japanese bunching onion, introgression breeding, organic agriculture, linkage map, AFLP, QTL analysis, Arbuscular Mycorrhizal Fungi, in vitro multiplicationA massive amount of synthetic fertilizers is needed to grow onions ( Allium cepa L.) due to their meager and inefficient root system. While the sustainability of such high-input systems is being questioned, low-input systems, such as organic agriculture, are gaining ground. For organic agriculture, plants have to be good nutrient scavengers. Therefore, productivity and stability of onion production in organic systems can be problematic. Plant breeding can improve the efficiency of onion roots, but breeding relies on available variation and there was no information about that in onions or in Allium. The aim of this thesis was to search for variation in root morphology in onion and in its allied species A. fistulosum L., to understand the role this variation could play in organic agriculture and to perform a genetic analysis of root traits. The variation found in root traits in onion was limited, although old onion cultivars had a higher root length density than modern ones. Huge variation was observed betweenonionand A. fistulosum . A. fistulosum developed substantially more stem-borne and lateral roots and, consequently, a much denser root system. Experiments carried out in an organic farm revealed that onion explored a smaller volume of soil and had a lower root density than A. fistulosum . In addition, onion, contrary to A. fistulosum , showed a reduction in total and fine root density when cultivated in a soil with low nitrogen content. It was also demonstrated that A. fistulosum was very responsive to indigenous and inoculated AMF (50 to 60% increase in both shoot biomass and root length). A Quantitative Trait Locus (QTL) analysis was done on the genetic linkage map of the progeny from the cross A. cepa x ( A. roylei x A. fistulosum ) to locate some of the genes respons