Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity

Abstract

The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23xAC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants.

Genetic mapping of a major gene affecting onion bulb fructan content

“…The EST-SSR marker ACM171, which is closely linked to the sucrose transporter RFLP locus API66C-E5-6.7/9.5 on chromosome 5 (Martin et al 2005), showed significant association with bulb DM (Table 4), as reported previously (Galmarini et al 2001). Only weak association of the chromosome 3 acid invertase locus API89 with bulb composition was observed (Table 4), in contrast to observations in 'BYG15-23 · AC43' (Galmarini et al 2001;Havey et al 2004).…”

“…Using variance components estimated with the REML analysis, narrow-sense heritability was calculated as described by Timmerman-Vaughan et al (2005). QTL analysis of total fructan content in the population 'BYG15-23' · 'AC43' was carried out with marker data used to construct the latest onion linkage map (Martin et al 2005) and phenotypic data from replicated field trials reported previously .…”

“…Chloroform:sec octanol (24:1) was used instead of phenol/chloroform/isoamyl alcohol and tissue homogenisation and DNA pellet washes were performed as described earlier (McCallum et al 2001b). EST-SSR and SSCP markers were developed and evaluated as described previously (Kuhl et al 2004;Martin et al 2005;McCallum et al 2001b). Primer sets not reported in these previous publications are shown in Table 1.…”

“…Allium fistulosum-shallot (A. cepa L. aggregatum group) alien addition line stocks (Shigyo et al 1996) were used for chromosomal assignment of markers as described by Martin et al (2005).…”

“…Analysis of phenotypic variation in several independent pedigrees showed common patterns of variation, suggesting segregation of a major gene affecting fructan content. Following identification of a linked marker, the onion linkage map (Martin et al 2005) was used to confirm that a major gene in the same genome region was the main determinant of fructan content in all these populations.…”