Mapping of Quantitative Trait Loci Controlling Seedling Growth in Bunching Onion (Allium fistulosum L.)

Abstract

Vigorous seedling growth is a desirable trait for machine-assisted transplanting using a plug nursery system in bunching onion. This study was undertaken to identify the quantitative trait loci (QTLs) controlling seedling growth and to elucidate the modes of gene action of the QTLs. Plant material was a set of reciprocally backcrossed populations (BC 1 ). These were produced from 2 inbred lines derived from the Senju group and Kujo group. Two corresponding BC 1 maps were constructed by adding co-dominant simple sequence repeat (SSR) markers to the previously reported amplified fragment length polymorphism (AFLP) based maps. Fresh weights of seedlings were measured in 3 seasons using BC 1 S 1 families. Remarkable heterosis was observed in F 1 and many BC 1 S 1 families. Many QTLs for seedling weight were detected on the 2 maps by composite interval mapping. The phenotypic variation explained by a single QTL was less than 25%. Of these, 3 QTLs on 3 linkage groups are considered to be consistently effective across different environmental conditions because they were detected in different years and seasons. Most QTLs were detected on one map, but were not detected in a corresponding region on the other map; however, the degree of dominance at each locus was calculated to determine whether the locus shows overdominance. Overdominance was observed at some loci, and the other loci showed an additive and dominant effect. It is suggested that remarkable heterosis for seedling weight in the present population is based on the accumulation of dominant and overdominant gene actions.

AlliumMap-A comparative genomics resource for cultivated Allium vegetables

“…The Ms locus conditioning restoration of male-fertility in S cytoplasm is the basis for most F 1 hybrid production in onion, and has been mapped to this chromosome [ 7 ], and we observed association of markers in this region with seed yield from selfed F 2 , due to segregation at Ms , plants (McCallum et al, unpublished observations) in the 'W202A x Texas Grano 438' family used to map bulb composition QTL [ 9 , 10 ]. QTL have been reported in an adjacent chromosomal region for onion bulb composition [ 45 ] and A. fistulosum seedling vigor [ 13 ]. This comparative view allows ready comparison between the QTL locations and linked markers from these studies and provides potential markers for more detailed studies of these regions in these or other genetic backgrounds.…”

“…These maps were used to conduct QTL analysis for seedling vigor [13]. More recently Tsukazaki and colleagues [14] reported a further A. fistulosum map based on A. fistulosum genomic SSR markers and onion EST-derived SNP and SSR markers, providing further scope for comparative studies between onion and A. fistulosum genomes.…”

“…The breeding systems of A. fistulosum have facilitated development of several larger mapping pedigrees and detailed genetic maps based initially on SSR and AFLP markers [ 11 , 12 ]. These maps were used to conduct QTL analysis for seedling vigor [ 13 ]. More recently Tsukazaki and colleagues [ 14 ] reported a further A. fistulosum map based on A. fistulosum genomic SSR markers and onion EST-derived SNP and SSR markers, providing further scope for comparative studies between onion and A. fistulosum genomes.…”

Phylogenetic and phylogenomic studies of wild onions (Allium, Amaryllidaceae) at three taxonomic scales

“…Allium by no means characterizes a model system that can be easily subjected to genetic analysis in order to understand the inheritance of phenotypic traits; it takes between one and three years for most species to reach reproductive maturity, and the size of nuclear genome is among the largest in angiosperms (Bennett and Leitch, 2011). Among economically important cultivated species, however, these impediments have not stood in the way of genetic analysis using quantitative trait loci (Ohara et al, 2009), and monosomic addition lines (Shigyo et al, 1996).…”