Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum)

Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. To establish a genetic basis for molecular breeding of bunching onion, we isolated 1,796 simple sequence repeat (SSR) clones by large-scale sequencing of SSR-enriched genomic DNA libraries. Of these, 1,331 (74.1%) contained (GT) _n repeats (n > 5), while 314 (17.5%) were (GA) _n -containing clones. The average number of SSR repeats was 10.5 and 10.4 in the (GT) _n - and (GA) _n -containing clones, respectively. In a sample of five bunching onion inbred lines, an average of 3.2 alleles were detected in the 100 SSR loci investigated, with the polymorphic information content averaging 0.55. These results indicate that bunching onion SSRs are very rich sources of highly informative genetic markers.     

Haploid induction from F1 hybrids between CMS shallot with Allium galanthum cytoplasm and common onion by unpollinated flower culture

The induction of haploid plants from F₁ hybrids between CMS shallot with Allium galanthum cytoplasm and common onion was examined. Starting with 535 unpollinated flowers cultured in B5 medium 25 seedlings from part henogenetic embryos were obtained of which 13 seedlings survived. Eleven seedlings were determined as haploid plants (2n = x = 8) and 2 seedlings were doubled haploid plants (2n = 2x = 16). All haploid and doubled haploid plants preserved chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) from A. galanthum. Segregation in different characters was observed among the haploid plants. The haploid and doubled haploid plants exhibited the different combinations of genes from shallot and common onion. Crossing of the doubled haploid plants with other shallot strains, common onion cultivars or related species may produce excellent F₁ hybrids for bulb production. This revised version was published online in July 2006 with corrections to the Cover Date.     

Chromosome and cytoplasm analyses of somatic hybrids between onion (Allium cepa L.) and garlic (A. sativum L.)

Chromosomes and cytoplasms were analyzed in two lines of a somatic hybrid between onion (Allium cepa L.) and garlic (A. sativum L.). One line of the somatic hybrid had 40 chromosomes and the other 41chromosomes. Genomic in situhybridization successfully revealed the chromosome constitution of the two lines. One line had 20 chromosomes from onion and17 chromosomes from garlic, and the other had 21 chromosomes from onion and 17chromosomes from garlic. Interestingly, both lines had three chimeric chromosomes. PCR-RFLP analyses of chloroplast and mitochondrial DNAs of both lines showed that these were identical to the onion parent. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic mapping of AFLP markers in Japanese bunching onion (<Emphasis Type="Italic">Allium fistulosum</Emphasis>)

Summary The first genetic linkage map of Japanese bunching onion (Allium fistulosum) based primarily on AFLP markers was constructed using reciprocally backcrossed progenies. They were 120 plants each of (P₁)BC₁ and (P₂)BC₁ populations derived from a cross between single plants of two inbred lines: D1s-15s-22 (P₁) and J1s-14s-20 (P₂). Based on the (P₂)BC₁ population, a linkage map of P₁ was constructed. It comprises 164 markers – 149 amplified fragment length polymorphisms (AFLPs), 2 cleaved amplified polymorphic sequences (CAPSs), and 12 simple sequence repeats (SSRs) from Japanese bunching onion, and 1 SSR from bulb onion (A. cepa) – on 15 linkage groups covering 947 centiMorgans (cM). The linkage map of P₂ was constructed with the (P₁)BC₁ population and composed of 120 loci – 105 AFLPs, 1 CAPS, and 13 SSRs developed from Japanese bunching onion and 1 SSR from bulb onion – on 14 linkage groups covering 775 cM. Both maps were not saturated but were considered to cover the majority of the genome. Nine linkage groups in P₂ map were connected with their counterparts in P₁ map using co-dominant anchor markers, 13 SSRs and 1 CAPS.     

Independent segregation of two isozyme markers and inter-plant differences in nuclear DNA content in the interspecific backcross (Allium fistulosum L. × A. cepa L.) × A. cepa L.

Summary From backcrosses of three interspecific hybrids (A. fistulosum x A. cepa) with a. cepa 14 diploid and 2 triploid plants were recovered.In this BC1 population introgression of A. fistulosum genetic material into the A. cepa nuclear genome was studied using two isozyme markers: Got-1 and Got-2. Both loci carried two alleles. A. cepa was monomorphic for both markers. A. fistulosum was polymorphic for Got-2. Based on their Got isozyme pattern seven out of the 14 diploid BC1 plants had a recombinant genotype. The loci appeared to be unlinked. Differences were observed in nuclear DNA contents between the diploid BC1 plants, indicating that gametes produced by the interspecific hybrids contained different combinations of chromosomal material from A. cepa and A. fistulosum.Abbreviations Adh alcohol dehydrogenase - Got glutamate oxaloacetate transaminase - Idh isocitrate dehydrogenase - Pgi phosphoglucoisomerase - Pgm phosphoglucomutase     

A new method for selecting cytochimeras by the maximum number of nucleoli per cell in Allium wakegi Araki and A. fistulosum L.

Summary A new method for determining ploidy levels in cytochimeral plants was developed by examining the maximum number of nucleoli per cell. Colchicine-treated plants of Allium wakegi Araki and A. fistulosum L., which have different ploidy levels in the first (LI), the second (LII), and the third (LIII) germ layer, were used together with untreated 2-2-2 plants of the same species. Nucleoli in guard cells for LI and in mesophyll cells for LII were stained in a 50% AgNO₃ aqueous solution at 55° C for three hours under dark, humid conditions. In both species the ploidy levels of LI determined by the maximum number of nucleoli per guard cell accorded well with those determined by guard cell length. In A. fistulosum the ploidy levels of LII determined by the maximum number of nucleoli per mesophyll cell clearly agreed with those determined by pollen size. This method provided more precise and efficient identification for LI and LII ploidy than the conventional methods of using guard cell length for LI and pollen size for LII.     

Introgression of leaf blight resistance from Allium roylei Stearn into onion (A. cepa L.)

Summary Segregation analysis in BC₁ and F₂ progenies from interspecific hybrids between Allium roylei and A. cepa demonstrated that leaf blight resistance is conditioned by one single dominant gene from A. roylei. This gene, designated Bs ₁ , was unlinked to the genes Pd ₁ and Pd ₂ determining downy mildew resistance. The prospects of exploiting A. roylei as a source for disease resistances in onion breeding are very promising.     

Variation in pollen viability in the onion (Allium cepa L.)

Summary The pollen viability of onions in a glasshouse was recorded from May to October 1975, using the fluorescein test. The average viability was 60–95% for most of this period but fell to less than 1% during the last two weeks of August. There was great variation in pollen viability between anthers within a flower and between flowers within a head. Attempts to induce pollen inviability by low temperature treatments at various stages of inflorescence development were unsuccessful. Low levels of pollen inviability appear to be a characteristic feature of onions, but the high level of inviability which was found both in this and in a previous season was associated particularly with the August period.     

Pollen competition in onion (Allium cepa L.)

Summary Pollen mixtures with two components, one of which carried a dominant marker gene for red or white bulb skin colour, were used to pollinate flowers on onion umbels from several cultivars. Scoring progenies for the marker revealed that pollen components differed in their ability to effect fertilization, suggesting that gametophytic competition can occur in onions. In many cases, self-pollen appeared to have a competitive advantage over cross-pollen. Both of the male components and the female parent played a part in determining the final ratio obtained from a mixed pollination.Crossed seeds were slightly but significantly heavier than selfed seeds in nine out of ten umbels studied.     

Pre- and post-fertilization barriers to backcrossing the interspecific hybrid between Allium fistulosum L. and A. cepa L. with A. cepa

Summary To facilitate the introgression of desirable traits of Allium fistulosum into the genome of A. cepa, several accessions of the hybrid between these species were pollinated with A. cepa as the recurrent parent, and in vitro ovary and ovule culture were performed to obtain an increase in the recovery of backcross progeny. Compared to the results obtained from seed development in planta, the increase in the number of backcross progeny was generally very limited, and in some cases even a decrease was found. Raising the sucrose concentration in the ovary culture medium resulted in a higher frequency of ovules developing back seed coats but this was not followed by an increase in the number of backcross progeny obtained. Pollen tube growth of A. cepa was disturbed in the styles of the interspecific hybrids. Per ovule, frequencies of micropylar penetration exceeded frequencies of backcross progeny only to a limited extent. Hence, it was concluded that in the tested interspecific hybrid accessions the attainable gain in viable backcross progeny by the application of in vitro culture techniques is limited by strong pre-fertilization barriers acting at the level of stylar incongruity.     

Chloroplast-DNA variation in the wild and cultivated olives (Olea europaea L.) of Morocco

The male sterile plants that segregated in a BC₅F₂ of `C. sericeus × C. cajan var. TT-5' population were maintained by sib mating. The male sterile plants were crossed with ICPL-85012.Approximately 50% of the F₁ plants were sterile. F₂ plants derived from the fertile F₁ plants did not segregate for male sterility. The reciprocal hybrid i.e. ICPL-85012 × Fertile derivatives from C. sericeus × TT-5, did not express male sterility. However, among the 12 F₂ plant to row progenies, two segregated 25% male sterile plants and remaining 10 did not segregate. The segregation pattern in subsequent progenies revealed that the sterility was under control of a single recessive allele. Studies on the backcross and their BC₁F₂ and BC₁F₃progenies revealed another sterility gene which was found to be dominant in inheritance. This paper shows that what was thought to be cytoplasmic male sterility from C. sericeus cytoplasm is actually a single dominant gene possibly acting in concert with a single recessive gene to mimic cytoplasmic male sterility. This revised version was published online in July 2006 with corrections to the Cover Date.     

SSR-tagged breeding scheme for allogamous crops: a trial in bunching onion (<Emphasis Type="Italic">Allium fistulosum</Emphasis>)

In several autogamous and vegetatively propagated crops, DNA markers have been used for cultivar identification. However, allogamous crops such as bunching onion (Allium fistulosum L.) are recalcitrant to marker-aided cultivar identification, as well as hybrid seed purity tests, due to the high degree of genetic heterogeneity within each cultivar. To aid cultivar identification and ensure its accuracy in bunching onion, we proposed the “SSR-tagged breeding” scheme in our previous study. The feasibility of this scheme was investigated here using a landrace of bunching onion with two populations tagged with two or four selected SSR markers. Compared with a control population, no significant differences were detected in the agronomic traits of the SSR-tagged populations. The targeted SSR loci were genetically uniform within each population whereas other loci maintained high heterogeneity. These results demonstrate that the SSR-tagged breeding scheme, even with a very small number of markers, is efficient for the identification of newly bred cultivars, and consequently for F₁ purity tests, in allogamous crops in which inbreeding depression is as severe as in bunching onion.     

Limitations of PCR‐based molecular markers to identify male‐sterile and maintainer plants from Indian onion (Allium cepa L.) populations

The main aim of this study was to validate PCR markers for determining cytoplasm and genotypes at the Ms locus in short‐day onion. Three cytoplasmic (OSN, MKFR and accD) and four nuclear (OPT, jnurf13, AcSKP1 and AcPMS1) markers were employed. Sel. 121‐1 had 100% S cytoplasm, whereas Sel. 121‐2, ‘Pusa Red’ and ‘Pusa Madhavi’ had 88%, 33% and 17% S cytoplasm, respectively. ‘Early Grano’ and ‘Pusa Riddhi’ did not possess S cytoplasm. Observations in 33 commercial varieties revealed two with sterile (S) cytoplasm. Nuclear markers were not found in linkage disequilibrium with the Ms locus, and the constitution of Ms alleles by OPT was different from other three markers, which were in conformity with each other. The other three markers predicted that most of the plants should be homozygous recessive. Anther colour also did not confirm the sterility status. It can be concluded that accD may be used for cytoplasm determination based on the ease of its use. For the Ms locus tagging, more markers are needed to be evaluated to isolate maintainer lines from open‐pollinated populations.     

Molecular and biological studies on male sterile cytoplasm in Cruciferae. II. The origin of Ogura male sterile cytoplasm inferred from the segregation pattern of male sterility in the F1 progeny of wild and cultivated radishes (Raphanus sativus L.)

Summary To determine the origin of Ogura male sterile cytoplasm in radish (Raphanus sativus L.), wild and cultivated radishes were crossed. Three types of progeny resulted from the F₁ hybrids between the wild radish from Kushikino with Ogura-type mtDNA and the cultivars (Uchiki-Gensuke or Comet). The segregation patterns of the male sterility were compared with those of Ogura cytoplasm. The male sterility induced in the F₁ hybrid was maintained by crossing with Uchiki-Gensuke, that maintains Ogura male sterility. In the two types of progeny, in which Comet (a restorer of Ogura cytoplasm) was used as one of the parents, both fertile and sterile plants segregated at the predicted ratio on the assumption that a single dominant fertility restoring gene exists in the restorer. From these results, we concluded that the Ogura cytoplasm is identical to that of the wild radish, and the former originated in a population of Japanese wild radish.     

Genetic studies on the interspecific cytoplasm substitution lines of japonica varieties of Oryza sativa L. and O. glaberrima Steud.

Summary Interspecific cytoplasm substitution lines of Oryza sativa and O. glaberrima, i.e. (sativa)-glaberrima and (glaberrima)-sativa, have been bred by means of successive backcrosses, using three japonica varieties of sativa and two glaberrima strains.In all the six substitution lines with the cytoplasm of the glaberrima strains, the fertility increased with succeeding backcrosses, and eventually completely fertile plants whith the characteristics of the parental japonica variety appeared. This indicates that the glaberrima cytoplasm exerted no effect on the genome manifestation of these japonica varieties. Of the five substitution lines with the cytoplasm of each of the japonica varieties, four lines produced male sterile (M.S.) plants only in the backcross generations. In the remaining substitution line with the cytoplasm of the japonica variety Akebono, there was simultaneous segregation for male sterile (M.S.) and pollen fertile plants bearing indehiscent anthers (ID.M.F.) in the backcross generations. In the compulsively selfed progeny of ID.M.F. plants, pollen fertile plants with dehiscent anthers (D.M.F.) occurred with M.S- and ID.M.F. plants. Morphologically, these three types were supposed to have the same genetic background as the glaberrima parent. It was established that D.M.F.-and ID.M.F. plants were homozygous and heterozygous for a dominant nuclear gene restoring pollen fertility, respectively, and the M.S. plants and the two glaberrima strains used in this study carried a recessive gene for pollen sterility in homozygous condition. The restorer gene was assumed to derive from the japonica variety Akebono. The expression of the restorer gene was of the sporophytic type. The pollen sterility of the substitution lines that possessed the cytoplasm of the japonica varieties was of cytoplasmon-genic nature.     

Linkage of downy mildew resistance genes Pd 1 and Pd 2from Allium roylei Stearn in progeny of its interspecific hybrid with onion (A. cepa L.)

Summary Male meiosis of the interspecific hybrid between Allium roylei and A. cepa is undisturbed relative to its parents. Based on meiotic data, A. roylei is concluded to be a closer relative of A. cepa than A. fistulosum. Segregation ratios for downy mildew resistance among BC₁ and F₂ progenies from the F₁ between A. roylei and A. cepa indicate the presence of two dominantly inherited, weakly linked nuclear resistance genes, Pd ₁ and Pd ₂, in A. roylei (recombination frequency 0.32±0.03). Presumably Pd ₁ and Pd ₂are the first genes described in Allium residing in one linkage group. The prospects of exploiting A. roylei in onion breeding seem very promising.     

Modified complementation test of male sterility mutants in pepper (Capsicum annuum L.): preliminary study to convert male sterility system from GMS to CMS

The male sterility system in hybrid seed production can eliminate the cost of emasculation and ensure seed hybridity through avoidance of self pollination. GMS and CMS are two types of male sterility system that currently employed in pepper breeding. Conversion from GMS to CMS will increase the male sterility proportion of female parent from 50 to 100%. In this study, segregation analysis of four male sterile mutants consisting of one CMS mutant (CA1) and three GMS mutants (GA1, GA3 and GA4) showed that each had single recessive gene inheritance. A modified complementation test was performed by replacing male sterile mutants with their maintainer line as male parent. The nuclear restorer gene for CMS was independent of all nuclear restorer genes for GMS and all nuclear restorer genes for GMS were independent each other. Further observation on CMS and GMS male sterility loci revealed that GA1 and GA3 had mutated in both nuclear restorer genes for CMS and GMS, while CA1 and GA4 each carried mutation in single male sterility system of nuclear restorer gene for CMS and GMS, respectively. Conversion from GMS to CMS in the case of lines carried mutations in both sterility systems required only S-type cytoplasm donor, while lines carried mutation in single nuclear restorer gene for GMS required not only S-type cytoplasm but also rf allele donors. The important finding is the broader function of maintainer line in certain male sterility system that can be used as a maintainer or restorer line for other male sterility systems. We also confirmed that line CC1 is the general restorer for both CMS and GMS systems.     

Characterization of CMS and maintainer lines in indica rice (Oryza sativa L.) based on RAPD marker analysis

Total DNA from WA type CMS lines: Zhenshan 97 A, Longtepu A and theirmaintainers Zhenshan 97 B, Longtepu B wasextracted by CTAB method. One hundredprimers were used for screening RAPDmarkers to distinguish CMS line (A) andmaintainer (B) plants at seedling stage.Results showed that under the conditions of37 ^°C annealing temperature and1.5 mM MgCl₂ concentration, in Zhenshan97 A, Longtepu A there was a 1600 bp DNAfragment in product amplified by primerOPA12, while in Zhenshan 97 B, and LongtepuB no 1600 bp fragment was found. The 1600 bpfragment was also found in DA type CMS lineXieqingzao A, but was absent in XieqingzaoB. Also in the restorer line, Minghui 63the 1600 bp fragment was absent. In F₁and F₂ generation of Zhenshan97A/Minghui 63, all plants investigated hadthe 1600 bp fragment. When mitochondrial DNA(mtDNA) was isolated from the three CMS (A)and their B lines and amplified by OPA12,results showed that the 1600 fragment wasfound in all the three A lines and wasabsent in the three B lines. In DA typeXieqingzao A, two other fragments (700 bp,1000 bp) were also found except the 1600 bp.These results indicate that the 1600 bpfragment derived from CMS mitochondrial DNAcan be used as a RAPD marker to distinguishA and B plants at seedling stage, and thefragments (700 bp, 1000 bp) can be used todistinguish WA and DA cytoplasms.     

Assessment of purity of rice CMS lines using cpDNA marker

AFLP technique was used to analyse the polymorphism between rice cytoplasmic male sterility (CMS) line Jin2A and its maintainer Jin2B. A stable differential band was discovered, and sequence analysis showed that Jin2A contained a more tandem repeat of 6 base pairs (AGAAAA) than Jin2B. Further studies confirmed that the diversity came from cpDNA and occurred at three kinds of abortive cytoplasmic genotypes. Accordingly, specific primers were designed and utilized to assess the purity of rice CMS lines during multiplication with pollen fertility and seed setting rates of bagged panicles as control. The result indicated that this cpDNA locus could be utilized to precisely distinguish maintainer plants from rice CMS lines. PCR analysis was consistent with that from Grow-out test in CMS line seed purity assessment during multiplication, despite it was helpless in distinguishing F₁ hybrids from CMS lines due to similar cytoplasms. Because of fewer hybrid and more maintainer off-plants, this cpDNA locus was still appropriate for seed purity assessment of rice CMS line during multiplication. This is first report that a marker on cpDNA could be utilized to assess the genetic purity of rice CMS lines with three abortive cytoplasmic genotypes.     

Geographical distribution of allozyme patterns in shallot (Allium cepa var. ascalonicum Backer) and wakegi onion (A. × wakegi Araki)

Summary Shallot and wakegi were collected in the main islands of Indonesia, and in Japan, Korea, Taiwan, Malaysia, Thailand and Bangladesh. Five isozyme resolutions, phosphoglucomutase (PGM), glutamate oxaloacetate (GOT), glutamate dehydrogenase (GDH), esterase (EST) and peroxidase (POX) were employed for demonstrating inter-and intraspecific differences. A dendrogram separated 189 collected accessions into 25 types of wakegi onion and 18 types of shallot. All accessions of Japan, Korea and Taiwan were determined to be wakegi onion, whereas those of Bangladesh, Malaysia and Thailand were shallot. Twenty-six out of 165 Indonesian accessions indicated wakegi onion distribution in Sumatra, West Java province and in Sulawesi Island. This confirmed that there is mixed-cultivation of the two Allium species with no distinction made between them. Japan and Indonesia had respectively 12 and eight unique types of wakegi onion, while Korea had only one type. West Java showed the most various type of wakegi onion, whereas East Java had many types of shallot. Shallots collected from Bangladesh were distinetly different from those of South East Asian types.