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  • Author or Editor: Michael J. Havey x
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The commercial production of onion (Allium cepa L.) inbreds, hybrids, and open-pollinated (OP) cultivars would benefit from a robust set of molecular markers that confidently distinguish among elite germplasms. Large-scale DNA sequencing has revealed that single nucleotide polymorphisms (SNPs), short insertion-deletion (indel) events, and simple sequence repeats (SSRs) are relatively abundant classes of codominant DNA markers. We identified 398 SNPs, indels, and SSRs among 35 elite onion ulations and observed that all populations could be distinguished. Phylogenetic analyses of simple-matching and Jaccard's coefficients for SSRs produced essentially identical trees and relationships were consistent with known pedigrees and previous marker evaluations. The SSRs revealed that elite germplasms from specific companies or breeding programs were often closely related. In contrast, phylogenetic analyses of SNPs and indels did not reveal clear relationships among elite onion populations and there was no agreement among trees generated using SNPs and indels vs. SSRs. This discrepancy was likely due to SNPs and indels occurring among amplicons from duplicated regions (paralogs) of the onion genome. Nevertheless, these PCR-based markers will be useful in the quality control of inbred, hybrid, and OP onion seed lots.

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Cytoplasmic-genic male sterility (CMS) is used to produce hybrid onion (Allium cepa L.) seed. For the most widely used source of onion CMS, male sterility is conditioned by the interaction of the male-sterile (S) cytoplasm and the homozygous recessive genotype at a nuclear male-fertility restoration locus (Ms). Maintainer lines are used to seed propagate male-sterile lines, possess normal (N) male-fertile cytoplasm, and are homozyous recessive at the Ms locus. Due to the biennial nature of onion, it takes 4 to 8 years of crossing and scoring of progeny phenotypes to establish if maintainer lines can be extracted from an uncharacterized population or family. Identification of nuclear markers tightly linked to the Ms locus would allow for molecular-facilitated selection of maintainer lines. We evaluated testcross progenies from a segregating family for nuclear restoration of male fertility over at least three environments. Although segregations in the F2 family fit the expected 1:2:1 ratio (P = 0.973), the proportion of male-sterile testcross progenies showed significant (P < 0.01) year effects and it is therefore imperative to score male-fertility restoration over environments. Too many male-sterile testcross progenies were often observed, indicating that the dominant allele conditioning male-fertility restoration for S cytoplasm may not show complete penetrance. Segregations of amplified fragment length polymorphisms and restriction fragment length polymorphisms (RFLPs) revealed RFLPs flanking the Ms locus at 0.9 and 8.6 cM. An onion cDNA showing highly significant homology to the aldehyde dehydrogenase conditioned by the rf2 locus of maize was identified and mapped to linkage group I, independent of the Ms locus. A sample of commercial onion germplasm was evaluated for putative allelic diversity at the RFLP loci linked to Ms. The genomic region corresponding to the cDNA (AOB272) revealing the closest RFLP to Ms was sequenced to reveal numerous single nucleotide polymorphisms. Single-stranded conformational polymorphisms and single nucleotide extensions were developed that revealed genomic variation at AOB272-EcoRI. The use of these molecular markers to select maintainer lines in onion is discussed.

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Although haploid induction has been used in onions (Allium cepa L.) for over 20 years, several obstacles limit its use in plant breeding programs. To address these limitations, we evaluated the responsiveness of doubled haploid (DH) lines and their selfed progenies, an alternative protocol for chromosome doubling using somatic regeneration of haploid lines, and pollen viability of DH lines. Twenty-one DH lines were self pollinated and tested for haploid induction in the second generation. Among the DH lines, 18 lines showed an average of 20% decrease in gynogenic responsiveness compared with the original lines, while three lines registered an average increase of 5.7%. Using a two-step induction/regeneration procedure, 8,589 somatic regenerants were obtained from 16,170 flower buds from haploid plants, and shoot culture was established. A more laborious procedure using extraction of ovaries in the regeneration stage was found equal to flower bud culture. Chromosome doubling via somatic regeneration was found to be 83% and 100% efficient when the source material was haploid or mixoploid, respectively. Based on the results achieved in this and previous studies, an alternative protocol for chromosome doubling of gynogenic haploids is proposed.

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Allium fistulosum L. (bunching onion) is resistant to many of the important diseases and pests of Allium cepa L. (bulb onion). Although the first interspecific hybrids were generated more than 50 years ago, there is no conclusive evidence that any desirable trait in bunching onion has been successfully transferred to bulb onion by backcrossing. We identified RFLPs in the chloroplast and nuclear genomes to assess DNA transfer from bunching to bulb onion by backcrossing an interspecific hybrid to a bulb onion. Polymorphisms in the chloroplast genome established that the interspecific hybrid and three putative backcross plants had the cytoplasm of a bunching onion. All 57 random cDNA probes detected polymorphisms between the bulb and bunching onion for at least one of two restriction enzymes. The backcross progenies always possessed the bulb-onion fragments and an excess of probes detected the bunching-onion fragments. Only one plant showed an acceptable fit to the expected 1:1 backcross ratio. Significant deviations from expected segregation ratios may be the result of abnormal meiosis in the interspecific hybrid. However, these observations could also be explained by a previously proposed nuclear-cytoplasmic interaction conditioning preferential survival in the bunching-onion cytoplasm of eggs carrying bunching-onion chromosomes.

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Pink root [PR (caused by Phoma terrestris)] is a major soil-borne disease of onion (Allium cepa) and reduces both yield and quality of bulbs. PR-resistant cultivars offer the best control option for this disease. The objectives of this study were to complete genetic analyses and mapping of PR resistances from independent sources. Segregating families were developed from different sources of PR resistance and evaluated using a seedling screen. PR severity in two segregating families from the same source of resistance mapped to one position on chromosome 4 with logarithm of odds (LOD) scores of 8.0 and 10.3, and explained 28% and 35% of the phenotypic variation, respectively. Estimates of additive and dominance effects revealed this source of PR resistance is codominantly inherited. PR resistance from a second source was assessed by percent survival in the seedling evaluation, showed codominance, and mapped to the same region on chromosome 4 at LOD 12.5 and explained 54% of the phenotypic variation. This research demonstrates that PR resistance from different sources mapped to the same chromosome region and showed similar modes of inheritance.

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Onion thrips (Thrips tabaci) is the main insect pest of onion (Allium cepa), and feeding damage routinely causes serious yield losses. Lower amounts of epicuticular waxes on onion leaves have been associated with fewer onion thrips and less feeding damage, and research is needed to assess the relationships between amounts and composition of epicuticular waxes and feeding damage by onion thrips. This study used gas chromatography mass spectroscopy to determine amounts and types of epicuticular waxes on the foliage of onion accessions that had been field-selected for lower damage from onion thrips. Hentriacontanone-16 (H16), octaconasol-1, and triacontanol-1 were the most prevalent waxes on the foliage of these selections. Amounts of H16 were significantly lower on selections visually classified as having glossy or semiglossy foliage. Semiglossy selections were identified with similar amounts of total epicuticular wax as waxy phenotypes, due primarily to lower amounts of H16 and higher amounts of other waxes. These semiglossy selections suffered significantly less feeding damage from onion thrips in a field evaluation, supporting the identification of unique wax profiles toward the development of thrips-resistant onion.

Open Access

Garlic has been propagated exclusively by asexual means since time immemorial. The recent discovery of male fertile garlic accessions allowed studies on genetics and garlic improvement. Single nucleotide polymorphism (SNP) and random amplified polymorphic DNA (RAPD) based genetic linkage map was developed for garlic using a segregating population derived from one plant of PI 540316. Progenies segregated for male fertility and other morphological characters. Distortion of segregation was observed for most of the markers. This was expected due to the segregation of recessive deleterious alleles present in the garlic genome. The map contained 23 loci distributed on five linkage groups. It covered 319 cM with the average of 18 cM between loci. Linkage with the male fertility (Mf) locus was established with SNP marker AOB155 (26.7 cM).

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Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

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Garlic (Allium sativum L.) has been cultivated by asexual propagation since time immemorial. The discovery of male-fertile garlic accessions has opened a venue for genetic studies and improvement through sexual recombination. An S1 family of 84 plants was generated from a single male-fertile heterozygous plant from the U.S. Dept. of Agriculture Plant Introduction 540316 and used to identify the first genetic linkages in garlic based on single nucleotide polymorphisms, simple sequence repeats, and randomly amplified polymorphic DNAs. Thirty-seven markers formed nine linkage groups covering 415 centimorgans (cM) with average distance of 15 cM between loci; other 16 loci remained unlinked. A male fertility locus was placed on the map. This first genetic map of garlic is a seminal step toward the genetic improvement of garlic and eventual marker-assisted breeding.

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