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  • Author or Editor: Michael J. Havey x
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PstI-genomic and cDNA clones revealing mapped restriction fragment-length polymorphisms (RFLP) in cucumber (Cucumis sativus L.) were sequenced in order to ensure that these clones remain available and to determine if any clones showing genetic linkage in cucumber are physically linked in Arabidopsis thaliana. Sequence comparisons using translated searches revealed that 80% of the cucumber cDNA clones showed significant (≤e-20) similarities to Arabidopsis expressed sequence tags (ESTs) or genomic sequences, as opposed to relatively few (32%) of the cucumber genomic clones. Two clones revealing RFLPs linked at 2 cM in cucumber showed significant (≤e-20) similarities to sequences separated by 347,616 basepairs on chromosome 4 of Arabidopsis.

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Restriction fragment length polymorphisms (RFLPs) in the chloroplast and nuclear genome are useful for estimation of phylogenetic relationships. Fifteen mutations at restriction enzyme sites in the chloroplast DNA were discovered. The wild species A. oschaninii and A. vavilovii were identical to A. cepa for all mutations. These species represent sources of wild germplasm closely related to the bulb onion. Nuclear RFLPs are now being used to estimate the genetic distances between accessions of A. oschaninii A. vavilovii, and open-pollinated populations of the cultivated bulb onion.

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The amounts and types of epicuticular waxes on onion (Allium cepa) leaves affect feeding damage by onion thrips (Thrips tabaci), a serious insect pest of onion. This study used gas chromatography mass spectrometry (GCMS) to measure amounts of epicuticular waxes on foliage of two plants from each of 50 plant introductions (PI) and inbred lines with high (waxy) and low (glossy) amounts of wax. Wax amounts on leaves of the same plants were measured twice (once in the greenhouse and once after moving plants outside) and were significantly (P < 0.01) correlated; however, wax amounts on leaves of plants grown in the greenhouse were approximately twice that of the same plants grown outside. Hentriacontanone-16 (H16) was the predominant wax on leaves of all PIs except PI 289689, and amounts of H16 were significantly correlated with amounts of fatty alcohols and total wax. Five plants from 17 of the PIs were grown in the greenhouse, wax amounts measured using GCMS, and results were significantly correlated with earlier evaluations. Results indicate that measurements of waxes on onion foliage should occur under protected conditions to better characterize phenotypic variation, and selection of higher amounts of waxes other than H16 may be effective toward the development onions suffering less thrips damage.

Open Access

The formation of onion (Allium cepa) bulbs is affected by photoperiod length and onion germplasm is commonly classified as short- (SD), intermediate-, or long-day (LD) types. The objectives of this study were to develop a segregating family from a cross between doubled haploids (DHs) of LD and SD onions and complete genetic analyses of bulb shape and volume, as well as daylength effects on bulbing. DH parents and F1 and F2 progenies were grown in a greenhouse under lengthening days. The diameters of the neck constriction and pseudostems were measured weekly and their ratio was used as the determinant of bulbing. Bulbs were harvested when the foliage collapsed and the diameters and heights of individual bulbs were measured and used to calculate a shape index (diameter divided by height) and bulb volume. Single nucleotide polymorphisms (SNPs) were genotyped and a genetic map of 112 SNPs constructed. Genetic analysis revealed two highly significant quantitative trait loci (QTL) affected bulbing under increasing daylengths, and both QTL showed significant additive effects with no dominance. One highly significant QTL was detected for bulb-shape index and explained 30% of phenotypic variation for bulb shape. Three additional QTL were slightly above the significance threshold, and together these four QTL explained over 50% of the phenotypic variation for bulb shape. No significant QTL were detected for bulb volume. These results reveal that bulb-shape and daylength effects on bulbing are relatively simply inherited, and this research should facilitate introgression of traits between onion populations of different daylength sensitivities and efforts to modify bulb shape.

Open Access

The most common bulb colors of onion (Allium cepa) are red, yellow, and white; chartreuse is a relatively rare bulb color conditioned by the homozygous recessive genotype at the G locus. In this research, plants with chartreuse bulbs were crossed with inbreds with yellow bulbs to develop segregating families for genetic mapping of the G locus. For all of 17 F2 families, segregations for yellow vs. chartreuse bulbs fit the expected 3:1 ratio (P > 0.05). DNAs were isolated from one F2 family and genotyped for single nucleotide polymorphisms (SNPs) to produce a genetic map of the G locus and 380 SNPs, of which 119 SNPs have not been previously mapped. Segregations for yellow vs. chartreuse bulbs placed the G locus at the end of chromosome 7 at 6.7 cM from the nearest SNP (isotig28625_2789). This codominant SNP marker linked to the G locus should be useful for introgression of recessive chartreuse bulb color into diverse onion populations for commercial production of this uniquely colored onion.

Open Access

Maintainer lines are used to seed propagate male-sterile lines for the development of hybrid onion (Allium cepa L.) cultivars. The identification of maintainer lines would be more efficient with molecular markers distinguishing genotypes at the nuclear male-fertility restoration (Ms) locus. Ms has been mapped to chromosome 2 of onion and linked genetic markers identified. However, linkages between these markers and Ms were detected using F2 or BC1 families at maximum linkage disequilibrium and, for many markers, their efficacy to predict genotypes at Ms in onion populations at or near linkage equilibrium remains unknown. In this research, near isogenic lines homozygous-dominant and -recessive at Ms were developed and screened for 930 single nucleotide polymorphisms (SNPs). Three SNPs tightly linked on chromosome 2 remained in linkage disequilibrium with genotypes at Ms among randomly selected plants from three open-pollinated populations of onion as well as among a collection of inbred lines. These SNPs should be useful for selection of the recessive ms allele to aid in the development of maintainer lines for hybrid onion development.

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Different sources of cytoplasmic male sterility (CMS) are used to produce hybrid onion seed. The most commonly used source of CMS in onion is S cytoplasm (S-CMS), and male fertility is restored by a dominant allele at the nuclear male-fertility restoration locus (Ms). Male-sterile plants possess S cytoplasm and have the homozygous recessive genotype at Ms; seed propagation of male-sterile plants is possible by crossing with a male-fertile maintainer plant or inbred possessing normal (N) male-fertile cytoplasm and the homozygous recessive at the Ms locus (N msms). Some commercially important onion populations possess S-CMS and high frequencies of the dominant Ms allele, eliminating the possibility to develop maintainer lines. An alloplasmic source of CMS (Gal-CMS) was developed by backcrossing the cytoplasm of Allium galanthum into the nuclear background of onion. The advantage of Gal-CMS is that the dominant allele at Ms does not restore male fertility, making this source of CMS useful for the development of male-sterile lines from populations possessing S cytoplasm and dominant allele(s) at Ms. In this research, a single nucleotide polymorphism unique to the cytoplasms of A. galanthum and Gal-CMS was identified, useful to distinguish Gal-CMS from other onion cytoplasms.

Open Access

Phytophthorainfestans is the casual agent of late blight and is a major threat to potato production worldwide. There are no curative control agents available and resistance genes offer promise in controlling late blight. To date, the primary source of late-blight resistance has been from hexaploid (6x) [4 Endosperm Balance Number (EBN)] Solanum demissum. Mexican diploid (2x) (1EBN) Solanum species possess a wealth of late-blight resistances, but have been neglected due to crossing barriers. Manipulation of EBN and ploidies should allow integration of 2x (1EBN) germplasm into cultivated potato. Synteny between late-blight resistance loci from Solanum species of disparate ploidies and EBNs may facilitate the identification of unique resistance alleles and loci. Isolate MSU96 (US8/A2) of P. infestans revealed a late-blight resistance locus (Rpi1) from 2x(1EBN) S. pinnatisectum (PI 253214) that mapped to chromosome seven (MGG 265:977-985). MSU96 was also avirulent on the late-blight differential R9-Hodgson 2573 (LB3), revealing the presence of the avirulence gene for R9 originating from S. demissum. To test the relationship between Rpi1 and R9, we evaluated a family segregating for R9 and revealed that it does not map to chromosome seven. The independent inheritance of R9 and Rpi1 indicates that Rpi1 is a unique resistance locus. We are conducting a variety of crossing schemes to introgress Rpi1 into cultivated potato.

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The bulb onion (Allium cepa L.) is a diploid with an very large nuclear genome of 15300 Mbp/1C (107× arabidopsis, 16× tomato, 6× maize). We developed a low-density genetic map with morphological, RAPD, and RFLP markers to examine genome organization and to study QTL controlling phenotypically correlated bulb quality traits. A mapping population of 58 F3 families was derived from a cross of the inbreds Brigham Yellow Globe 15-23 (BYG) × Alisa Craig 43 (AC). These inbreds are distinct in solids, storability, pungency, and bulb shape. Analysis of 580 RAPD primers detected 53 (9%) polymorphisms between BYG and AC, but only 12 (2%) segregated at expected ratios among F3 families. Using probes from onion cDNA libraries and four restriction enzymes, 214 RFLPs were identified between mapping parents. A 112-point map includes 96 RFLPs, 13 RAPDs, a locus controlling complementary red bulb color, and two loci hybridizing with a clone of the enzyme alliinase (EC 4.4.1.4), which produces the flavors characteristic of Allium species. Duplicated loci were detected by ≈25% of RFLP probes and were unlinked, loosely linked (2 to 30 cM), or tightly linked (<2 cM). This frequency of duplication was comparable to species with polyploid ancestors (paleopolyploids) and was higher than that found in most true diploids. However, the distribution of duplicated loci suggests that, in contrast to whole genome duplications typical of paleopolyploids, the contemporary size and structure of the onion genome may be a product of intrachromosomal duplications (cryptopolyploidy) and subsequent structural rearrangements.

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Natural variation exists in onion (Allium cepa L.) for amounts and types of epicuticular waxes on leaves. Wild-type waxy onion possesses copious amounts of these waxes, whereas the foliage of semiglossy and glossy phenotypes accumulates significantly less wax. Reduced amounts of epicuticular waxes have been associated with resistance to onion thrips (Thrips tabaci Lindeman), an important insect pest of onion. A segregating family from the cross of waxy and semiglossy onions was used to map single nucleotide polymorphisms (SNPs) and identify chromosome regions affecting amounts and types of epicuticular waxes as measured by gas chromatography–mass spectrometry. The amount of the primary epicuticular wax on onion leaves, hentriacontanone-16, was controlled by one region on chromosome 5. One region on chromosome 2 affected concentrations of several primary fatty alcohols. Results indicate that the region on chromosome 2 may be associated with the acyl reduction pathway, and the region on chromosome 5 may affect the decarbonylation pathway of epicuticular wax biosynthesis. Because lower amounts of epicuticular waxes are recessively inherited, SNPs tagging regions on chromosomes 2 and 5 will be useful for marker-assisted breeding to vary amounts and types of epicuticular waxes on onion foliage with the goal to develop cultivars resistant to onion thrips.

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