A low-density genetic map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome

 The bulb onion, Allium cepa L., is a diploid (2n=2x=16) plant with a huge nuclear genome. Previous genetic and cytogenetic analyses have not supported a polyploid origin for onion. We developed a low-density genetic map of morphological markers, randomly amplified polymorphic DNAs (RAPD), and restriction fragment length polymorphisms (RFLP) as a tool for onion improvement and to study the genome organization of onion. A mapping population of 58 F₃ families was produced from a single F₁ plant from the cross of two partially inbred lines (Brigham Yellow Globe 15-23 and Alisa Craig 43). Segregations were established for restoration of male fertility in sterile cytoplasm, complementary light-red bulb color, 14 RAPDs, 110 RFLPs revealed by 90 anonymous cDNA clones, and 2 RFLPs revealed by a cDNA clone of alliinase, the enzyme responsible for the characteristic Allium flavors. Duplicated RFLP loci were detected by 21% of the clones, of which 53% were unlinked (>30 cM), 5% loosely linked (10–30 cM), and 42% tightly linked (<10 cM). This duplication frequency is less than that reported for paleopolyploids but higher than for diploid species. We observed 40% dominant RFLPs, the highest yet reported among plants. Among duplicated RFLP loci, 19% segregated as two loci each with two codominant alleles, 52% segregated as one locus with codominant alleles and one locus with only a dominant fragment, and 29% segregated as two loci with only dominant fragments. We sequenced cDNAs detecting duplicated RFLPs; 63% showed homology to known gene families (e.g., chlorophyll binding proteins, ubiquitin, or RuBISCO), and 37% were unique clones showing significant homology to known genes of low-copy number or no homology to database sequences. Duplicated RFLPs showing linkage could be due to retroviral-like sequences in adjacent coding regions or intrachromosomal, as opposed to whole genome, duplications. Previous cytological analyses and this genetic map support intrachromosomal duplication as a mechanism contributing to the huge onion genome. Received: 3 July 1997 / Accepted: 8 August 1997     

Hydroxyapatite fractionation procedures in the study of the mammalian genome

Three methods of fractionating DNA are described, in which DNA fragments are separated on the basis (1) of their base composition, (2) of the ability of denatured DNA to renature after incubation, and (3) of the presence of intrastrand secondary structure in denatured DNA. The ability of some of these fractions to form specific duplexes with whole denatured DNA isolated from the same and from a different mammal has been investigated. The results are presented to demonstrate how the fractionation procedures described may provide new information about the organization of the mammalian genome.     

Relationship between longevity of spermatozoa after insemination and the percentage of normal embryos in brown marsupial mice (Antechinus stuartii)

Twenty-six female brown marsupial mice in a laboratory colony were mated at intervals ranging from 1 to 20 days between coitus and ovulation. The numbers of corpora lutea and normal embryos were counted. A multiple regression model examined the parabolic relationship between the proportion of normal embryos and the time from coitus to ovulation. The proportion of normal embryos increased until a mean of 9.5 days and decreased thereafter. This relationship was independent of the year of breeding and the number of corpora lutea. After survival of spermatozoa for up to 13 days in the female reproductive tract, the fertility levels of females was 88-92%. Low fertility levels after 13 days appeared to be due to a decrease in the number of spermatozoa. Reproductive tracts from 7 females killed after insemination and examined histologically showed many spermatozoa in the isthmus of the oviduct and the uterus at 5 days post coitum; spermatozoa confined to the isthmus between 6 and 13 days; and few spermatozoa in the isthmus at 14 days after copulation. A comparison between the fertility levels in the females which had been inseminated once and a further 17 females which had been inseminated 2 or 3 times suggested that spermatozoa from 2nd and 3rd inseminations can contribute spermatozoa for fertilization. In these females fertility levels did not decline with time after the first mating.     

Fourier transform magnitudes are unique pattern recognition templates

Fourier transform magnitudes are commonly used in the generation of templates in pattern recognition applications. We report on recent advances in Fourier phase retrieval which are relevant to pattern recognition. We emphasise in particular that the intrinsic form of a finite, positive image is, in general, uniquely related to the magnitude of its Fourier transform. We state conditions under which the Fourier phase can be reconstructed from samples of the Fourier magnitude, and describe a method of achieving this. Computational examples of restoration of Fourier phase (and hence, by Fourier transformation, the intrinsic form of the image) from samples of the Fourier magnitude are also presented.     

The effects of genotype on physiological and behavioural responses related to the welfare of pregnant pigs

Plasma free-corticosteroid concentrations, aggressive behaviour and levels of motivation to socially interact and explore a novel arena were observed in an experiment to examine whether differences previously observed between pigs in neck-tethers and groups are shown by pigs of different genotypes. Thirty-two pregnant gilts of 2 genotypes were housed in either tether stalls or groups. The 2 genotypes were mainly Large White×Landrace stock, but one had been intensively selected on the basis of growth performance.

Genotypic differences had previously been observed in protein and energy metabolism, and the present experiment also showed differences in their behaviour (increased activity and a decreased motivation to socially interact in the intensively selected genotype) and free-corticosteroid concentrations (40% lower in the intensively selected genotype). In spite of these differences, the behavioural and physiological responses to housing treatments were similar. In tether stalls, pigs of both genotypes had a higher frequency of retaliation and a lower frequency of withdrawal in response to aggressive interactions than group-housed pigs. There were 50 and 56% increases in free-corticosteroid concentrations in response to tether housing in the 2 genotypes, providing evidence of a chronic stress response of a magnitude sufficient to suggest a risk to welfare in the design of tether stall used in this experiment.     

Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing

The construction of the first genetic map in autotetraploid blueberry has been made possible by the development of new SNP markers developed using genotyping by sequencing in a mapping population created from a cross between two key highbush blueberry cultivars, Draper × Jewel (Vaccinium corymbosum). The novel SNP markers were supplemented with existing SSR markers to enable the alignment of parental maps.  In total, 1794 single nucleotide polymorphic (SNP) markers and 233 simple sequence repeat (SSR) markers exhibited segregation patterns consistent with a random chromosomal segregation model for meiosis in an autotetraploid. Of these, 700 SNPs and 85 SSRs were utilized for construction of the ‘Draper’ genetic map, and 450 SNPs and 86 SSRs for the ‘Jewel’ map.  The ‘Draper’ map comprises 12  linkage groups (LG), associated with the haploid chromosome number for blueberry, and totals 1621 cM while the ‘Jewel’ map comprises 20 linkage groups totalling 1610 cM. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents. Tentative alignments of the two parental maps have been made on the basis of shared SSR alleles and linkages to double-simplex markers segregating in both parents.     

Sulfur and nitrogen fertility affects flavour of field-grown onions

Although glasshouse studies have conclusively demonstrated that S nutrition can affect onion (Allium cepaL.) pungency this has been rarely observed in field-based studies due to difficulties in controlling S nutrition and lack of efficient methods for measurement of flavour bioactives. We have developed a rapid automated method for determination of onion lachrymatory factor ((Z, E)-thiopropanal-S-oxide; LF) based on juice extraction into dichloromethane and gas chromatography (GC) analysis with flame photometric detection. We evaluated this in a field trial of a mild (cv. ‘Encore’) and a pungent (cv. ‘Kojak’) onion cultivar grown on a low S soil with and without S addition, under high or low N treatments. No treatments significantly affected bulb fresh weight but S fertilisation significantly increased bulb total S, sulfate, pungency, LF and flavour precursor levels in both varieties. Analysis of bulb flavour precursors by HPLC confirmed that juice LF levels paralleled levels of the flavour precursor S-1-propenyl cysteine sulfoxide. The pungent cultivar also exhibited significant N main effects on bulb LF, total S and sulfate. We also assayed the key S-assimilatory enzyme, APS reductase (APR) in leaves before and during bulbing. Specific activities in the range of 1 to 11 nmol mg⁻¹·min⁻¹ were observed in youngest leaves, but only the milder cultivar exhibited significant stage × N × S effects. These findings suggest that sulfur metabolism of mild and pungent onions respond differently to N fertility, and that GC of LF is practical for field-based studies of onion flavour.     

Expressed sequence markers for genetic analysis of bulb onion (Allium cepa L.)

Sequencing of cDNA clones previously screened for ability to reveal RFLPs in bulb onion has been completed and a further 128 ESTs from 111 clones have been deposited in public databases. A putative function was assigned to 66% (84/128) of ESTs by BLASTX searches against public databases and FASTA comparisons were used to determine similarity among clones, including those which detected linked RFLP loci. Cleavage amplified polymorphisms (CAPs) and single-stranded conformation polymorphisms (SSCP) were evaluated as strategies for converting onion expressed sequence tags (ESTs) into PCR-based assays for gene mapping. We screened 14 ESTs with 8 to 12 restriction enzymes and detected two CAPs, which mapped in the ’Brigham Yellow Globe’ (BYG15–23)×’Ailsa Craig’ (AC43) mapping population. A wider survey of CAPs for ESTs among eight bulb onion populations with six frequently cutting restriction enzymes detected variation, but too little to be practical for routine gene mapping. By contrast, non-radioactive SSCP of amplicons from 3′ UTRs of ESTs was found to detect useful levels of variation within bulb onion germplasm. In addition to SSCPs, homo- and hetero-duplex polymorphisms (duplex polymorphisms) were also frequently observed on the same gels. Of a total of 31 ESTs surveyed, 26 exhibited SSCP/duplex variation among bulb onion populations. SSCP/duplex polymorphisms in 11 ESTs were mapped in the ’BYG15–23’×’AC43’ family and, of these, ten were linked to an RFLP locus revealed by the original cDNA. The SSCP/duplex assays of five additional ESTs showed Mendelian segregations in the ’Colossal Grano’×’Pukekohe Longkeeper’ (P12) F₂ population. Two of these markers were linked, as predicted from linkage of their corresponding RFLPs in the ’BYG15–23’×’AC43’ family. Ninety two percent (12/13) of EST PCR products that amplified in Allium roylei exhibited marked differences in SSCP patterns from bulb onion. ESTs for invertase and sucrose-sucrose fructosyltransferase were mapped by SSCP and an ATP sulfurylase gene cloned by RT-PCR revealed SSCP/ duplex polymorphism within bulb onion. These results demonstrate that SSCP/duplex is an efficient and economical technique for exploiting onion EST information for gene mapping in onion. Received: 18 September 2000 / Accepted: 15 February 2001