John Mccallum

John Mccallum
Plant and Food Research · Department of Breeding and Genomics

PhD, Dip. App. Stats.

About

212
Publications
24,759
Reads
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2,898
Citations
Additional affiliations
July 2015 - present
University of Otago
Position
  • Snior Lecturer
October 1989 - April 1992
University of British Columbia - Vancouver
Position
  • PostDoc Position

Publications

Publications (212)
Article
Full-text available
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed A. chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa 'Hayward', is hexaploid (2n = 6x = 174). Advance...
Article
Full-text available
Pseudomonas syringae pv. actinidiae (Psa) biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2×) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Ps...
Article
Full-text available
During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or lo...
Preprint
Full-text available
During analysis of kiwifruit derived from hybrids between the high AsA species Actinidia eriantha and A. chinensis var chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis we performed whole-genome sequencing on pools of high and low AsA fruit from tetraploid A. chinensis v...
Article
Full-text available
Background Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a region of non-recombination. To better understand early sex chromosome evolution, it is important to determine the process by whic...
Preprint
Full-text available
Pseudomonas syringae pv. actinidiae (Psa) Biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2x) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Ps...
Article
Bulb onion (Allium cepa L.) is a challenging subject for experimental studies because of its slow growth, genetic heterogeneity, and sensitivity to environmental and biotic stresses. Sharing of common germplasm and controlled propagation practices has underpinned research on model plants, such as Arabidopsis and tomato, but not in onion. To encoura...
Chapter
Ability to conduct molecular analyses in Allium species was previously limited by the power of available technologies to sample very large heterozygous genomes in a cost-effective manner. The emergence of third-generation long-read sequencing technologies, coupled with maturing strategies for population genomics in non-model systems provides exciti...
Chapter
During evolution, plant genomes have undergone duplications, deletions and rearrangements resulting in a wide variation in genome size and number of gene family members between different species. The variation in gene families is an important mechanism for adaptation to different environmental conditions. Allium species, such as bulb onion (Allium...
Article
BACKGROUND To facilitate faster phenotyping of onions (Allium cepa L.), Fourier‐transform mid infrared (FT‐MIR) spectroscopy with partial least squares (PLS) regression modelling was evaluated for determination of pungency (pyruvate), sweetness (free sugars) and fructan in juice samples (n = 605) expressed from bulbs from breeding populations. RES...
Article
Full-text available
Background: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb...
Article
Full-text available
Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite bein...
Article
Full-text available
Researchers working on model plants have derived great benefit from developing genomic and genetic resources using ‘reference’ genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we...
Data
Description of samples used and their NCBI SRA links. (DOCX)
Data
Sequences in FASTA of bulb onion orthologues of rice genes involved in male fertility and floral development identified using BLAST searches. (XLSX)
Data
List of primer Sequences used in present investigation. (DOCX)
Article
Full-text available
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing tech- nologies to inform conservation policy and the manage- ment of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective a...
Article
Full-text available
Bulb onion (Allium cepa L.) is an ancient crop that is thought to have originated in Central Asia and has been cultivated for over 5000 years. Classical genetic and plant breeding approaches have been used to improve onion yield, quality, and resistance against biotic and abiotic stresses. However, its biennial life cycle, cross-pollinated nature a...
Article
Full-text available
Not so long ago identifying genes in a non-model species was a large task; since the development of high throughput sequencing technologies, it is now relatively simple. As molecular biologists our task has now switched to not only to understanding gene function, but also to understanding how allelic variation contributes to the huge diversity of p...
Article
Full-text available
Species of the genus Podocarpus are primarily found in the Southern Hemisphere. In New Zealand, there are four endemic species—Podocarpus acutifolius, Podocarpus nivalis, Podocarpus totara and Podocarpus cunninghamii. The last mentioned two species, tōtara and Hall's tōtara, are the most economically and culturally important and have been used exte...
Article
Full-text available
Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. Although expressed sequence tag (EST)-derived markers for bulb onion (A. cepa L.) have been developed from medium-scale sequencing, comparable EST sequences in bunching onion are lacking. In this study, we obtained 54,903 bunching onion unigenes using transcript...
Chapter
Sulfite reductase (SiR) and nitrite reductase (NiR) belong to a family of oxidoreductases with conserved siroheme and iron-sulfur cluster domains. While functional redundancy has been characterized extensively between the two enzymes in prokaryotes, not much work has been done in characterizing the functional redundancy between assimilatory SiR and...
Article
Full-text available
Onion (Allium cepa L.) is a biennial crop that in temperate regions is planted in the spring and, after a juvenile stage, forms a bulb in response to the lengthening photoperiod of late spring/summer. The bulb then overwinters and in the next season it flowers and sets seed. FLOWERING LOCUS T (FT) encodes a mobile signaling protein involved in regu...
Article
Full-text available
Key message We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology. Abstract Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a b...
Article
Background: Non-structural carbohydrate (NSC; glucose, fructose, sucrose and fructan) composition of onions (Allium cepa L.) varies widely and is a key determinant of market usage. To analyse the physiology and genetics of onion carbohydrate metabolism and to enable selective breeding, an inexpensive, reliable and practicable sugar assay is requir...
Data
##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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GenBank staff is unable to verify sequence and/or annotation provided by the submitter. ##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
Data
##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Assembly Method :: newbler v. 1.0 Sequencing Technology :: 454 ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
Most people experience the lachrymatory smell that is emitted when a bulb of onion (Allium cepa) is cut with a knife in a kitchen. The lachrymatory factor (LF), identified as propanthial-S-oxide more than 40 years ago, is produced during the enzymatic conversion of 1-propenyl sulfenic acid, a putative reaction product of alliinase acting on trans-1...
Article
Full-text available
Background Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research ha...
Data
Table S1. Genetic Marker assays and map locations. Genbank accessions denote accession number of contigs or read identifier for singleton reads in SRA accession SRX031645.
Data
Table S2. Bin mapped genetic marker assays targeting TF-like sequences and genomic SSR.
Article
Full-text available
Improved understanding of genetic diversity in onion and shallot (Allium cepa L.) is required to inform breeding and genetic resource conservation, and to enable development of association genetics and seed quality assurance methods. To develop quantitative estimates of diversity we estimated within- and among-population heterozygosity in a set of...
Article
Genomic and cDNA sequences corresponding to a ferredoxin-sulfite reductase (SiR) have been cloned from bulb onion (Allium cepa L.) and the expression of the gene and activity of the enzyme characterized with respect to sulfur (S) supply. Cloning, mapping and expression studies revealed that onion has a single functional SiR gene and also expresses...