Papers by Kenneth McNally
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Rice (New York, N.Y.), 2015
Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a ... more Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus subpopulation and modern improved cultivars from Bangladesh. Cultivars from the OryzaSNP set and Rice Diversity Panel 1 (RDP1) were also included for reference. The population analysis program STRUCTURE was used to infer putative population groups in the panel, revealing four groups: indica (76 cultivars), japonica (55) and two distinct groups within the aus subpopulation (aus-1 = 99, aus-2 = 151). Principal Component Analysis was used to confirm the four population groups identified by STRUCTURE. The analysis revealed cultivars that belonged to neither aus-1 nor aus-2 but which are clearly aus based on the combined probabilities of their membership of the two aus groups which have been termed aus-admix (96). Information obtained from the panel of 511...
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Current Genetics, 1992
The small subunit ribosomal RNA gene (SSU rDNA) from the euryhaline yeast Debaryomyces hansenii h... more The small subunit ribosomal RNA gene (SSU rDNA) from the euryhaline yeast Debaryomyces hansenii has been isolated and sequenced. After appropriate alignment of this sequence with SSU rDNA sequences from 30 other taxa, phylogenetic reconstruction using distance matrix and maximum parsimony methods indicates that D. hansenii is most closely affiliated with Candida albicans, and occurs in the cluster of the yeasts Saccharomyces cerevisiae, Torulaspora delbruekii, Candida glabrata, and Kluyveromyces lactis. It appears that the capacity to tolerate high salt is independent of phylogenetic affiliations based on SSU rDNA analyses.
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Journal of Phycology, 1994
... from the hydrocoral Millepora dichotoma (from the Gulf of Aqaba), and Amphidinium belauense T... more ... from the hydrocoral Millepora dichotoma (from the Gulf of Aqaba), and Amphidinium belauense Trench from the acoel flatworm Haplodiscus sp. (from Belau) have been amplified by the polymerase chain reaction, cloned, and sequenced. ...
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The rapid progress in rice genotyping must be matched by advances in phenotyping. A better unders... more The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7–40.7 Mb) and on chromosome
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Background: Rice, Oryza sativa L., is the staple food for half the world's population. By 2030, t... more Background: Rice, Oryza sativa L., is the staple food for half the world's population. By 2030, the production of rice must increase by at least 25% in order to keep up with global population growth and demand. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land, as well as to ensure a stable global food supply.
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Journal of Agronomy and Crop Science, 2012
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Current Genetics, 1992
The complete sequence of the small subunit ribosomal RNA (SSU rRNA) gene was determined for the s... more The complete sequence of the small subunit ribosomal RNA (SSU rRNA) gene was determined for the symbiotic dinoflagellate Symbiodinium pilosum. This sequence was compared with sequences from two other dinoflagellates (Prorocentrum micans and Crypthecodinium cohnii), five Apicomplexa, five Ciliata, five other eukaryotes and one archaebacterium. The corresponding structurally conserved regions of the molecule were used to determine which portions of the sequences could be unambiguously aligned. Phylogenetic relationships were inferred from an analysis of distance matrices, where pair-wise distances were determined using a maximum likelihood model for transition and transversion ratios, and from maximum parsimony analysis, with bootstrap resampling. By either analytical approach, the dinoflagellates appear distantly related to prokaryotes, and are most closely related to two of the Apicomplexa, Sarcocystis muris and Theileria annulata. Among the dinoflagellates, C. cohnii was found to be more closely affiliated with the Apicomplexa than either P. micans or S. pilosum.
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Theoretical and Applied Genetics, 2010
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Proceedings of the National Academy of Sciences, 2003
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Current Genetics, 1990
The complete 94,192 bp sequence of the mitochondrial genome from race s of Podospora anserina is ... more The complete 94,192 bp sequence of the mitochondrial genome from race s of Podospora anserina is presented (1 kb=103 base pairs). Three regions unique to race A are also presented bringing the size of this genome to 100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group II introns (3 in race A). Analysis shows that the group I introns can be categorized according to families both with regard to secondary structure and their open reading frames. All identified genes are transcribed from the same strand. Except for the lack of ATPase 9, the Podospora genome contains the same genes as its fungal counterprts, N. crassa and A. nidulans. About 20% of the genome has not yet been identified. DNA sequence studies of several excision-amplification plasmids demonstrate a common feature to be the presence of short repeated sequences at both termini with a prevalence of GGCGCAAGCTC.
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Current Genetics, 1989
The 5,969 by (base pair) DNA sequence of the apocytochrome b mitochondrial (mt) gene of race A Po... more The 5,969 by (base pair) DNA sequence of the apocytochrome b mitochondrial (mt) gene of race A Podospora anserina was located in a 8.5 Kbp region. This gene contained a 2,499 by subgroup IB and a 1,306 by subgroup ID intron as well as a 990 bp subgroup IB intron which is present in race A but not race s. The large subgroup IB intron and the race A specific IB intron both contained potential alternate splice sites which brought their open reading frames into phase with their upstream exon sequences. All three introns were compared with regard to their secondary structures and open reading frames to the other 30 group I introns in Podospora anserina, as well as to other fungal introns. We detected a new family of intronic ORFs comprising seven P. anserina introns, several N. crassa introns, as well as the T4td bacteriophage intron. Sequence similarities to intron-encoded endonucleases were noteworthy. The DNA sequences reported here and in the accompanying paper complete the analysis of race s and race A mitochondrial DNA.
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... and TILLING Ramesh S. Bhat1, Narayana M. Upadhyaya2, Abed Chaudhury2, Chitra Raghavan3, Fulin... more ... and TILLING Ramesh S. Bhat1, Narayana M. Upadhyaya2, Abed Chaudhury2, Chitra Raghavan3, Fulin Qiu3, Hehe Wang3, Jianli Wu3, Kenneth McNally3, Hei Leung3, Brad Till4, Steven Henikoff4, and Luca Comai4,5 Reviewed by Phil Larkin ...
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Molecular Breeding, 2007
TILLING (Targeting Induced Local Lesions IN Genomes) exploits the fact that CEL I endonuclease cl... more TILLING (Targeting Induced Local Lesions IN Genomes) exploits the fact that CEL I endonuclease cleaves heteroduplexes at positions of single nucleotide or small indel mismatches. To detect single nucleotide polymorphisms (SNPs) across a population, DNA pools are created and a target locus under query is PCR-amplified and subjected to heteroduplex formation, followed by CEL I cleavage. Currently, the common method used to detect cleaved products is by polyacrylamide gel electrophoresis using a high-throughput genotyping platform. Exact SNPs are then determined by sequencing. We sought to simplify the detection of CEL I-cleaved products on conventional agarose gels to make the technique more accessible to collaborating partners in developing countries where access to instrumentation could be limiting. Here, we used a panel of stress-related genes to evaluate SNP detection across 48 rice genotypes by contrasting them individually against IR64 and Nipponbare. SNP detection calls corresponded perfectly with those obtained from the Li-Cor genotypers. We were able to detect SNPs in pools of eight DNA templates, suggesting that the agarose gel system could be used to screen for SNPs with comparable throughput as that of the Li-Cor genotypers and showed that the throughput can be increased by analyzing larger amplicons (∼3 kb). The agarose method offers a significant advantage by alleviating the need for labeled primers. We further demonstrated that the agarose method can be effectively used in gene mapping, an application particularly useful for parental lines with low levels of polymorphism. The lower cost and simplicity of the technique make it possible for broader applications of SNP-based markers for germplasm characterization and mapping studies.
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International Journal of Plant Genomics, 2008
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BMC Bioinformatics, 2008
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Rice, 2010
We present an overview of a research platform that provides essential germplasm, genotypic and ph... more We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our long-term goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.
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Journal of Integrative Plant Biology, 2006
Diversity array technology (DArTTM) was a genotyping tool characterized gel-independent and high ... more Diversity array technology (DArTTM) was a genotyping tool characterized gel-independent and high throughput. The main purpose of present study is to validate DArT for rice (Oryza sativa L.)genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a general-purpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc (Numerical taxonomy system for cluster and ordination analysis, v. 2.02j) software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple sequence repeats genotyping outline and varieties' pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.(Managing editor: Ya-Qin Han)
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Papers by Kenneth McNally