Works (28)
Updated: November 18th, 2024 11:06
2024 article
Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in <i>Alternaria linariae</i> from Tomato
Adhikari, T. B., Olukolu, B. A., Paudel, R., Pandey, A., Halterman, D., & Louws, F. J. (2024, February 22). PHYTOPATHOLOGY, Vol. 2.
author keywords: asexual reproduction; linkage disequilibrium; population biology; population differentiation
TL;DR:
Evidence of a high level of population genetic differentiation in A. linariae is provided, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. Linariae.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: March 18, 2024
2024 journal article
Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato
HORTICULTURE RESEARCH, 11(7).
open access via academic.oup.com (publisher PDF)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: July 17, 2024
2023 article
Development of NIRS calibration curves for sugars in baked sweetpotato
Amankwaah, V. A., Williamson, S., Reynolds, R., Ibrahem, R., Pecota, K. V., Zhang, X., … Yencho, G. C. (2023, July 12). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Vol. 7.
author keywords: sweetpotato storage roots; NIRS; high-throughput phenotyping; consumer preferences; nutritional quality; storage root
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: July 24, 2023
2023 journal article
Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection
FRONTIERS IN PLANT SCIENCE, 13.
author keywords: sweetpotato; convolvulaceae; USDA germplasm; SNPs; DAPC; breeder subsets; genotyping-by-sequencing (GBS); polyploid
TL;DR:
The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germ plasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 20, 2023
2023 article
Interrelations of & alpha;- and & beta;-amylase activity with starch, sugars, and culinary and nutritional quality attributes in sweetpotato storage roots
Amankwaah, V. A. A., Williamson, S., Olukolu, B. A. A., Truong, V.-D., Carey, E., Ssali, R., & Yencho, G. C. (2023, July 27). Interrelations of & alpha;- and & beta;-amylase activity with starch, sugars, and culinary and nutritional quality attributes in sweetpotato storage roots. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Vol. 7.
author keywords: sweetpotato; consumer preferences; curing; root storage; root quality traits
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 27, 2023
2023 journal article
Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes
BRIEFINGS IN BIOINFORMATICS, 24(6).
author keywords: metagenomics; microbiome; reduced representation sequencing; exact matching; MegaBLAST
TL;DR:
An automated pipeline, quantitative metagenomic alignment and taxonomic exact matching (Qmatey), that performs a fast exact matching-based alignment and integration of taxonomic binning and profiling that interrogates large databases without using metagenome-assembled genomes, curated pan-genes or k-mer spectra.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: September 20, 2023
2022 journal article
A chromosome-length genome assembly and annotation of blackberry (<i>Rubus argutus</i>, cv. “Hillquist”)
G3 Genes|Genomes|Genetics, 11(ue 2).
Ed(s): T. Pyhäjärvi
author keywords: Rubus; blackberry; Rosaceae; Rosoideae; biennial flowering; annual flowering; primocane-fruiting; chromosome-length genome assembly; Hi-C; annotation; repetitive content
MeSH headings : Rubus / genetics; Tetraploidy; Plant Breeding; Chromosome Mapping; Chromosomes, Plant / genetics; Molecular Sequence Annotation
TL;DR:
The utility of the ‘Hillquist’ genome has been demonstrated here by the development of the first genotyping-by-sequencing based linkage map of tetraploid blackberry and the identification of several possible candidate genes for primocane-fruiting within the previously mapped locus.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, Crossref, NC State University Libraries, ORCID
Added: December 16, 2022
2022 journal article
Combining ability and heritability analysis of sweetpotato weevil resistance, root yield, and dry matter content in sweetpotato
Frontiers in Plant Science, 13.
author keywords: clones; crosses; families; mixed models; Cylas spp; Ipomoea batatas
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: October 3, 2022
2021 journal article
A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(43).
author keywords: maize; teosinte; domestication; evolution; selection
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 13, 2021
2021 journal article
Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)
Theoretical and Applied Genetics, 134(7), 1945–1955.
Contributors: B. Oloka n , G. Silva Pereira *, V. Amankwaah n, M. Mollinari n , K. Pecota n , B. Yada *, *, Z. Zeng n, G. Craig Yencho n
MeSH headings : Animals; Chromosome Mapping; Disease Resistance / genetics; Genetic Linkage; Genotype; Ipomoea batatas / genetics; Ipomoea batatas / parasitology; Plant Diseases / genetics; Plant Diseases / parasitology; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Tylenchoidea / pathogenicity
TL;DR:
A major dominant QTL for root-knot nematode (RKN) resistance is discovered using a high-density integrated genetic linkage map of hexaploid sweetpotato, which represents a significant step forward in understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding inSweetpotato breeding programs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: April 4, 2021
2021 journal article
Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte
PLOS GENETICS, 17(12).
Contributors: L. Samayoa n, *, C. Yang *, Q. Chen* , M. Stetter *, A. York *, J. Jesus Sanchez-Gonzalez *, J. Glaubitz*
Ed(s): B. Walsh
MeSH headings : Domestication; Genes, Plant; Genetic Variation / genetics; Inbreeding Depression / genetics; Phenotype; Plant Breeding; Plant Proteins / genetics; Quantitative Trait Loci / genetics; Selection, Genetic / genetics; Zea mays / genetics; Zea mays / growth & development
TL;DR:
This work compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte, and identified quantitative trait loci representing large-effect rare variants carried by only a single parent, which were more important in teOSinte than maize.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 28, 2022
2021 journal article
ngsComposer: an automated pipeline for empirically based NGS data quality filtering
BRIEFINGS IN BIOINFORMATICS, 22(5).
author keywords: quality score; demultiplexing; buffer sequence; qRRS (quantitative reduced representation sequencing); short-read pre-processing; OmeSeq
MeSH headings : Algorithms; Computational Biology / methods; Computer Simulation; High-Throughput Nucleotide Sequencing / methods; Humans; Reproducibility of Results; Sequence Analysis, DNA / methods; Software
TL;DR:
The ngsComposer pipeline leverages known sequence motifs to enable empirical estimation of error rates, detection of erroneous base calls and removal of contaminating adapter sequence, and was validated with read compression rates as an unbiased metric.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 23, 2021
2020 journal article
Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations
Nature Genetics, 52(11), 1256–1264.
MeSH headings : Algorithms; Chromosomes, Plant; Computer Simulation; Genetic Linkage; Genome, Plant; Genotype; Ipomoea / genetics; Plant Breeding; Poaceae / genetics; Polyploidy; Protein Array Analysis; Solanum tuberosum / genetics
TL;DR:
PolyGembler, a method for grouping and ordering contigs into complete pseudomolecules by combining long-read sequencing and genotype information from an outbred mapping population, improves the accuracy for assembly of polyploidy plant genomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: November 24, 2020
2020 journal article
The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication
PLOS GENETICS, 16(5).
Contributors: Q. Chen* , L. Samayoa n, C. Yang *, P. Bradbury *, *, M. Neumeyer *, M. Romay *, Q. Sun *
Ed(s): R. Mauricio
MeSH headings : Domestication; Gene Flow; Gene Frequency; Genes, Plant; Genetic Variation; Genetics, Population; Quantitative Trait Loci; Quantitative Trait, Heritable; Selection, Genetic; Zea mays / classification; Zea mays / genetics
TL;DR:
A strongly reduced number of QTL for domestication traits in maize relative to teosinte is observed, consistent with the previously reported depletion of additive variance by selection during domestication, and genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 22, 2020
2018 journal article
Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly
Frontiers in Plant Science, 9.
author keywords: Convolvulaceae; genotyping-by-sequencing; GBSpoly; polyploid; SNPs; sweetpotato; USDA germplasm
TL;DR:
In this study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions were determined using single nucleotide polymorphisms identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: October 19, 2018
2018 journal article
Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement
Nature Communications, 9(1).
MeSH headings : Base Sequence; Carotenoids / metabolism; Diploidy; Ecotype; Genetic Variation; Genome, Plant; Genomics; Ipomoea batatas / genetics; Molecular Sequence Annotation; Multigene Family; Phylogeny; Plant Breeding; Polyploidy; Repetitive Sequences, Nucleic Acid / genetics
TL;DR:
Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: November 26, 2018
2018 journal article
Identification of a locus in maize controlling response to a host-selective toxin derived from Cochliobolus heterostrophus, causal agent of southern leaf blight
Theoretical and Applied Genetics, 131(12), 2601–2612.
Contributors: X. Xiaodong*, n, Q. Yang n & P. Balint-Kurti n
MeSH headings : Alleles; Ascomycota / pathogenicity; Chromosome Mapping; Genetic Association Studies; Host-Pathogen Interactions / genetics; Mycotoxins; Plant Diseases / genetics; Plant Diseases / microbiology; Quantitative Trait Loci; Zea mays / genetics; Zea mays / microbiology
TL;DR:
A host-selective, proteinaceous maize toxin was identified from the culture filtrate of the maize pathogenCochliobolus heterostrophus, and a significant correlation (− 0.58) was observed between SLB susceptibility and CF-sensitivity in seedlings.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: December 3, 2018
2016 journal article
A Genome-Wide Association Study for Partial Resistance to Maize Common Rust
PHYTOPATHOLOGY, 106(7), 745–751.
Contributors: n, W. Tracy n, R. Wisser n, B. De Vries n & P. Balint-Kurti n
author keywords: association analysis; disease resistance; linkage disequilibrium; QTL
MeSH headings : Basidiomycota / physiology; Genome-Wide Association Study; Host-Pathogen Interactions; Plant Diseases / immunology; Plant Immunity / genetics; Zea mays / genetics; Zea mays / immunology
TL;DR:
Resistance to common rust was found to be moderately correlated with resistance to three other diseases and with the severity of the hypersensitive defense response previously assessed in the same population.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
The Genetics of Leaf Flecking in Maize and Its Relationship to Plant Defense and Disease Resistance
Plant Physiology, 172(3), 1787–1803.
Contributors: n, Y. Bian n, B. De Vries *, W. Tracy *, R. Wisser *, J. Holland n , P. Balint-Kurti n
MeSH headings : Alleles; Chromosome Mapping; Disease Resistance / genetics; Genetics, Population; Genome-Wide Association Study; Inbreeding; Light; Phenotype; Plant Diseases / genetics; Plant Diseases / immunology; Plant Leaves / genetics; Plant Leaves / radiation effects; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci / genetics; Reactive Oxygen Species / metabolism; Seeds / genetics; Zea mays / genetics; Zea mays / radiation effects
TL;DR:
Evidence is presented suggesting that mild flecking could be used as a selection criterion for breeding programs trying to incorporate broad-spectrum disease resistance and positive correlations were found between increased flecking, stronger defense response, increased disease resistance, and increased pest resistance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2015 journal article
Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel
BMC PLANT BIOLOGY, 15(1).
Contributors: L. Samayoa *, R. Malvar *, n, J. Holland n & A. Butrón *
author keywords: Candidate genes; Corn borer; Genome-wide association study; Insect resistance; Maize; Mixed linear models; Sesamia nonagrioides
MeSH headings : Animals; Genes, Plant; Genome-Wide Association Study; Moths / physiology; Polymorphism, Single Nucleotide; Zea mays / genetics; Zea mays / parasitology
TL;DR:
Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Maize homologs of hydroxycinnamoyltransferase, a key enzyme in lignin biosynthesis, bind the nucleotide binding leucine-rich repeat Rp1 proteins to modulate the defense response
Plant Physiology, 169(3), 2230–2243.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes
BMC GENOMICS, 16.
author keywords: Chestnut; Comparative genomics; Blight resistance; Synteny; Plant genomics; Physical map; Genetic map
MeSH headings : Computational Biology; Evolution, Molecular; Genome, Plant; Genomics / methods; Magnoliopsida / classification; Magnoliopsida / genetics; Phylogeny; Physical Chromosome Mapping; Quantitative Trait Loci; Synteny / genetics
TL;DR:
Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
The genetic basis of flecking and its relationship to disease resistance in the IBM maize mapping population
THEORETICAL AND APPLIED GENETICS, 128(11), 2331–2339.
Contributors: V. Vontimitta*, n, B. Penning *, G. Johal * & P. Balint-Kurti*
MeSH headings : Chromosome Mapping; Crosses, Genetic; DNA, Plant / genetics; Disease Resistance / genetics; Phenotype; Plant Diseases / genetics; Plant Leaves; Quantitative Trait Loci; Zea mays / genetics
TL;DR:
The genetic architecture controlling leaf flecking in maize is determined and its relationship to disease resistance and the defense response is investigated and several quantitative trait loci for flecking were identified.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2012 journal article
A Connected Set of Genes Associated with Programmed Cell Death Implicated in Controlling the Hypersensitive Response in Maize
GENETICS, 193(2), 609-+.
Contributors: *, A. Negeri, R. Dhawan, B. Venkata *, P. Sharma *, A. Garg*, E. Gachomo *, S. Marla *
MeSH headings : Alleles; Apoptosis / genetics; Crosses, Genetic; Disease Resistance / genetics; Genes, Plant; Genetic Markers; Genetic Variation; Genome-Wide Association Study; Linear Models; Linkage Disequilibrium; Phenotype; Physical Chromosome Mapping; Polymorphism, Single Nucleotide; Zea mays / genetics; Zea mays / physiology
TL;DR:
An association mapping strategy based on the Mutant Assisted Gene Identification and Characterization approach to identify naturally occurring allelic variants associated with phenotypic variation in HR, and the extent of genome-wide LD is examined.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
3. Good Health and Well-being
(OpenAlex)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2012 journal article
A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map
TREE GENETICS & GENOMES, 9(2), 525–537.
author keywords: Castanea spp.; Chestnut; BAC library; HICF fingerprinting; Physical map; Comparative genomics; Chestnut blight resistance
TL;DR:
Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2012 journal article
A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)
Tree Genetics & Genomes, 9(2), 557–571.
author keywords: Fagaceae; Castanea spp.; Chestnut; Genetic map; Comparative genomics; Disease resistance
TL;DR:
A highly informative genetic map was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science; OpenAlex)
Sources: Crossref, Web Of Science
Added: August 6, 2018
2011 journal article
Genetic diversity in Bambara groundnut (Vigna subterranea (L.) Verdc.) as revealed by phenotypic descriptors and DArT marker analysis
Genetic Resources and Crop Evolution, 59(3), 347–358.
author keywords: Germplasm; Phylogeny; Population structure; Vigna subterranea
TL;DR:
Higher genetic diversity was observed for the Cameroon/Nigeria region relative to other regions, in agreement with the hypothesis that this region is the centre of origin for Bambara groundnut.
(via Semantic Scholar)
Source: Crossref
Added: June 6, 2020
2010 journal article
Comparison of gene order in the chromosome region containing a TERMINAL FLOWER 1 homolog in apricot and peach reveals microsynteny across angiosperms
Plant Science, 179(4), 390–398.
author keywords: Apricot; BAC contig; Gene order; Microsynteny; Peach; TFL1
TL;DR:
Sequence analysis revealed that the apricot and peach TFL1 genes display a similar exon–intron organization to homologs from other eudicot species and the defined amino acid domains are preserved.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: June 6, 2020
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