Alan E. Pepper
YOU?
Author Swipe
View article: Plastomic studies inform the mechanisms of edaphic adaptation in North American species in the tribe Thelypodieae (Brassicaceae)
Plastomic studies inform the mechanisms of edaphic adaptation in North American species in the tribe Thelypodieae (Brassicaceae) Open
Premise Adaptation to edaphic environments is vital for plant survival. The tribe Thelypodieae (Brassicaceae) thrives in diverse edaphic conditions, including harsh serpentine soils. A robust phylogeny is essential to understanding the eda…
View article: Diversity across the border: Genetic study of a highly disjunct occurrence of the U.S. federally-endangered plant species Physaria thamnophila, Brassicaceae (Zapata bladderpod) discovered in Mexico
Diversity across the border: Genetic study of a highly disjunct occurrence of the U.S. federally-endangered plant species Physaria thamnophila, Brassicaceae (Zapata bladderpod) discovered in Mexico Open
Taxonomy, genetics and biogeography each make key contributions to biological conservation. However, integrating these disciplines to obtain a coherent account of the status of a taxon of concern not always straightforward. This is the cas…
View article: Accurate identification of de novo genes in plant genomes using machine learning algorithms
Accurate identification of de novo genes in plant genomes using machine learning algorithms Open
De novo gene birth—the evolution of new protein-coding genes from ancestrally noncoding DNA—is increasingly appreciated as an important source of genetic and phenotypic innovation. However, the frequency and overall biological impact of de…
View article: Casola et al. de novo genes plans MLAs
Casola et al. de novo genes plans MLAs Open
Gene datasets from three plant species regarding features of DNA and protein sequences
View article: Comparative Analysis of Temporal Transcriptome Reveals the Relationship Between Pectin Degradation and Pathogenicity of Defoliating Verticillium Dahliae to Upland Cotton (Gossypium Hirsutum)
Comparative Analysis of Temporal Transcriptome Reveals the Relationship Between Pectin Degradation and Pathogenicity of Defoliating Verticillium Dahliae to Upland Cotton (Gossypium Hirsutum) Open
Background: Verticillium wilt (VW), caused by Verticillium dahliae Kleb., is a major plant disease that causes heavy annual losses around the world, especially in Upland cotton ( Gossypium hirsutum ). The disease-causing pathogen can be cl…
View article: Comparative analysis of temporal transcriptome reveals the relationship between pectin degradation and pathogenicity of defoliating<i>Verticillium dahliae</i>to Upland cotton (<i>Gossypium hirsutum</i>)
Comparative analysis of temporal transcriptome reveals the relationship between pectin degradation and pathogenicity of defoliating<i>Verticillium dahliae</i>to Upland cotton (<i>Gossypium hirsutum</i>) Open
Verticillium wilt (VW), caused by Verticillium dahliae Kleb., is a major plant disease that causes heavy annual losses around the world, especially in Upland cotton ( Gossypium hirsutum ). The disease-causing pathogen can be classified int…
View article: Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)
Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower) Open
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, …
View article: Development of 15 microsatellite loci in the endangered <i>Streptanthus glandulosus</i> subsp. <i>niger</i> (Brassicaceae)
Development of 15 microsatellite loci in the endangered <i>Streptanthus glandulosus</i> subsp. <i>niger</i> (Brassicaceae) Open
Premise of the Study The endangered Streptanthus glandulosus subsp. niger (Brassicaceae) is endemic to a single peninsula in California and threatened by fragmentation. We developed microsatellite markers to investigate genetic diversity i…
View article: Genes regulating gland development in the cotton plant
Genes regulating gland development in the cotton plant Open
Summary In seeds and other parts of cultivated, tetraploid cotton ( Gossypium hirsutum L.), multicellular groups of cells lysigenously form dark glands containing toxic terpenoids such as gossypol that defend the plant against pests and pa…
View article: Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant
Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant Open
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have …
View article: QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt
QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt Open
Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population…
View article: Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line
Genome-wide identification and characterization of microRNAs differentially expressed in fibers in a cotton phytochrome A1 RNAi line Open
Cotton fiber is an important commodity throughout the world. Fiber property determines fiber quality and commercial values. Previous studies showed that silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium …
View article: Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (&lt;i&gt;Gossypium hirsutum&lt;/i&gt;) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants
Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (<i>Gossypium hirsutum</i>) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants Open
Silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with improved fiber quality (longer, stronger and finer fiber). To reveal molecular mechanisms …
View article: Additional file 4: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array
Additional file 4: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array Open
Distribution of SNP minor allele frequency across groups of germplasm. Categories of minor allele frequency are used to show the relative polymorphism of SNPs within a set of germplasm. The values shown are the fraction of all SNPs within …
View article: Additional file 5: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array
Additional file 5: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array Open
Matrix showing numbers of different and identical SNPs for all pairwise combinations of 395 samples. Values above the diagonal represent the count of homozygous differences between pairs of samples. Values below the diagonal represent the …
View article: Additional file 2: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array
Additional file 2: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array Open
List of Gossypium samples genotyped for SNP diversity analyses. The table includes information for seed source, improved/wild classification, assigned categories for improved breeding regions, assigned categories for wild race types, avail…
View article: Additional file 3: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array
Additional file 3: of Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array Open
Individual matrices with numbers of different and identical SNPs for entries with the same name. These values were extracted directly from Additional file 5. Values above the diagonal represent the count of homozygous differences between p…
View article: RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.)
RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.) Open
RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antise…