A5010103643- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Genetics and Plant Breeding
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Plant Disease Resistance and Genetics
- Wheat and Barley Genetics and Pathology
- Crop Yield and Soil Fertility
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- CRISPR and Genetic Engineering
- Plant Taxonomy and Phylogenetics
- Plant pathogens and resistance mechanisms
- Genetic and Environmental Crop Studies
- Genetically Modified Organisms Research
- Viral Infectious Diseases and Gene Expression in Insects
- Evolution and Genetic Dynamics
- Plant and soil sciences
- Molecular Biology Techniques and Applications
- Bioenergy crop production and management
- Genomics and Chromatin Dynamics
- Plant tissue culture and regeneration
- Microbial infections and disease research
- RNA modifications and cancer
Iowa State University
2016-2025
University of Missouri
2023
University of California, Davis
2008-2015
Plant (United States)
2012-2014
University Medical Center
1997
Indiana University – Purdue University Indianapolis
1997
Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) provide an opportunity comprehensive annotation of TEs. Numerous methods exist each class TEs, but their relative performances not been systematically compared. Moreover, a pipeline needed produce non-redundant library TEs species lacking this resource generate whole-genome TE...
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. results demonstrate ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres revealed additional variation major...
The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation the genome-wide effects these phenomena only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize conspecific wild teosinte Zea mays ssp. mexicana, (hereafter, mexicana) are known hybridize in fields highland Mexico. Despite widespread evidence gene flow, mexicana maintain distinct...
The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, gene flow wild relatives. interplay between selection shaped diversity across populations genomes.We investigate these processes using high-depth resequencing data from 31 landraces spanning the pre-Columbian distribution maize, four teosinte individuals (Zea mays ssp. parviglumis). Genome-wide analyses reveal that experienced...
Abstract A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a assembly maize with each chromosome entirely traversed in single contig. The 2,178.6 Mb T2T Mo17 base accuracy over 99.99% unveiled structural features all repetitive regions genome. There were several super-long simple-sequence-repeat arrays having consecutive...
Foraging range, an important component of bee ecology, is considerable interest for insect-pollinated plants because it determines the potential outcrossing among individuals. However, long-distance pollen flow difficult to assess, especially when plant also relies on self-pollination. Pollen movement can be estimated indirectly through population genetic data, but complementary data pollinator flight distances necessary validate such estimates. By using radio-tracking cowpea return flights,...
The genome of maize (Zea mays ssp.mays) consists mostly transposable elements (TEs) and varies in size among lines.This variation extends to other species the genus Zea: although Zea luxurians diverged only ;140,000 years ago, their genomes differ by ;50%.We used paired-end Illumina sequencing evaluate potential contribution TEs difference between these two species.We aligned reads both a filtered gene set an exemplar database unique repeats representing 1,514 TE families; ;85% mapped...
Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and genetics evolution complex traits. To examine how domestication has reshaped transcriptome maize seedlings, we used expression profiling 18,242 genes 38 diverse genotypes 24 teosinte genotypes. We detected evidence more than 600 having significantly different levels in...
Since the advent of modern plant breeding in 1930s, North American maize has undergone a dramatic adaptation to high-input agriculture. Despite importance genetic contributions historical yield increases, little is known about underlying genomic changes. Here we use high-density SNP genotyping characterize set lines spanning history breeding. We provide unique analysis genome-wide developments diversity, ancestry, and selection. The marked by steady increase differentiation linkage...
Abstract A possible consequence of planting genetically modified organisms (GMOs) in centres crop origin is unintended gene flow into traditional landraces. In 2001, a study reported the presence transgenic 35S promoter maize landraces sampled 2000 from Sierra Juarez Oaxaca, Mexico. Analysis large sample taken same region 2003 and 2004 could not confirm existence transgenes, thereby casting doubt on earlier results. These two studies were based different sampling analytical procedures are...
Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization the genetic basis adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, an understanding population structure potential selection pressures. Here, we used single-nucleotide polymorphism genotyping data on numerous variables describe in 21 populations teosinte, wild ancestor maize. We found complex hierarchical...
Abstract Creating gapless telomere-to-telomere assemblies of complex genomes is one the ultimate challenges in genomics. We use two independent and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed 63 contigs contig N50 162 Mb. This includes chromosome 3 (236 Mb) 9 (162 Mb), 53 Mb Ab10 meiotic drive haplotype. The data also reveal internal structure seven centromeres five heterochromatic knobs, showing that major tandem repeat arrays (CentC, knob180, TR-1)...
Genome assemblies are foundational for understanding the biology of a species. They provide physical framework mapping additional sequences, thereby enabling characterization of, example, genomic diversity and differences in gene expression across individuals tissue types. Quality metrics genome gauge both completeness contiguity an assembly help confidence downstream biological insights. To compare quality multiple assemblies, set common typically calculated then compared to one or more...