A5085102532- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Legume Nitrogen Fixing Symbiosis
- Genetic diversity and population structure
- Sunflower and Safflower Cultivation
- Plant Molecular Biology Research
- Nematode management and characterization studies
- Agronomic Practices and Intercropping Systems
- Soybean genetics and cultivation
- Remote Sensing in Agriculture
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Gene expression and cancer classification
- Animal Nutrition and Physiology
- Plant Disease Resistance and Genetics
- Plant nutrient uptake and metabolism
- Agriculture and Biological Studies
- Plant and animal studies
- Lipid metabolism and biosynthesis
- Adipose Tissue and Metabolism
- Plant Gene Expression Analysis
- Research in Cotton Cultivation
- Phytase and its Applications
- Hops Chemistry and Applications
University of Nebraska–Lincoln
2020-2024
China Agricultural University
2006-2022
State Key Laboratory of Plant Physiology and Biochemistry
2019
Guangdong Academy of Agricultural Sciences
2013
Massachusetts Institute of Technology
2011
A better understanding of the extent convergent selection among crops could greatly improve breeding programs. We found that quantitative trait locus KRN2 in maize and its rice ortholog, OsKRN2, experienced selection. These orthologs encode WD40 proteins interact with a gene unknown function, DUF1644, to negatively regulate grain number both crops. Knockout or OsKRN2 increased yield by ~10% ~8%, respectively, no apparent trade-offs other agronomic traits. Furthermore, genome-wide scans...
Abstract Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent potentially powerful, unbiased method identify microbes sensitive host genotype and connect them with that influence their colonization. Here, we conducted population-level analysis rhizospheres 200 sorghum genotypes. Using 16S rRNA amplicon...
Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced structure. We generated reference-level genome assemblies the founders and genotyped all 18K-rice through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to 16 traits were identified, including
Summary Improvement of grain yield is an essential long‐term goal maize ( Zea mays ) breeding to meet continual and increasing food demands worldwide, but the genetic basis remains unclear. We used 10 different recombination inbred line RIL populations genotyped with high‐density markers phenotyped in multiple environments dissect architecture ear traits. Three methods were map quantitative trait loci QTL s) affecting found 17–34 minor‐ or moderate‐effect that influence traits, little...
Abstract DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines the maize genome, but variation and evolution landscape during domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) bisulfite (WGBS) data on populations modern maize, landrace, teosinte ( Zea mays ssp. parviglumis) to estimate epimutation rates selection coefficients. We find weak evidence for direct any context, thousands differentially methylated regions (DMRs) are...
SUMMARY Maize ( Zea mays ssp. ) populations exhibit vast ranges of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number projects sought to measure differences between within maize using whole‐genome resequencing strategies, identifying millions segregating single‐nucleotide polymorphisms (SNPs) insertions/deletions (InDels). Unlike older genotyping strategies like microarrays by sequencing, should, in principle, frequently identify score common variants....
The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of rhizobiome is governed by intraspecific variation in host genetics field degree which selection can reshape rhizobiome. Here, we quantify rhizosphere microbial communities associated with a replicated diversity panel 230 maize (Zea mays L.) genotypes grown agronomically relevant conditions under high N (+N) low (-N)...
Abstract Advancements in the use of genome‐wide markers have provided unprecedented opportunities for dissecting genetic components that control phenotypic trait variation. However, cost‐effectively characterizing agronomically important traits on a large scale remains bottleneck. Unmanned aerial vehicle (UAV)‐based high‐throughput phenotyping has recently become prominent method, as it allows numbers plants to be analyzed time‐series manner. In this experiment, 233 inbred lines from maize (...
Genome engineering using single-stranded oligonucleotides is an efficient method for generating small chromosomal and episomal modifications in a variety of host organisms. The efficiency this allelic replacement strategy highly dependent on avoidance the endogenous mismatch repair (MMR) machinery. However, global MMR inactivation generally results significant accumulation undesired background mutations. Here, we present novel oligos containing chemically modified bases (2′-Fluoro-Uridine,...
The nutritional traits of maize kernels are important for human and animal nutrition, these have undergone selection to meet the diverse needs humans. However, our knowledge genetic basis selecting kernel is limited. Here, we identified both single epistatic quantitative trait loci (QTLs) that contributed differences oil carotenoid between teosinte. Over half teosinte alleles QTLs increased values detected traits. Based on pleiotropism or linkage information QTLs, constructed a trait-locus...
Maize (Zea mays L. ssp. mays) was domesticated from teosinte parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication adaptation processes over past two decades, but efforts been limited either sample size or genetic diversity. To better understand these processes, we conducted genome-wide survey 982 inbred lines 190 accessions using 40,000 single-nucleotide polymorphism markers.Population...
Abstract Mapping genotype to phenotype is an essential topic in genetics and genomics research. As the Omics data become increasingly available, 2-variable methods have been widely applied associate with (genome-wide association study), gene expression (transcriptome-wide expression. However, signals detected by these suffer from low mapping resolution or inexplicit causality between phenotype, making it challenging interpret validate molecular mechanisms of underlying genomic variations...
Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which chromatin environment affects this bias not explored. Here, we compared dominant subgenome (maize1) and recessive (maize2) with respect patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, accessible regions (ACRs). Our data show that between subgenomes for all...
Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) emerging as an important contributor to both phenotypic variability disease susceptibility. Herein, we performed genome-wide CNV scan in 96 chickens 12 diversified breeds, benefiting high-density Affymetrix 600 K SNP arrays. We identified total 231 autosomal regions (CNVRs) encompassing 5.41 Mb chicken genome...
Chicken is considered to be an excellent model for genetic studies of phenotypic and genomic evolution, with large effective population size, specialized commercial lines, strong human-driven selection. High-density chicken SNP chips can help achieve a better understanding the selection mechanisms in artificially selected populations. We performed genome-wide tests signature 385 White Leghorn hens mapped positively regions genome annotations. Ten QTL related egg production, quality, growth,...
Abstract Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little known about prevalence such their effects on phenotypic traits in context modern breeding. To address this, we examined number frequency 350 elite maize inbred lines developed over past few decades China United States. Our findings reveal an accumulation weakly a decrease strongly mutations, indicating dominant genetic drift...
The sunflower (Helianthus annuus L.) is one of the most essential oil crops in world. Several component traits, including flowering time, plant height, stem diameter, seed weight, and kernel determine yield. Although genetic mechanisms governing variation these yield-related traits have been studied using various approaches, genome-wide association studies (GWAS) not widely applied to sunflowers. In this study, a set 342 accessions was evaluated 2019 2020 an incomplete randomized block...
Abstract Sunflower ( Helianthus annuus L.) plays an essential role in meeting the demand for edible oil worldwide. The yield of sunflower seeds encompasses several component traits, including disc diameter. Over three consecutive years, 2019, 2020, and 2022, we assessed phenotypic variation diameter across a diverse set accessions (N = 342) replicated field trials. Upon aggregating data from multiple estimated broad sense heritability H 2 ) trait to be 0.88. A subset N 274 was genotyped by...
Thyroid hormone responsive Spot 14 (THRSP) is suggested as a transcription factor involved in the regulation of adipogenic enzymes by 3 thyroid response elements promoter region. In chicken genome, THRSP gene was identified to duplicate into 2 paralogs, THRSPα and THRSPβ. current study, cDNA sequences duplicated duck genes were cloned real-time PCR rapid amplification ends. Duck THRSPβ predicted encode peptides with 133 amino acids, which had 74 68% sequence identity at level, 78 74% acid...
DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines the genome are methylated. Recently, major progress has been made describing molecular mechanisms driving methylation, yet variation and evolution landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) whole bisulfite (WGBS) on populations modern landrace, teosinte ( Zea mays ssp. parviglumis ) to investigate adaptive phenotypic consequences...
Epigenetic modification is widely known to be involved in embryo development, aging, tumorigenesis, and many complex diseases. Both hypermethylation of CpG islands at the gene promoters global hypomethylation are initiation progression carcinogenesis. However, only a small portion occurs leads overexpression certain oncogenes. To determine whether DNA methylation plays role tumorigenesis Marek's disease, we selected one putative oncogene 8 tumor suppressor genes from expression profile for...
Mapping genotype to phenotype is an essential topic in genetics and genomics research. As the Omics data become increasingly available, genome-wide association study (GWAS) has been widely applied establish relationship between phenotype. However, signals detected by GWAS usually span broad genomic regions with many underneath candidate genes, making it challenging interpret validate molecular functions of genes. Under context research, we hypothesized a causal chain from partially mediated...