Huihui Yu

University of Nebraska at Lincoln | NU · Center for Plant Science Innovation

Background Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. Result We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core p...

Hybrid rice has made considerable contributions to achieve the ambitious goal of food security for the world population. Hybrid rice from indica/xian and japonica/geng subspecies shows much higher heterosis and is thereby an important innovation in promoting rice production in the next decade. However, such inter-subspecific hybrid rice has long su...

A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum ( Paspalum vaginatum ) is a self-incompatible and multiply stress-tolerant wild...

Cytoplasmic male sterility (CMS) determined by mitochondrial genes and restorer of fertility ( Rf ) controlled by nuclear-encoded genes provide the breeding systems of many hybrid crops for the utilization of heterosis. Although several CMS/ Rf systems have been widely exploited in rice, hybrid breeding using these systems has encountered difficult...

Environmental factors, including different stresses, can have an impact on the expression of genes and subsequently the phenotype and development of plants. Since a large number of genes are involved in response to the perturbation of the environment, identifying groups of co-expressed genes is meaningful. The gene co-expression network models can...

It is challenging to identify the smallest microexons (≤15-nt) due to their small size. Consequently, these microexons are often misannotated or missed entirely during genome annotation. Here, we develop a pipeline to accurately identify 2,398 small microexons in 10 diverse plant species using 990 RNA-seq datasets, and most of them have not been an...

Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as ce...

A number of crop wild relatives can tolerate extreme stressed to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild...

MicroRNAs (miRNAs) are essential regulators of gene expression in metazoans and plants. In plants, most miRNAs are generated from primary miRNA transcripts (pri‐miRNAs), which are processed by the Dicer‐like 1(DCL1) complex along with accessory proteins. Serrate‐Associated Protein 1 (SEAP1), a conserved splicing‐related protein, has been studied in...

Pre‐mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome‐wide association studies (GWAS), we developed a software tool to quantify and visualize Variations of Splicing in Population (VaSP). VaSP can quantify splicing variants from short‐read RNA‐seq dataset...

Speciation has long been regarded as an irreversible process once the reproductive barriers had been established. However, unlike in natural populations, artificial selection might either accelerate or prevent speciation processes in domesticated species. Asian cultivated rice is a target crop for both domestication and artificial breeding; it cont...

MADS-box transcription factors (TFs) are subdivided into type-I and II based on phylogenetic analysis. The type II’s regulate floral organ identity and flowering time, but type I’s are relatively less characterized. Here, we report functional characterization of two type-I MADS-box TFs in rice (Oryza sativa), MADS78 and MADS79. Transcript abundance...

Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co‐expression network...

In many applications, such as gene co-expression network analyses, data arises with a huge number of covariates while the size of sample is comparatively small. To improve the accuracy of prediction, variable selection is often used to get a sparse solution by forcing coefficients of variables contributing less to the observed response variable to...

Key message Pyramiding ofS5-nandf5-ncumulatively improved seed-setting rate ofindica–japonicahybrids, which provided an effective approach for utilization of inter-subspecific heterosis in rice breeding. Abstract Breeding for indica–japonica hybrid rice is an attractive approach to increase rice yield. However, hybrid sterility is a major obstacle...

Blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the big problems in rice production in China, especially for high yield hybrid varieties made from a two-line system in which thermo-sensitive genic male sterile (TGMS) lines are used. In this study, we report the introgression of a rice blast resistance gene Pi2 from VE6219 i...

Background: Mechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds. Results: A set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 va...

Background Soil phosphorus (P) deficiency is one of the major limiting factors to crop production. The development of crop varieties with improved P use efficiency (PUE) is an important strategy for sustainable agriculture. The objectives of this research were to identify quantitative trait loci (QTLs) linked to PUE traits using a high-density sing...

The ability to reveal the regulatory architecture of genes at the whole-genome level by constructing a regulatory network is critical for understanding the biological processes and developmental programmes of organisms. Here, we conducted an eQTL-guided function-related co-expression analysis to identify the putative regulators and construct gene r...

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred...

A high density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecular breeders. With the accumulation of huge amounts of genomic resequencing data and available technologies for accurate SNP detection, it is possible to design high density and high quality rice SNP arrays. Here we report the development of...

The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics-based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic backg...

The completed gnome sequences of rice subspecies, indica and japonica, as well as the characterization of a large number of important trait-related genes, laid a sound foundation for genomics-based breeding. Re-sequencing thousands of rice germplasm accessions by next-generation sequencing technologies provided breeders with enormous amount of sequ...

Grain weight, one of the three major components of rice yield, is largely determined by grain size, which is controlled by quantitative trait loci (QTLs). In a previous study, we identified qGS5 as a major QTL for grain width. Here, we report our identification of two more major grain-size QTLs (qGL3 and qGW2a) by using a recombinant inbred line (R...

Rice is a staple food crop and has become a reference of monocot plant for functional genomic research. With the availability of high quality rice genome sequence, there has been rapid accumulation of functional genomic resources, including: large mutant libraries by T-DNA insertion, transposon tagging, and chemical mutagenesis; global expression p...

Leaf size is a major determinant of plant architecture and yield potential in crops. A previous study showed that the genomic region of chromosome 1 contains a major quantitative trait locus (QTL) for flag leaf size in a set of backcross recombinant inbred lines derived from two elite parental lines (Zhenshan 97 and 93-11). In the present study, th...

Auxin is an indispensable hormone throughout the lifetime of nearly all plant species. Several aspects of plant growth and development are rigidly governed by auxin, from micro to macro hierarchies; auxin also has a close relationship with plant-pathogen interactions. Undoubtedly, precise auxin levels are vitally important to plants, which have man...

Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL) analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (R...

QTLs identified for yield and yield-component traits in four trials from the RIL population of the Zhenshan 97/Minghui 63 cross using the ultra-high density SNP bin map. Trial 1, in 1997 from Xing et al [16] (Xing1997); Trial 2, in 1998 from Xing et al [16] (Xing1998); Trial 3, in 1998 from Hua et al [17]–[18] (Hua1998); Trial 4, in 1999 from Hua e...

QTLs identified for grain length and grain width for the data of 1998 and 2008 from the RIL population of the Zhenshan 97/Minghui 63 cross, using the RFLP/SSR map. (XLS)

Distribution of 270,820 high quality SNPs identified from low-coverage sequences of 241 RILs. The physical positions on each chromosome are based on rice TIGR6.1. The short blue lines indicate the SNP density (SNPs/50-kb). The average density is about 36 SNPs/50-kb (∼1 SNP/1.37-kb). A height more than 150 SNPs/50-kb is set to 150 SNPs/50-kb. The pi...

QTLs identified for yield and yield-component traits in four trials from the RIL population of the Zhenshan 97/Minghui 63 cross using the RFLP/SSR genetic map. Trial 1, in 1997 from Xing et al [16] (Xing1997); Trial 2, in 1998 from Xing et al [16] (Xing1998); Trial 3, in 1998 from Hua et al [17]–[18] (Hua1998); Trial 4, in 1999 from Hua et al [17]–...

Number of QTLs identified for yield and yield-component traits for the data of four trials from the RIL population of the Zhenshan 97/Minghui 63 cross using the RFLP/SSR (map1) and ultra-high density SNP bin (map2) maps, with LOD threshold 3.0. (XLS)

Distribution of 1,619 recombinant bins based on the SNP markers in the rice genome. Physical positions are based on rice TIGR6.1. Adjacent bins are separated by short lines on each chromosome. Yellow arrows indicate centromeres. Red boxes indicate bins of more than 2 Mb in length. (TIF)

Map information for the 220 polymorphic loci detected by RFLP/SSR markers for the 210 RILs from the Zhenshan 97/Minghui 63 cross. (XLS)

Map information for all 1,619 bins for the 210 RILs from the Zhenshan 97/Minghui 63 cross based on high quality SNPs obtained from population sequencing. (XLS)

The main objective of this study was to identify the genes causing etiolation in a rice mutant, the thylakoids of which were scattered. Three populations were employed to map the genes for etiolation using bulked segregant analysis. Genetic analysis confirmed that etiolation was controlled by two recessive genes, et11 and et12, which were fine mapp...

Breeding crops with the quality of broad-spectrum disease resistance using genetic resources is one of the principal goals of crop improvement. However, the molecular mechanism of broad-spectrum resistance remains largely unknown. Here, we show that GH3-2, encoding an indole-3-acetic acid (IAA)-amido synthetase, mediates a broad-spectrum resistance...

Analyses of quantitative trait loci (QTLs) for expression levels (eQTLs) of genes reveal a genetic relationship between expression variation and the regulator, thus unlocking information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and trans...

Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in...

Peptide transporter (PTR) family whose member can transport di-/tripeptides and nitrate is important for plant growth and development. Although the rice (Oryza sativa L.) genome has been sequenced for a few years, a genomic survey, characterization and expression profile analysis of the PTR family in this species has not been reported. In this stud...

TM prediction result of OsPTR proteins by TMHMM. The predicted TM regions are marked with red rectangle and their probabilities are list in the Y-axis. Length: the length of the protein sequence. Number of predicted TMs: The number of predicted TM helices. Total prob of N-in: The total probability that the N-term is on the cytoplasmic side of the m...

Hierarchical cluster display of expression profile for 50 AtPTR genes with corresponding probes. Color key at the left represents log2 expression values. Developmental stages (list in the table below) used for expression profiling are mentioned on bottom of each column. On the left side of expression map, cluster dendrogram is shown.

Hierarchical cluster display of expression profile for 81 OsPTR genes with corresponding probes in ZS97. Color key represents log2 expression values. Developmental stages (Additional file 9) used for expression profiling are mentioned on bottom of each column. On the left side of expression map, cluster dendrogram is shown. On the right side, five...

Detailed information of rice samples used in microarray analysis

The detailed information of each OsPTR gene and corresponding protein.

Domain composition and structures of OsPTR proteins predicted by SMART. The graphical presentations are: transmembrane segments as predicted by the TMHMM program (blue vertical rectangle); segments of low compositional complexity determined by the SEG program (pink rectangle); signal peptides determined by the SignalP program (red rectangle); disor...

Results of differential expression analysis in 7 d-old seedlings subjected to three phytohormone (NAA, GA3 and KT) treatments and plumule or radicle with light/dark regulation in MH63 and ZS97

Phylogenetic relationship of rice and Arabidopsis PTR proteins. The unrooted tree was generated using ClustalX program by neighbor-joining method. Bootstrap values from 1000 replicates are indicated at each node. The orthologous proteins are marked with red circles and the AtPTR proteins are marked with blue triangles. The tree can be divided into...

Average microarray signal values of 81 OsPTR genes in MH63 and ZS97

Ankyrin repeat (ANK) containing proteins comprise a large protein family. Although many members of this family have been implicated in plant growth, development and signal transduction, only a few ANK genes have been reported in rice. In this study, we analyzed the structures, phylogenetic relationship, genome localizations and expression profiles...