Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis.

Introduction: Maize ( L.) is one of the most important crops worldwide, the kernel size-related traits are the major components of maize grain yield.

Methods: To dissect the genetic architecture of four kernel-related traits of 100-kernel weight, kernel length, kernel width, and kernel diameter, a genome-wide association study (GWAS) was conducted in the waxy and sweet maize panel comprising of 447 maize inbred lines re-sequenced at the 5× coverage depth.

Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses.

Elite inbred line 18-599 was developed via triple test cross from introduced hybrid P78599 and used as parents of dozens of maize hybrids adapting to the diverse ecological conditions of the maize ecological region in Southwest China. In this study, its genomic DNA was resequenced and aligned with the B73 genome sequence to identify single nucleotide polymorphism (SNP), and insertion (In) and deletion (Del) loci. These loci were aligned with those between B73 and 1020 inbred lines in the HapMap database to identify specific variation loci of 18-599.

Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses.

CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues.

Complete Genome Sequence Data of Novel Strain CQUSa03, a Potential Biological Control Agent for Potato Oomycete and Fungal Diseases.

CQUSa03 was recently isolated from the rhizosphere soil of a potato resistant variety, which showed strong biocontrol activity against potato late blight and other fungal diseases. To elucidate the biocontrol mechanism, the whole genome of CQUSa03 was sequenced using second-generation Illumina and third-generation Nanopore sequencing technologies. The assembled genome of CQUSa03 was 8,107,672 bp, containing one chromosome and three plasmids, with an average GC content of 72.

Characterization of phenylalanine ammonia-lyase genes facilitating flavonoid biosynthesis from two species of medicinal plant .

Background: and , belong to the genus, have been used for Chinese herbal drugs as well as health food. Phenylalanine ammonia-lyase (PAL), the key enzyme in primary metabolism and phenylpropanoid metabolism, produces secondary metabolites (flavonoids) in plants, which are beneficial for the biosynthesis of phenylpropanoid metabolites.

Methods: The genes were cloned from and according to our previous transcriptomic analysis.

Zinc Transporter ZmLAZ1-4 Modulates Zinc Homeostasis on Plasma and Vacuolar Membrane in Maize.

Zinc is an essential micronutrient for plant growth and development, and functions as a cofactor for hundreds of transcription factors and enzymes in numerous biological processes. Zinc deficiency is common abiotic stress resulting in yield loss and quality deterioration of crops, but zinc excess causes toxicity for biological systems. In plants, zinc homeostasis is tightly modulated by zinc transporters and binding compounds that uptake/release, transport, localize, and store zinc, as well as their upstream regulators.

Alternative Splicing Variants Negatively Regulate Drought Tolerance in Maize.

Serine/threonine protein phosphatase 2C (PP2C) dephosphorylates proteins and plays crucial roles in plant growth, development, and stress response. In this study, we characterized a clade B member of maize PP2C family, i.e.

Identification and fine mapping of a major QTL (qRtsc8-1) conferring resistance to maize tar spot complex and validation of production markers in breeding lines.

A major QTL of qRtsc8-1 conferring TSC resistance was identified and fine mapped to a 721 kb region on chromosome 8 at 81 Mb, and production markers were validated in breeding lines. Tar spot complex (TSC) is a major foliar disease of maize in many Central and Latin American countries and leads to severe yield loss. To dissect the genetic architecture of TSC resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid population were used for GWAS and selective genotyping analysis, respectively.

Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum.

Background: The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported.

Genomic Prediction of Resistance to Tar Spot Complex of Maize in Multiple Populations Using Genotyping-by-Sequencing SNPs.

Tar spot complex (TSC) is one of the most important foliar diseases in tropical maize. TSC resistance could be furtherly improved by implementing marker-assisted selection (MAS) and genomic selection (GS) individually, or by implementing them stepwise. Implementation of GS requires a profound understanding of factors affecting genomic prediction accuracy.

Genetic Dissection of Quantitative Resistance to Common Rust () in Tropical Maize ( L.) by Combined Genome-Wide Association Study, Linkage Mapping, and Genomic Prediction.

Common rust is one of the major foliar diseases in maize, leading to significant grain yield losses and poor grain quality. To dissect the genetic architecture of common rust resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid (DH) population, DH1, were used to perform GWAS and linkage mapping analyses. The GWAS results revealed six single-nucleotide polymorphisms (SNPs) significantly associated with quantitative resistance of common rust at a very stringent threshold of value 3.

Isolation and characterization of maize gene promoter in drought-response.

The clade A members of serine/threonine protein phosphatase 2Cs (PP2Cs) play crucial roles in plant growth, development, and stress response via the ABA signaling pathway. But little is known about other PP2C clades in plants. Our previous study showed that maize the , a clade B member of , negatively regulated drought tolerance in transgenic .

Maize ZmBES1/BZR1-5 Decreases ABA Sensitivity and Confers Tolerance to Osmotic Stress in Transgenic .

The BRI1-EMS suppressor 1 (BES1)/brassinazole-resistant 1 (BZR1) transcription factors, key components in the brassinosteroid signaling pathway, play pivotal roles in plant growth and development. However, the function of BES1/BZR1 in crops during stress response remains poorly understood. In the present study, we characterized ZmBES1/BZR1-5 from maize, which was localized to the nucleus and was responsive to abscisic acid (ABA), salt and drought stresses.

Identification and characterization of the TCA cycle genes in maize.

Background: The tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear.

Results: In this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig.

Metabolite Profiling and Transcriptome Analyses Provide Insights into the Flavonoid Biosynthesis in the Developing Seed of Tartary Buckwheat ().

Tartary buckwheat () seeds are rich in flavonoids. However, the detailed flavonoid compositions and the molecular basis of flavonoid biosynthesis in tartary buckwheat seeds remain largely unclear. Here, we performed a combined metabolite profiling and transcriptome analysis to identify flavonoid compositions and characterize genes involved in flavonoid biosynthesis in the developing tartary buckwheat seeds.

Isolation and identification of a vegetative organ-specific promoter from maize.

To avoid the unregulated overexpression of the exogenous genes, specific or inducible expression is necessary for some exogenous genes in transgenic plants. But little is known about organ- or tissue-specific promoters in maize. In the present study, the expression of a maize pentatricopeptide repeat (PPR) protein encoding gene, , was analyzed by RNA-sequencing data and confirmed by quantitative real time PCR.

Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.).

A set of RIL population was used to detect QTL associated with the sizes of eight consecutive leaves, across different environments, and ten QTL clusters were identified as main QTLs. One of the important parameters of the maize leaf architecture that affects light penetration into the canopy, leaf size, has long attracted breeders' attention for optimizing the plant type of maize and for maximizing the grain yield (GY). In this study, we used 253 RIL lines derived from a cross between B73 and SICAU1212 to investigate the leaf widths (LWs), leaf lengths (LLs), and leaf areas (LAs) of eight consecutive leaves of maize below the tassel and GY across different environments and to identify quantitative traits loci (QTLs) controlling the above-mentioned traits, using inclusive interval mapping for single-environment analysis plus a mixed-model-based composite interval mapping for joint analysis.

Development of Genome-Wide Insertion and Deletion Polymorphism Markers from Next-Generation Sequencing Data in Rice.

Background: Next-generation sequencing technologies enable the re-sequencing of a large number of genomes and provide an unprecedented opportunity to discover numerous DNA polymorphisms throughout the genome of a species. As the second most abundant form of genetic variation, InDels, with characteristics of co-dominance, multiple alleles and high stability and density and that are easy to genotype, have received an increasing amount attention.

Results: In this work, a total of 2,329,544 InDels were identified in 1767 rice genomes; these InDels were dispersed across all 12 rice chromosomes, with one InDel marker found, on average, every 160.

Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data.

Background: Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species.

A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data.

Background: Maize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world.

Clinical outcomes of treatment for spinal cord compression due to primary non-Hodgkin lymphoma.

Background Context: Primary non-Hodgkin lymphoma of the spine (PNHLS) with spinal cord compression is an extremely rare disease in clinical practice. The optimal treatment options for this disease have been controversial and pose a challenge for the clinicians.

Purpose: To provide some useful insight into the treatments, outcomes, and prognostic factors of PNHLS.

Higher-order ocular aberrations caused by crystalline lens waterclefts.

Purpose: To compare visual acuity and ocular higher-order aberrations (HOAs) in eyes with waterclefts, a type of crystalline lens opacity, and in normal eyes.

Setting: Department of Ophthalmology, Kanazawa Medical University, Ishikawa, Japan, and Faculty of Medicine, University of Iceland, Reykjavik, Iceland.

Methods: In this nested case-control study of subjects attending the third examination of the Reykjavik Eye Study in 2008, eyes with pure waterclefts and control eyes with no lenticular opacity were evaluated.