Association study of crude seed protein and fat concentration in a USDA pea diversity panel.

Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources.

Genetic diversity and population structure of bermudagrass ( spp.) revealed by genotyping-by-sequencing.

Bermudagrass ( spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 accessions consisting of 193 common bermudagrass ( var.

Genes and genetic mechanisms contributing to fall armyworm resistance in maize.

Maize (Zea mays L.) is a crop of major economic and food security importance globally. The fall armyworm (FAW), Spodoptera frugiperda, can devastate entire maize crops, especially in countries or markets that do not allow the use of transgenic crops.

Comparative Analysis of Multiple GWAS Results Identifies Metabolic Pathways Associated with Resistance to Infection and Aflatoxin Accumulation in Maize.

Aflatoxins are carcinogenic secondary metabolites produced by several species of , including , an important ear rot pathogen in maize. Most commercial corn hybrids are susceptible to infection by , and aflatoxin contaminated grain causes economic damage to farmers. The creation of inbred lines resistant to fungal infection or the accumulation of aflatoxins would be aided by knowing the pertinent alleles and metabolites associated with resistance in corn lines.

Genetic Variability Assessment of Tropical Indica Rice ( L.) Seedlings for Drought Stress Tolerance.

Drought stress is one of the most devastating abiotic factors limiting plant growth and development. Devising an efficient and rapid screening method at the seedling stage is vital in identifying genotypes best suited under drought conditions. An experiment was conducted to assess 74 rice genotypes for drought tolerance using specially designed mini-hoop structures.

Three types of genes underlying the Gametophyte factor1 locus cause unilateral cross incompatibility in maize.

Unilateral cross incompatibility (UCI) occurs between popcorn and dent corn, and represents a critical step towards speciation. It has been reported that ZmGa1P, encoding a pectin methylesterase (PME), is a male determinant of the Ga1 locus. However, the female determinant and the genetic relationship between male and female determinants at this locus are unclear.

Target-oriented prioritization: targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding.

Genomic prediction in crop breeding is hindered by modeling on limited phenotypic traits. We propose an integrative multi-trait breeding strategy via machine learning algorithm, target-oriented prioritization (TOP). Using a large hybrid maize population, we demonstrate that the accuracy for identifying a candidate that is phenotypically closest to an ideotype, or target variety, achieves up to 91%.

Population genomics of Zea species identifies selection signatures during maize domestication and adaptation.

Background: Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp.

Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species.

Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology ("DArTseq"). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs.

Assessment of agro-morphological, physiological and yield traits diversity among tropical rice.

Rice ( L.) is an essential staple food crop, but the per acre average rice yield is less than its substantial potential in many countries. Rice breeders and growers would benefit from a robust genotypes with better morpho-physiological and yield-related traits.

Reference Gene Selection for RT-qPCR Analysis in Maize Kernels Inoculated with .

Resistance against infection by the fungus Link in commercial maize ( L.) is the topic of many studies, but few studies have investigated the effects of infection on gene expression levels in ear kernels. A crucial component of gene expression profiling by RT-qPCR is having a reliable set of reference genes that show relatively constant expression across the treatments and phenotypes under study.

The genetic mechanism of heterosis utilization in maize improvement.

Background: In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits.

Results: We show that, although yield heterosis is correlated with the widespread, minor-effect epistatic QTLs, it may be resulted from a few major-effect additive and dominant QTLs in early developmental stages.

Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis.

Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F1 hybrids by crossing 488 diverse inbred lines with two elite testers.

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.

To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O.

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information.

Recently, a new implementation of a previously described method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and released. The Pathway Association Study Tool (PAST) was developed to address concerns with user-friendliness and slow-running analyses. This new user-friendly tool has been released on Bioconductor and Github.

Breeding Crops for Enhanced Food Safety.

An increasing global population demands a continuous supply of nutritious and safe food. Edible products can be contaminated with biological (, bacteria, virus, protozoa), chemical (, heavy metals, mycotoxins), and physical hazards during production, storage, transport, processing, and/or meal preparation. The substantial impact of foodborne disease outbreaks on public health and the economy has led to multidisciplinary research aimed to understand the biology underlying the different contamination processes and how to mitigate food hazards.

CUBIC: an atlas of genetic architecture promises directed maize improvement.

Background: Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders.

Results: Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait.

PAST: The Pathway Association Studies Tool to Infer Biological Meaning from GWAS Datasets.

In recent years, a bioinformatics method for interpreting genome-wide association study (GWAS) data using metabolic pathway analysis has been developed and successfully used to find significant pathways and mechanisms explaining phenotypic traits of interest in plants. However, the many scripts implementing this method were not straightforward to use, had to be customized for each project, required user supervision, and took more than 24 h to process data. PAST (Pathway Association Study Tool), a new implementation of this method, has been developed to address these concerns.

Evaluating rice for salinity using pot-culture provides a systematic tolerance assessment at the seedling stage.

Background: Rice (Oryza sativa L.) is one of the major staple food crops consumed globally. However, rice production is severely affected by high salinity levels, particularly at the seedling stage.

Leveraging GWAS data to identify metabolic pathways and networks involved in maize lipid biosynthesis.

Maize (Zea mays mays) oil is a rich source of polyunsaturated fatty acids (FAs) and energy, making it a valuable resource for human food, animal feed, and bio-energy. Although this trait has been studied via conventional genome-wide association study (GWAS), the single nucleotide polymorphism (SNP)-trait associations generated by GWAS may miss the underlying associations when traits are based on many genes, each with small effects that can be overshadowed by genetic background and environmental variation. Detecting these SNPs statistically is also limited by the levels set for false discovery rate.

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs.

Using interspecific crosses involving Steud. as donor and L. as recurrent parents, rice breeders at the Africa Rice Center developed several 'New Rice for Africa (NERICA)' improved varieties.

Genome-Wide Association and Metabolic Pathway Analysis of Corn Earworm Resistance in Maize.

Maize ( L.) is a staple crop of economic, industrial, and food security importance. Damage to the growing ears by corn earworm [ (Boddie)] is a major economic burden and increases secondary fungal infections and mycotoxin levels.

Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination.

Many projects have identified candidate genes for resistance to aflatoxin accumulation or infection and growth in maize using genetic mapping, genomics, transcriptomics and/or proteomics studies. However, only a small percentage of these candidates have been validated in field conditions, and their relative contribution to resistance, if any, is unknown. This study presents a consolidated list of candidate genes identified in past studies or in-house studies, with descriptive data including genetic location, gene annotation, known protein identifiers, and associated pathway information, if known.