Sampling Maize () Seed Endophytes.

For most farmers, the production of maize grain is the ultimate goal of the entire field season. From the point of view of plant microbiome studies, seeds are particularly interesting in that they are the only avenue for vertical transmission of microbes from parent to offspring, though microbes can also enter maize seeds via wounds or silks. Although the presence of seed endophytes is well documented, their role, if any, in seed health and their effects on the next generation of plants are largely unknown.

Manipulating the Maize () Microbiome.

Maize () is a multifaceted cereal grass used globally for nutrition, animal feed, food processing, and biofuels, and a model system in genetics research. Studying the maize microbiome sometimes requires its manipulation to identify the contributions of specific taxa and ecological traits (i.e.

Sampling and Analysis of the Maize Microbiome.

Maize is an important plant for both global food security and genetics research. As the importance of microorganisms to plant health is becoming clearer, there is a growing interest in understanding the relationship between maize and its associated microbiome; i.e.

Sampling Root-Associated Microbiome Communities of Maize ().

The soil microbiome of maize shapes its fitness, sustainability, and productivity. Accurately sampling maize's belowground microbial communities is important for identifying and characterizing these functions. Here, we describe a protocol to sample the maize rhizosphere (including the rhizoplane and endorhizosphere) and root zone (still influential but further from the root) in a form suitable for downstream analyses like culturing and DNA extractions.

Preparation of Illumina 16s Amplicon Sequencing Libraries with Peptide Nucleic Acids (PNAs) for the Analysis of Maize-Associated Microbiomes.

One of the most common methods to survey bacterial communities is targeted amplification of the hypervariable regions of the 16s rRNA gene followed by sequencing. This protocol details Illumina library preparation of such amplicons from communities isolated from maize. We include both staggered PCR primers to improve Illumina base calling and peptide nucleic acids (PNAs) to reduce the presence of plant organelles.

Soybean microbiome composition and the impact of host plant resistance.

Microbial communities play an important role in the growth and development of plants, including plant immunity and the decomposition of complex substances into absorbable nutrients. Hence, utilizing beneficial microbes becomes a promising strategy for the optimization of plant growth. The objective of this research was to explore the root bacterial profile across different soybean genotypes and the change in the microbial community under soybean cyst nematode (SCN) infection in greenhouse conditions using 16S rRNA sequencing.

kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS.

Genome-wide association studies (GWAS) have been widely used to identify genetic variation associated with complex traits. Despite its success and popularity, the traditional GWAS approach comes with a variety of limitations. For this reason, newer methods for GWAS have been developed, including the use of pan-genomes instead of a reference genome and the utilization of markers beyond single-nucleotide polymorphisms, such as structural variations and k-mers.

Yield prediction through integration of genetic, environment, and management data through deep learning.

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models.

Identification of small effect quantitative trait loci of plant architectural, flowering, and early maturity traits in reciprocal interspecific introgression population in cotton.

Plant architecture, flowering time and maturity traits are important determinants of yield and fiber quality of cotton. Genetic dissection of loci determining these yield and quality components is complicated by numerous loci with alleles conferring small differences. Therefore, mapping populations segregating for smaller numbers and sizes of introgressed segments is expected to facilitate dissection of these complex quantitative traits.

Genome-wide association mapping of resistance to the sorghum aphid in Sorghum bicolor.

Since 2013, the sorghum aphid (SA), Melanaphis sorghi (Theobald), has been a serious pest that hampers all types of sorghum production in the U.S. Known sorghum aphid resistance in sorghum is limited to a few genetic regions on SBI-06.

Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions.

High consumer demand for cannabidiol (CBD) has made high-CBD hemp () an extremely high-value crop. However, high demand has resulted in the industry developing faster than the research, resulting in the sale of many hemp accessions with inconsistent performance and chemical profiles. These inconsistencies cause significant economic and legal problems for growers interested in producing high-CBD hemp.

Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain.

Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel.

Genome-Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet.

Developed genome-wide SNP marker data for kodo, proso, and little millet Marker data used to analyze genetic diversity Heritability results of various traits used to validate genetic data Millets are a diverse group of small-seeded grains that are rich in nutrients but have received relatively little advanced plant breeding research. Millets are important to smallholder farmers in Africa and Asia because of their short growing season, good stress tolerance, and high nutritional content. To advance the study and use of these species, we present genome-wide marker datasets and population structure analyses for three minor millets: kodo millet (Paspalum scrobiculatum L.

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics.

Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.

Large-scale replicated field study of maize rhizosphere identifies heritable microbes.

Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples.

Mapping a male-fertility restoration locus for the A cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map.

Background: Pearl millet (Pennisetum glaucum (L.) R. Br.

A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize.

Maize abnormal chromosome 10 (Ab10) encodes a classic example of true meiotic drive that converts heterochromatic regions called knobs into motile neocentromeres that are preferentially transmitted to egg cells. Here, we identify a cluster of eight genes on Ab10, called the Kinesin driver (Kindr) complex, that are required for both neocentromere motility and preferential transmission. Two meiotic drive mutants that lack neocentromere activity proved to be kindr epimutants with increased DNA methylation across the entire gene cluster.

Genetic Analysis of Fiber Quality Traits in Reciprocal Advanced Backcross Populations.

In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L.

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain.

Tocopherols, tocotrienols, and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot , which has green, photosynthetic seeds, but our understanding of tocochromanol accumulation in major crops, whose seeds are nonphotosynthetic, remains limited.

Maize Genes and Regulate Plant Architecture.

Leaf architecture directly influences canopy structure, consequentially affecting yield. We discovered a maize () mutant with aberrant leaf architecture, which we named (). Pleiotropic mutations in affect leaf length and width, leaf angle, and internode length and diameter.

Genotyping-by-Sequencing.

Genotyping-by-sequencing (GBS) refers to a suite of related methods that obtain genotype data from samples by using restriction enzyme digestion followed by high-throughput sequencing. GBS is a refinement of restriction site-associated DNA sequencing (RADseq) methods, with a goal of being able to perform library preparations quickly, cost-effectively, and in a high-throughput manner. This protocol contains the steps necessary to go from purified DNA to Illumina-ready libraries.