Exploiting historical agronomic data to develop genomic prediction strategies for early clonal selection in the Louisiana sugarcane variety development program.

Genomic selection can enhance the rate of genetic gain of cane and sucrose yield in sugarcane (Saccharum L.), an important industrial crop worldwide. We assessed the predictive ability (PA) for six traits, such as theoretical recoverable sugar (TRS), number of stalks (NS), stalk weight (SW), cane yield (CY), sugar yield (SY), and fiber content (Fiber) using 20,451 single nucleotide polymorphisms (SNPs) with 22 statistical models based on the genomic estimated breeding values of 567 genotypes within and across five stages of the Louisiana sugarcane breeding program.

MicroRNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156-squamosa promoter binding protein (SBP) and zma-miR398/zma-miR394-F -box combinations involved in resistance mechanisms.

Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungus Aspergillus flavus that can produce the carcinogenic metabolite aflatoxin (AF) especially under climate change induced abiotic stressors that favor mold growth. Several studies have used "-omics" approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction.

QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population.

Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant U.S.

Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with resistance in maize.

Aflatoxin (AF) contamination, caused by , compromises the food safety and marketability of commodities, such as maize, cotton, peanuts, and tree nuts. Multigenic inheritance of AF resistance impedes conventional introgression of resistance traits into high-yielding commercial maize varieties. Several AF resistance-associated quantitative trait loci (QTLs) and markers have been reported from multiple biparental mapping and genome-wide association studies (GWAS) in maize.

Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice.

While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice () is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance.

Whole-Genome Sequencing of KMR3 and -Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice.

The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.

A Reappraisal of Polyploidy Events in Grasses (Poaceae) in a Rapidly Changing World.

Around 80% of megaflora species became extinct at the Cretaceous-Paleogene (K-Pg) boundary. Subsequent polyploidy events drove the survival of thousands of plant species and played a significant historical role in the development of the most successful modern cereal crops. However, current and rapid global temperature change poses an urgent threat to food crops worldwide, including the world's big three cereals: rice, wheat, and maize, which are members of the grass family, Poaceae.

Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore?

The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light-dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network.

An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane.

Sugarcane crop is important for both sugar and biofuels. A world collection of sugarcane and related grasses (WCSRG) maintained at Miami, FL contains > 1,200 non-redundant clones of different species and genera within the Saccharum complex. However, linkage of undesirable alleles with useful genes in wild species has hindered its efficient utilization in sugarcane breeding.

Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice.

Background: Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services.

Identification of QTLs for Resistance to Head Blight Using a Doubled Haploid Population Derived from Southeastern United States Soft Red Winter Wheat Varieties AGS 2060 and AGS 2035.

head blight (FHB), caused primarily by the fungus , is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high inoculum pressure from corn stubble contribute to frequent FHB epidemics in the southern United States. The soft red winter wheat variety AGS 2060 is moderately susceptible (as opposed to susceptible) to FHB and regularly found in pedigrees of resistant breeding lines.

The 21st Century Agriculture: When Rice Research Draws Attention to Climate Variability and How Weedy Rice and Underutilized Grains Come in Handy.

Rice, the first crop to be fully sequenced and annotated in the mid-2000s, is an excellent model species for crop research due mainly to its relatively small genome and rich genetic diversity. The 130-million-year-old cereal came into the limelight in the 1960s when the semi-dwarfing gene , better known as the "green revolution" gene, resulted in the establishment of a high-yielding semi-dwarf variety IR8. Deemed as the miracle rice, IR8 saved millions of lives and revolutionized irrigated rice farming particularly in the tropics.

Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions.

Improving drought resistance in crops is imperative under the prevailing erratic rainfall patterns. Drought affects the growth and yield of most modern rice varieties. Recent breeding efforts aim to incorporate drought resistance traits in rice varieties that can be suitable under alternative irrigation schemes, such as in a (semi)aerobic system, as row (furrow-irrigated) rice.

Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection.

Sugarcane is an economically important crop for both food and biofuel industries. Marker-assisted breeding in sugarcane is becoming a reality with the recent development and deployment of markers linked with disease resistance genes. Large linkage disequilibrium in sugarcane makes genome-wide association studies (GWAS) a better alternative to biparental mapping to identify markers associated with agronomic traits.

Natural and targeted isovariants of the rice actin depolymerizing factor 2 can alter its functional and regulatory binding properties.

Actin depolymerizing factors (ADFs) are ubiquitous actin-binding proteins that play essential roles in maintaining cellular actin dynamics by depolymerizing/severing F-actin. Plant ADF isoforms show functional divergence via differential biochemical and cellular properties. We have shown previously that ADF2 of rice (OsADF2) and smooth cordgrass (SaADF2) displayed contrasting biochemical properties and stress response in planta.

Identification of Genomic Regions Controlling Leaf Scald Resistance in Sugarcane Using a Bi-parental Mapping Population and Selective Genotyping by Sequencing.

Leaf scald, caused by , is a major sugarcane disease worldwide. The disease is managed primarily with resistant cultivars obtained through classical breeding. However, erratic symptom expression hinders the reliability and reproducibility of selection for resistance.

Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes.

The H2A.Z histone variant plays a role in the modulation of environmental responses, but the nature of the associated mechanisms remains enigmatic. We investigated global H2A.

Correction: Genome-wide microarray analysis leads to identification of genes in response to herbicide, metribuzin in wheat leaves.

[This corrects the article DOI: 10.1371/journal.pone.

Sugarcane Cell Wall-Associated Defense Responses to Infection by .

The plant cell wall is known to be the first barrier against plant pathogens. Detailed information about sugarcane cell wall-associated defense responses to infection by the causal agent of smut, , is scarce. Herein, (immuno)histochemical analysis of two smut resistant and two susceptible sugarcane cultivars was conducted to understand host cell wall structural and compositional modifications in response to fungal infection.

An actin-depolymerizing factor from the halophyte smooth cordgrass, Spartina alterniflora (SaADF2), is superior to its rice homolog (OsADF2) in conferring drought and salt tolerance when constitutively overexpressed in rice.

Actin-depolymerizing factors (ADFs) maintain the cellular actin network dynamics by regulating severing and disassembly of actin filaments in response to environmental cues. An ADF isolated from a monocot halophyte, Spartina alterniflora (SaADF2), imparted significantly higher level of drought and salinity tolerance when expressed in rice than its rice homologue OsADF2. SaADF2 differs from OsADF2 by a few amino acid residues, including a substitution in the regulatory phosphorylation site serine-6, which accounted for its weak interaction with OsCDPK6 (calcium-dependent protein kinase), thus resulting in an increased efficacy of SaADF2 and enhanced cellular actin dynamics.

Identification of candidate resistance genes of cotton against infection using a comparative transcriptomics approach.

A comparative transcriptome analysis was performed using the genes significantly differentially expressed in cotton, corn and peanut in response to aflatoxin producing fungus with an objective of identifying candidate resistance genes in cotton. Two-way analyses identified 732 unique genes to be differentially regulated by the fungus with only 26 genes common across all three crops that were considered candidate resistance genes with an assumption that these genes have specific roles in conferring the resistance trait. Genes of membrane cellular component involved in DNA binding with involvement in defense responses were highly represented among the differentially expressed unique genes.

Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression.

Background: Formation of nucleosomes along eukaryotic DNA has an impact on transcription. Major transcriptional changes occur in response to low external phosphate (Pi) in plants, but the involvement of chromatin-level mechanisms in Pi starvation responses have not been investigated.

Results: We mapped nucleosomes along with transcriptional changes after 24-h of Pi starvation in rice (Oryza sativa) by deep sequencing of micrococcal nuclease digested chromatin and ribosome-depleted RNA.

Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions.

Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits.

Genome-wide microarray analysis leads to identification of genes in response to herbicide, metribuzin in wheat leaves.

Herbicides are an important component of weed management in wheat, particularly in the southeastern US where weeds actively compete with wheat throughout the winter for nutrients and reduce tillering and ultimately the yield of the crop. Some wheat varieties are sensitive to metribuzin, a low-cost non-selective herbicide, leading to leaf chlorosis, stand loss, and decreased yield. Knowledge of the genetics of herbicide tolerance in wheat is very limited and most new varieties have not been screened for metribuzin tolerance.