Corrigendum: Sparse testing designs for optimizing predictive ability in sugarcane populations.

[This corrects the article DOI: 10.3389/fpls.2024.

Sequencing vs. amplification for the estimation of allele dosages in sugarcane ( spp.).

Premise: Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane ( spp.).

Sparse testing designs for optimizing predictive ability in sugarcane populations.

Sugarcane is a crucial crop for sugar and bioenergy production. Saccharose content and total weight are the two main key commercial traits that compose sugarcane's yield. These traits are under complex genetic control and their response patterns are influenced by the genotype-by-environment (G×E) interaction.

Genetic association analysis in sugarcane (Saccharum spp.) for sucrose accumulation in humid environments in Colombia.

Background: Sucrose accumulation in sugarcane is affected by several environmental and genetic factors, with plant moisture being of critical importance for its role in the synthesis and transport of sugars within the cane stalks, affecting the sucrose concentration. In general, rainfall and high soil humidity during the ripening stage promote plant growth, increasing the fresh weight and decreasing the sucrose yield in the humid region of Colombia. Therefore, this study aimed to identify markers associated with sucrose accumulation or production in the humid environment of Colombia through a genome-wide association study (GWAS).

Corrigendum: The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization.

[This corrects the article DOI: 10.3389/fpls.2022.

The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization.

The OMICAS alliance is part of the Colombian government's Scientific Ecosystem, established between 2017-2018 to promote world-class research, technological advancement and improved competency of higher education across the nation. Since the program's kick-off, OMICAS has focused on consolidating and validating a multi-scale, multi-institutional, multi-disciplinary strategy and infrastructure to advance discoveries in plant science and the development of new technological solutions for improving agricultural productivity and sustainability. The strategy and methods described in this article, involve the characterization of different crop models, using high-throughput, real-time phenotyping technologies as well as experimental tissue characterization at different levels of the omics hierarchy and under contrasting conditions, to elucidate epigenome-, genome-, proteome- and metabolome-phenome relationships.

Modern Approaches for Transcriptome Analyses in Plants.

The collection of all transcripts in a cell, a tissue, or an organism is called the transcriptome, or meta-transcriptome when dealing with the transcripts of a community of different organisms. Nowadays, we have a vast array of technologies that allow us to assess the (meta-)transcriptome regarding its composition (which transcripts are produced) and the abundance of its components (what are the expression levels of each transcript), and we can do this across several samples, conditions, and time-points, at costs that are decreasing year after year, allowing experimental designs with ever-increasing complexity. Here we will present the current state of the art regarding the technologies that can be applied to the study of plant transcriptomes and their applications, including differential gene expression and coexpression analyses, identification of sequence polymorphisms, the application of machine learning for the identification of alternative splicing and ncRNAs, and the ranking of candidate genes for downstream studies.

Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid.

Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940.

NGSEP3: accurate variant calling across species and sequencing protocols.

Motivation: Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features.

Results: Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats.

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

In the version of this article originally published, the accession codes listed in the data availability section were incorrect and the section was incomplete. The text for this section should have read "The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. The data can also be downloaded from the following link: http://www.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined.

The Seed Biotinylated Protein of Soybean (Glycine max): A Boiling-Resistant New Allergen (Gly m 7) with the Capacity To Induce IgE-Mediated Allergic Responses.

Soybean is a common allergenic food; thus, a comprehensive characterization of all the proteins that cause allergy is crucial to the development of effective diagnostic and immunotherapeutic strategies. A cDNA library was constructed from seven stages of developing soybean seeds to investigate candidate allergens. We searched the library for cDNAs encoding a seed-specific biotinylated protein (SBP) based on its allergenicity in boiled lentils.

Hypoallergenic legume crops and food allergy: factors affecting feasibility and risk.

Currently, the sole strategy for managing food hypersensitivity involves strict avoidance of the trigger. Several alternate strategies for the treatment of food allergies are currently under study. Also being explored is the process of eliminating allergenic proteins from crop plants.