Correction: Salazar-Cubillas, K.C.; Dickhoefer, U. Evaluating the Protein Value of Fresh Tropical Forage Grasses and Forage Legumes Using In Vitro and Chemical Fractionation Methods. Animals 2021, 11, 2853

The authors wish to make the following correction to their paper [...]

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment​, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods Some 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. Key Results Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs​. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions We suggest a new coherent nomenclature for the genomes present​. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses

Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.

Evaluating the Protein Value of Fresh Tropical Forage Grasses and Forage Legumes Using In Vitro and Chemical Fractionation Methods

The objectives of the present study were (1) to assess the adequacy of the in vitro and chemical methods to predict post-ruminal crude protein supply (PRCP) from fresh tropical forage, and (2) to identify PRCP supply predictors. Twenty-three fresh forage grasses and 15 forage legumes commonly used in domestic cattle feeding in the tropics and subtropics were incubated in the rumen of cows to determine ruminal crude protein (CP) degradation. The PRCP supply was calculated from in situ rumen-undegraded CP and in vitro organic matter digestibility (i.e., reference method), from ammonia-nitrogen release during in vitro incubation (i.e., in vitro method), and from the concentrations of chemical CP fractions (i.e., chemical method). The adequacy was evaluated using error-index and dimensionless parameters, and stepwise regression was used to select PRCP predictors. Adequacy ranged from poor to moderate (0.53 to 0.74) for the in vitro method being lower for forage legumes at a slow rumen passage rate (0.20), and even poorer (0.02 to 0.13) for the chemical method. Hence, the in vitro method can estimate PRCP supply in tropical forages with moderate to high but not with slow passage rates. Equations developed in the present study appear to predict PRCP supply with reasonable adequacy.