Biology subjects

Castiblanco, V.

Publications and source records attributed to Castiblanco, V..

7 recordsLinked to original sources

bioRxiv2025

Integrating image-based phenotyping and GWAS to map tolerance to Spittlebug nymphs in interspecific Urochloa grasses

Urochloa grasses are among the most widely used forage grasses across the tropics. Spittlebugs (Hemiptera: Cercopidae) are major pests of tropical Urochloa (syn. Brachiaria) pastures, severely reducing forage productivity and quality. Understanding the genetic basis of host-plant resistance is essential for developing durable resistant cultivars. Here, we combined high-throughput image-based phenotyping and genome-wide association studies (GWAS) to dissect the genetic architecture of tolerance to Aeneolamia varia nymphs in 339 interspecific F hybrids derived from crosses between resistant sexual and susceptible apomictic Urochloa parents. Digital image analysis using both unsupervised (DQU) and supervised (DTR) quantification pipelines enabled precise estimation of plant damage, yielding moderate to high broad-sense heritability estimates (H{superscript 2} = 0.49-0.66). In contrast, insect survival (NTS) exhibited low to moderate correlations with all damage traits and lower heritability estimates (H{superscript 2} = 0.42). Using 57,051 high-quality SNPs aligned to the genome of the hybrid cultivar Basilisk, GWAS models identified 18 quantitative trait loci (QTL) for plant damage traits, but none for insect survival (antibiosis). Six robust QTL on chromosomes 1, 6, 7, 27, 29, and 36 were consistently detected across models and phenotyping methods, explaining up to 21.5% of phenotypic variance. Candidate gene analysis revealed proteins involved in hormone signalling, oxidative stress response, and cell wall modification, suggesting multifaceted tolerance mechanisms. These results provide a foundational set of molecular markers associated with spittlebug tolerance in Urochloa, useful for marker-assisted and genomic selection in our forage breeding programme.

plant biology↗

bioRxiv2021

The five Urochola spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

Background and AimsUrochloa (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochloa spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvement, following the example from other crop genera. MethodsWe explored the genetic make-up and population structure in 111 accessions, which comprise the five Urochloa species used for the development of commercial cultivars. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq, averaging 40M reads per accession, to generate 1,167,542 stringently selected SNP markers that tentatively encompassed the complete Urochloa gene pool used in breeding. Key ResultsWe identified ten subpopulations, which had no relation with geographical origin and represented ten independent gene pools, and two groups of admixed accessions. Our results support a division in U. decumbens by ploidy, with a diploid subpopulation closely related to U. ruziziensis, and a tetraploid subpopulation closely related to U. brizantha. We observed highly differentiated gene pools in U. brizantha, which were not related with origin or ploidy. Particularly, one U. brizantha subpopulation clustered distant from the other U. brizantha and U. decumbens subpopulations, so likely containing unexplored alleles. We also identified a well-supported subpopulation containing both polyploid U. decumbens and U. brizantha accessions; this was the only group containing more than one species and tentatively constitutes an independent "mixed" gene pool for both species. We observed two gene pools in U. humidicola. One subpopulation, "humidicola-2", was much less common but likely includes the only known sexual accession in the species. ConclusionsOur results offered a definitive picture of the available diversity in Urochloa to inform breeding and resolve questions raised by previous studies. It also allowed us identifying prospective founders to enrich the breeding gene pool and to develop genotyping and genotype-phenotype association mapping experiments. HIGHLIGHTWe clarified the genetic make-up and population structure of 111 Urochloa spp. forage grasses to inform cultivar development.

plant biology↗

bioRxiv2021

Flow cytometry-based determination of ploidy from dried leaf specimens in genomically complex collections of the tropical forage grass Urochloa s. l.

We aimed to develop an optimized approach to determine ploidy for dried leaf material in a germplasm collection of a tropical forage grass group, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. The methods enable robust identification of ploidy levels (coefficient of variation, CV, typically <5%). Ploidy of some 353 forage grass accessions (ploidy range from 2 to 9), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes used in the current breeding programs at CIAT and EMBRAPA: the brizantha and humidicola agamic complexes are variable, with multiple ploidy levels and DNA content. U. brizantha has odd level of ploidy (x=5), and the relative differences in nuclear DNA content between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed some aneuploidy.

genomics↗

bioRxiv2021

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

Background and AimsDiploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. 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. MethodsSome 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 with in situ hybridization to chromosomes were used to identify chromosomes and genomes in Urochloa accessions belonging to the different agamic complexes. Key ResultsGenome 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. ConclusionsWe 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. 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.

genomics↗

bioRxiv2020

Allele Mining in Diverse Accessions of Urochloa and Megathyrsus spp. Tropical Grasses to Improve Forage Quality and Reduce Environmental Impact

The C4 Urochloa spp (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease amount of land required per unit production and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We studied allelic diversity of 20 target genes (11 for digestibility, 9 for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha, U. decumbens, U. humidicola, U. ruziziensis and M. maximum. We used RNAseq and then bait-capture DNA-seq to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence. We found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified 7 putative LOF alleles with high confidence, including ones in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme. HighlightWe found gene variants in a collection of tropical grasses that could help reduce environmental impact of cattle production.

plant biology↗

bioRxiv2020

Digital imaging outperforms traditional scoring methods of spittlebug tolerance in Urochloa humidicola hybrids

American spittlebug complex (Hemiptera: Cercopidae) is a critical pest for existing Urochloa humidicola cultivars in the neotropical savannas. The U. humidicola breeding program of the International Center for Tropical Agriculture aims to increase tolerance to spittlebugs. To develop U. humidicola genotypes with superior tolerance to spittlebugs than existing cultivars, adequate screening methods ought to be deployed. Currently, visual scores of plant damage by spittlebugs is the standard method to screen for variation in plant tolerance. However, visual scoring is prone to human bias, is of medium throughput and relies of the expertise of well-trained personnel. In this study, we compared estimations of plant damage from two alternative methods (SPAD measurements and digital images) and visual scoring from an inexpert evaluator with the plant damage estimated from an expert. This information should instruct if different methods could be implemented in the U. humidicola breeding program. Time needed to evaluate damage was recorded for each method. Lins correlation coefficient, Pearsons correlation coefficient and broad sense heritability values were also calculated. Overall, damage estimated from digital images showed the highest throughput (twice as fast as visual scoring from an expert); high correlations with visual scoring (r > 0.80, p < 0.0001); and heritability values for plant damage as good or better (> 0.7) than those obtained by visual scoring from an expert. Our results indicate that digital imaging is a phenotyping method that might improve the efficiency of breeding for increased tolerance to spittlebugs in U. humidicola. HighlightDigital imaging outperformed standard scoring method of spittlebug tolerance in Urochloa humidicola, suggesting that this method might improve the efficiency of breeding for such stress.

plant biology↗

bioRxiv2019

A new Brachiaria reference genome and its application in identifying genes associated with natural variation in tolerance to acidic soil conditions among Brachiaria grasses

Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as a forage in the tropics because of their resilience and low demand for nutrients, have a greater tolerance to high concentrations of aluminium cations than most other grass crops. In this work, we explored the natural variation in tolerance to aluminium cations (Al3+) between high and low tolerant Brachiaria species and characterised their transcriptional differences during stress. We also identified three QTLs associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we have identified 30 genes responsible for Al3+ tolerance in Brachiaria. We also observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition and vesicle location genes homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which are associated with external tolerance mechanisms to Al3+ stress in other grasses. The contrasting regulation of RNA translation and response signalling suggests response phasing is critical to Al3+ tolerance. HIGHLIGHTWe identified QTLs, genes and molecular responses in high and low tolerant Brachiaria grasses associated with aspects of response to aluminium stress, such as regulation, cell-wall composition and active transport.

genomics↗