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Genetic parameters were estimated for frosty pod rot resistance and yield components in cacao using a linear mixed model approach (restricted maximum likelihood and best linear unbiased prediction). Two progeny trials established in the Rosario Izapa Experimental Field of the INIFAP in Chiapas, Mexico, were evaluated for frosty pod rot incidence and yield components, including the number of pods per tree, bean dry weight per tree, number of beans per pod, bean dry weight per pod, seed index, and pod index, for 4 years. Genetic correlations, age-age correlations, and heritabilities were estimated. The narrow-sense heritability for frosty pod rot resistance was 0.46, and for the yield components, it ranged from 0.14 to 0.99. Backward selection, using UF-273 and Pa-169 as parents for new combinations, resulted in a reduction from −36.54 to −29.05% in frosty pod rot, respectively. The genetic correlations between bean dry weight per tree and frosty pod rot, number of pods per tree, number of beans per pod and pod index were −0.72, 0.89, 0.25, and 0.40, respectively (all significant at p < 0.01). Age-age correlations and heritabilities from data subsets indicated that the first 2 years of evaluation and evaluating for only two specific months (August to September) in the year should result almost in the same genetic estimates as using all 4 years data, for key traits, including frosty pod rot resistance, reducing the costs, and accelerating breeding decisions.

In Mexico, cacao production is endangered by pathogenic fungi, such as Phytophthora spp. and Moniliophthora rorei, that cause black pod rot and moniliasis, respectively. In this study the biocontrol agent Paenibacillus sp. NMA1017 was tested in cacao fields against the previous diseases. The treatments applied were shade management, inoculation of the bacterial strain with or without an adherent, and use of chemical control. The statistical analysis showed that the incidence of black pod rot in tagged cacao trees diminished when the bacterium was applied (reduction of 44.24 to 19.11%). The same result was observed with moniliasis when the pods were tagged (reduction of 66.6 to 27%). The use of Paenibacillus sp. NMA1017 with an integrated management might be a solution to cacao diseases and to having a sustainable production of cacao in Mexico.

Cacao ( Theobroma cacao L. ) production is significantly influenced by genotype-environment interactions, which affect key agronomic traits such as yield, fruit quality, and disease resistance. Despite advances in cacao breeding, one of the main challenges remains the identification of stable, high-performing clones that can adapt to different environmental conditions while maintaining desirable agronomic characteristics. In particular, the introduction of improved clones with high productivity and tolerance to diseases such as frosty pod rot is essential to ensure sustainable production. However, limited information exists on the environmental influence on these traits, making it crucial to assess the performance of new cacao clones in diverse agroecological conditions before their large-scale adoption. With the objective of evaluating the genotype-environment interaction of cacao clones generated by INIFAP and introduced for their tolerance to diseases (frosty pod rot), high yield, and quality, 23 cacao clones were established in three environments: (1) Campo Experimental Rosario Izapa-Tuxtla chico, Chiapas; (2) Ejido Umoa, Tapachula, Chiapas y (3) Vicente Guerreo, Teapa, Tabasco. The cacao clones were established in a Randomized Block Experimental Design with three replications and five trees per block. Statistical analysis was conducted in R 4.4.1 using the statgenGxE package and hierarchical clustering. The variance analysis showed highly significant differences among the genotypes for all the evaluated variables, indicating considerable genetic variability in terms of fruit length (FL), fruit weight (FW), total number of seeds (TNS), individual seed dry weight (ISDW), and pod index (PI). Environment 1, located in Rosario Izapa, Chiapas, stood out as the best for the variables FL, TNS, and ISDW. On the other hand, environment 3, situated in Vicente Guerrero, Teapa, Tabasco, proved to be the most suitable for FW and PI. In contrast, environment 2, located in Ejido Umoa, Tapachula, Chiapas, ranked as the worst for most of the variables, particularly for FL, FW, and TNS. The sensitivity analysis of the cacao genotypes depended on the type of variable; for the fruit variables, genotype 5 stood out for FL, genotype 18 for FW, genotype 4 for TNS, genotype 9 for ISDW, and genotype 15 for PI. In general, the best genotype for fruit variables was genotype 25 (F19P3). Finally, it was observed that among the 23 promising cacao genotypes, most exhibited interaction with the environment, suggesting that it is very important to consider the environmental conditions where the varieties will be established. The findings of this study provide valuable insights into the influence of environmental conditions on cacao productivity and quality, highlighting the need for site-specific clone selection. The identification of high-yielding and stable genotypes can facilitate more efficient breeding strategies and better decision-making for cacao producers and researchers. By understanding how different environments impact agronomic traits, this research contributes to the sustainable intensification of cacao cultivation, helping to optimize yields while mitigating the risks associated with environmental variability. These results are particularly relevant for breeding programs aimed at developing resilient cacao varieties suited to diverse agroecological regions.

Cacao represents an important source of income for farmers in the south of Mexico. However, phytosanitary problems have disrupted the production over the years. The use of antagonistic microorganisms as biocontrol agents might improve the production of cacao. In this study, Paenibacillus polymyxa NMA1017, isolated from the rhizosphere of Opuntia ficus-indica L., was used as a biocontrol agent for black pod rot of Theobroma cacao L. cultivated in Chiapas, Mexico. The experiments were carried in vitro and in vivo using pear fruit (Pyrous communis) as model and cacao pods in the field, respectively. The effect of NMA1017 on the phytopathogen was observed by electron microscopy and the production of enzymes was tested as a potential mechanism of action. The bacterium inhibited the radial growth of Phytophthora tropicalis PtCa-14 by 85.9 ± 0.12%. The strain NMA1017 affected mycelial development, as observed by the damage to the cell wall of the oomycete. In pear fruit, the biocontrol agent controlled the production of mycelium on the pear fruit surface, indicating an inhibitory effect exerted. Cacao pods infected with P. tropicalis in the field resulted in a reduction in disease incidence from 86 to 33% and in infection from 68 to 6%. Moreover, strain NMA1017 produced hydrolytic enzymes such as cellulases, xylanases, chitinases and proteases. The results obtained highlight P. polymyxa NMA1017 as an organism of interest for the biocontrol of P. tropicalis, as a method to rescue this important crop in Mexico.

The prickly pear cactus (Opuntia ficus-indica L.) is an emblematic crop for Mexico’s economy, gastronomy, and culture. Microbial communities play an important role in the health, development, and productivity of crops. This study used 16S rRNA high-throughput sequencing and bioinformatic analyses to evaluate the rhizosphere microbiome of prickly pear cactus across an altitudinal gradient in Milpa Alta (Mexico). A microbial core consisting of Bacillus, Acidibacter, and Sphingomonas was detected, reflecting strong co-adaptation between plants and soil microorganisms under different agroecosystems. However, in the lower-altitude zones, Conexibacter, Agromyces, Domibacillus, Pedomicrobium, and Rokubacteriales predominated, which are associated with humid environments and high organic matter content. In contrast, in the middle-altitude zones, Acidothermus, Gemmatimonas, Mesorhizobium, and Pseudoxanthomonas were enriched, which are involved in carbon and nitrogen cycles. Higher-altitude zones exhibited greater bacterial specialization, with genera adapted to more extreme conditions such as Halocella, Solirubrobacter, Rhodomicrobium, Phenylobacterium, Roseomonas, Pseudarthrobacter, Crossiella, Aquicella, and others. Overall, our data show that altitude acts as an ecological filter structuring soil microbial communities associated with prickly pear cactus, influencing the diversity and functional potential. This study on microbial diversity not only provides insights into the health of the agroecosystem but also represents a valuable source of microorganisms with functional potential for sustainable agriculture.

The microbiota associated with Vanilla planifolia grown in three production systems in Puebla, México, was evaluated: shade cloth, cocuite, and acahual. Rhizosphere and soil samples were analyzed, from which bacteria, fungi, yeasts, and actinomycetes were isolated. The bacterial and actinomycete isolates were characterized morphologically and biochemically, and their potential as growth promoters was evaluated. Morphological and microscopic characteristics identified the fungi. In parallel, agronomic variables were measured in five plants per system, and the data were analyzed using ANOVA and Tukey’s test (p ≤ 0.05). The results showed that the shade cloth favored a greater number of internodes, total leaves, and biomass, although with a higher incidence of diseased leaves. The cocuite presented intermediate values, while the acahual had lower leaf density but fewer leaf health problems. Microbial composition varied across systems, with potentially beneficial bacteria and actinomycetes, as well as both beneficial and pathogenic fungi, being prominent. These findings demonstrate the influence of the management system on the microbiota and health of V. planifolia, providing a basis for more sustainable production strategies for vanilla cultivation in Mexico.

Abstract In the present study, phenotypic correlations and direct and indirect effects were estimated in a breeding population of cacao involving 22 full-sib families from 14 reciprocals and 8 direct crosses to obtain information aiming to increase selection efficiency for higher production. Path analysis was used to obtain estimates at the family level, within families, and the individual level. High phenotypic correlation coefficients were found between the total number of pods per tree and frosty pod rot incidence, with bean dry weight per tree, at the family (r = 0.91 and − 0.84, p < 0.001) and individual levels (r = 0.89 and − 0.50, p < 0.001), respectively. Path analysis revealed that the total number of pods per tree had the highest positive direct effects (0.66 to 1.05) on bean dry weight per tree expression. Likewise, indirect effects via the total number of pods per tree were important to explain the significant association of the other variables with the bean dry weight yield per tree. Variations in the correlation significance and direct and indirect effect magnitudes were observed among sample size, families, reciprocal and direct crosses, years, and bimonthly. However, beyond the influence of these, the total number of pods per tree had the greatest effects on production. These results suggest that indirect selection on the total number of pods per tree would improve selection efficiency for high bean yield in these breeding populations, accelerating and reducing costs than using a larger number of traits. The low heritability associated with the number of pods per tree might be beneficial in the second step of the selection process, considering other yield components of higher heritability as bean dry weight per pod. Also, extrapolation of the results should be done with care, considering that genetic parameter estimates are strictly valid for the population and environment studied, especially here that the number of parents used is a small sample (although important) of the parents used in cacao breeding programs.

Sechium edule (Jacq.) Sw. (Cucurbitaceae) is a species native to Mexico and Central America. The collection, characterization, and evaluation of accessions maintained in genebanks is essential for the conservation of this species. However, there are no specific varietal descriptors that differ from those used in a phenetic approach and are adapted to international registration guidelines to help distinguish, improve, cluster, and protect intraspecific variants of common use and those obtained by breeding. Therefore, 65 morphological descriptors (qualitative and quantitative) were evaluated in 133 accessions obtained from Mexico, Guatemala, and Costa Rica located in the National Germplasm Bank of S. edule in Mexico. These characteristics were observed to be phenetically stable for five generations under the same agroclimatic conditions. In addition, an analysis of amplified fragment length polymorphism (AFLP) was applied to 133 samples from a set of 245 accessions. According to the multivariate analysis, 26 of the 65 descriptors evaluated (qualitative and quantitative) enabled differentiation of varieties of S. edule. The AFLP analysis showed a high level of polymorphism and genetic distance between cultivated accessions and their corresponding wild ancestor. The variations in S. edule suggest that the morphological characteristics have differentiated from an essentially derived initial edible variety (ancestral original variety), but unlike other cucurbits, there is no evidence of the ancestral edible for Sechium since the seed is unorthodox and there are no relicts.

Se estudió la respuesta a la selección masal para componentes del rendimiento de grano y la estabilidad en dos variedades originales de maíz, Zacatecas 58 y Cafime, en las cuales se aplicaron 19 y 16 ciclos de selección masal para resistencia a sequía, respectivamente. Ambos materiales genéticos se evaluaron en dos localidades (Montecillo y Tecámac, Estado de México) con tres ambientes de humedad del suelo (riego, temporal y sequía). Los estimadores del avance genético por ciclo de selección y los parámetros de estabilidad utilizados indican que en el ambiente de sequía se encontraron los avances genéticos más altos por ciclo para ambas variedades, pero la mayor ganancia acumulada en unidades para los caracteres evaluados, se obtuvo en condiciones de riego. Los compuestos de selección de Cafime fueron más consistentes que los de Zacatecas 58. El peso de mazorca promedio por planta se incrementó conforme aumentó el número de ciclos de selección en las dos variedades y de manera concomitante se incrementó el coeficiente de regresión. Se deduce que al aumentar la selección masal visual aumenta el rendimiento y la sensibilidad ambiental lineal (b i), pero no la sensibilidad ambiental no lineal (S²d i). Finalmente, el aumento del rendimiento y de sus componentes estuvo positivamente correlacionado con el coeficiente de regresión lineal del rendimiento sobre el número de ciclos de selección, pero no hubo correlación con las desviaciones de regresión.

In Mexico, cacao production is endangered by pathogenic fungi, such as Phytophthora spp. and Moniliophthora rorei, that cause black pod rot and moniliasis, respectively. In this study the biocontrol agent Paenibacillus sp. NMA1017 was tested in cacao fields against the previous diseases. The treatments applied were shade management, inoculation of the bacterial strain with or without an adherent, and use of chemical control. The statistical analysis showed that the incidence of black pod rot in tagged cacao trees diminished when the bacterium was applied (reduction of 44.24 to 19.11%). The same result was observed with moniliasis when the pods were tagged (reduction of 66.6 to 27%). The use of Paenibacillus sp. NMA1017 with an integrated management might be a solution to cacao diseases and to having a sustainable production of cacao in Mexico.