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Background Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. Methods We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. Results The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. Conclusion Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Revaluation of Criollo mango peels for use in the food industry would generate an environmentally sustainable impact on the circular economy. This research seeks evaluation temperature (T) and time (t) of mango peel pre-cooking (PMP) and effect of drying on the concentration functional compounds (CFC). For this, a 22-type experimental design with a central point was implemented to evaluate the effects temperature (80, 89, and 98 °C) and time (5, 12.5, and 20 min) on the PMP the Criollo variety. The analyses performed included quantification total polyphenols (TP), total flavonoids (TF), antioxidant capacity (AC), and vitamin C (VC). This study, the effect conventional drying at three temperatures (45, 55, and 65 °C) was evaluated over 10 hours. The main findings study indicated that, after optimization to maximize CFC, the best values were obtained PMP of temperature and time, with 80 °C and 5 minutes, respectively. During the drying process, it was observed that, under the temperatures examined, there was no significant change in most of the samples. This study serves as a starting point for reevaluating Criollo mango skins through implementation circular economy and their application in products such as cookies made with mango peel. Revaluation of Criollo mango peels for use in the food industry would generate an environmentally sustainable impact on the circular economy. This research seeks evaluation temperature (T) and time (t) of mango peel pre-cooking (PMP) and effect of drying on the concentration functional compounds (CFC). For this, a 22-type experimental design with a central point was implemented to evaluate the effects temperature (80, 89, and 98 °C) and time (5, 12.5, and 20 min) on the PMP the Criollo variety. The analyses performed included quantification total polyphenols (TP), total flavonoids (TF), antioxidant capacity (AC), and vitamin C (VC). This study, the effect conventional drying at three temperatures (45, 55, and 65 °C) was evaluated over 10 hours. The main findings study indicated that, after optimization to maximize CFC, the best values were obtained PMP of temperature and time, with 80 °C and 5 minutes, respectively. During the drying process, it was observed that, under the temperatures examined, there was no significant change in most of the samples. This study serves as a starting point for reevaluating Criollo mango skins through implementation circular economy and their application in products such as cookies made with mango peel.

Lameness is one of the main causes of clinical manifestations of injuries in horses, and is characterized by an asymmetry of movement. This study assessed the influence of the saddle and two different riders on the symmetry of movements in Criollo horses. We used twenty Criollo horses in training for the Freio de Ouro competitions. An objective evaluation was carried out when moving at a trot in a straight line, in order to compare the saddle and rider effects in the asymmetry of horses trotting in a straight line. We evaluated inertial measurement units, obtaining data from the asymmetric side, as well as the amplitude of the asymmetry, using inertial sensor software. There was no significant difference in the objective measurements between the groups assessed in the VECTOR SUM, DIFF MIN of the head, DIFF MAX and DIFF MIN of the pelvis, but one of the riders showed a statistical difference in the DIFF MAX of the head compared to the situations. In this study, it was observed that one of the riders influenced the horse’s head movement, suggesting the possibility that riders can indeed impact the movements and asymmetries of horses during riding. RESUMO: A claudicação é uma das principais causas de manifestação clínica de lesões em equinos, e é caracterizada por ser uma assimetria do movimento. O objetivo deste trabalho é avaliar a influência da sela e de dois diferentes cavaleiros na simetria dos movimentos de equinos da raça Crioula. Foram utilizados 20 equinos da raça Crioula em treinamento para competições de Freio de Ouro. Foi realizada uma avaliação objetiva ao se deslocar em trote em linha reta, a fim de comparar o efeito da sela e do cavaleiro na simetria do movimento, modificando os parâmetros avaliados pela avaliação objetiva, obtendo dados do lado assimétrico, bem como a amplitude da assimetria, utilizando software de sensor inercial. Não houve diferença significativa nas medidas objetivas entre os grupos avaliados no VECTOR SUM, DIFF MIN da cabeça, DIFF MAX e DIFF MIN da pelve, porém um dos cavaleiros apresentou diferença estatística no DIFF MAX da cabeça comparado às demais situações. Nesse estudo, observou-se que um dos cavaleiros teve influência no movimento da cabeça do cavalo, sugerindo a possibilidade que os cavaleiros podem, de fato, impactar os movimentos e as assimetrias dos cavalos durante a montaria.

Grafting induces precocity and maintains clonal integrity in fruit tree crops. However, the complex rootstock × scion interaction often precludes understanding how the tree phenotype is shaped, limiting the potential to select optimum rootstocks. Therefore, it is necessary to assess (1) how seedling progenies inherit trait variation from elite ‘plus trees’, and (2) whether such family superiority may be transferred after grafting to the clonal scion. To bridge this gap, we quantified additive genetic parameters (i.e., narrow sense heritability— h 2 , and genetic-estimated breeding values—GEBVs) across landraces, “criollo”, “plus trees” of the super-food fruit tree crop avocado ( Persea americana Mill.), and their open-pollinated (OP) half-sib seedling families. Specifically, we used a genomic best linear unbiased prediction ( G -BLUP) model to merge phenotypic characterization of 17 morpho-agronomic traits with genetic screening of 13 highly polymorphic SSR markers in a diverse panel of 104 avocado “criollo” “plus trees.” Estimated additive genetic parameters were validated at a 5-year-old common garden trial (i.e., provenance test), in which 22 OP half-sib seedlings from 82 elite “plus trees” served as rootstocks for the cv. Hass clone. Heritability ( h 2 ) scores in the “criollo” “plus trees” ranged from 0.28 to 0.51. The highest h 2 values were observed for ribbed petiole and adaxial veins with 0.47 (CI 95%0.2–0.8) and 0.51 (CI 0.2–0.8), respectively. The h 2 scores for the agronomic traits ranged from 0.34 (CI 0.2–0.6) to 0.39 (CI 0.2–0.6) for seed weight, fruit weight, and total volume, respectively. When inspecting yield variation across 5-year-old grafted avocado cv. Hass trees with elite OP half-sib seedling rootstocks, the traits total number of fruits and fruits’ weight, respectively, exhibited h 2 scores of 0.36 (± 0.23) and 0.11 (± 0.09). Our results indicate that elite “criollo” “plus trees” may serve as promissory donors of seedling rootstocks for avocado cv. Hass orchards due to the inheritance of their outstanding trait values. This reinforces the feasibility to leverage natural variation from “plus trees” via OP half-sib seedling rootstock families. By jointly estimating half-sib family effects and rootstock-mediated heritability, this study promises boosting seedling rootstock breeding programs, while better discerning the consequences of grafting in fruit tree crops.

provides precious products such as polyphenol-rich beans that are useful for nutraceutical purposes. The geographical area may influence the chemical composition of raw cocoa beans in terms of the polyphenols and biological qualities of the products. This work aimed to investigate the biological properties and the chemical composition of two different samples of Criollo var. cocoa raw beans coming from two areas (Indonesia; Peru). Beans underwent biphasic extraction obtaining lipophilic and hydroalcoholic extracts. The extracts were tested for antiradical, antimutagenic, and antigenotoxic effects. Cell viability inhibition toward breast, gastric/esophageal colorectal adenocarcinoma, and hepatoblastoma human cell lines was evaluated. Extracts were chemically investigated through UV-Vis spectroscopy and ultra-high-pressure liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-Q TOF MS/MS). Results showed that the Indonesian bean hydroalcoholic extracts were able to scavenge 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) cation radical better than the Peruvian hydroalcoholic extracts (ECs : 72.63 vs. 322.20 μg/mL). Extracts showed antimutagenic and antigenotoxic activity. The viability inhibitory effect on breast and hepatic cancer cells was reached only for the Indonesian hydroalcoholic extracts at hundreds of μg/mL. Phenylpropenoyl-L-amino acids, hydroxycinnamoyl aminoacids conjugates, and procyanidin compounds were found mainly in the hydroalcoholic extracts, whereas fatty acids and lyso-phospholipids were found mainly in lipophilic fractions. Fatty acid and ( )catechins appeared to be affected by different environmental conditions of the geographical areas.

Background: Genes and their variants associated with milk and beef production traits in cattle can be identified through molecular markers. Calpain gene CAPN1316 has been associated with meat tenderness in several breeds. Tropical Milking Criollo males not selected as breeders are usually destined to commercial beef production. Objective: To estimate genotypic and allelic frequencies of calpain CAPN1316 gene associated with meat tenderness in Tropical Milking Criollo cattle breed. Methods: Molecular marker microsatellites of single sequence repeats (SSR) from DNA were extracted from blood samples of 423 purebred animals from three farms to identify variants of CAPN1316 using polymerase chain reaction (PCR). Genotypic and allelic frequencies within populations, genetic distance, heterozygosity, and Xi squared (X2) test were performed using POPGENE software. Results: Genotypic frequencies of the whole population were CC 0.31, GG 0.18, and CG 0.51. Allelic frequencies of variant C per farm were 0.62, 0.60, and 0.52. Genotypic and allelic frequencies of the CAPN1316 polymorphisms were in HardyWeinberg equilibrium (X2, p>0.05). The CC genotype showed indication of greater meat tenderness. Conclusion: The C variant of CAPN1316 gene favorable to meat tenderness has higher frequency than the G variant in Tropical Milking Criollo cattle.

The introduction of Iberian cattle in the Americas after Columbus’ arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD) and Ne Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross‐population extended haplotype homozygosity (XP‐EHH) and population differentiation (FST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic Ne contraction. NeS analysis provided insights into short‐term complexity in population change and depicted a decrease/expansion episode at the end of the ABC‐inferred expansion, as well as several additional fluctuations in Ne with the attainment of the current small Ne only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future‐proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change.

The esbarrada and volta sobre patas manoeuvres are critical in Criollo horse equestrian activities, yet their kinematics remain largely unexplored. This observational study aimed to kinematically describe the manoeuvres in Criollo breed horses and explore the relationship between static goniometry and dynamics. A 2D kinematic analysis was conducted on 31 Criollo horses performing the manoeuvres using high-speed cameras. Joint angles were measured using static goniometry and analysed in relation to dynamic performance. The esbarrada covered a distance of 4.28 ± 0.99 m in 1.15 ± 0.11 s at a velocity of 3.77 ± 0.55 m/s. Joint angles showed a mean fetlock extension of 75.4° ± 5.3° and hock flexion of 43.2° ± 4.1°. In the volta sobre patas, significant differences were found in turn duration (first: 0.96 ± 0.07 s, second: 1.12 ± 0.09 s, p = 0.03) and thoracic limb suspension (first: 0.23 ± 0.02 s, second: 0.28 ± 0.03 s, p = 0.02). Static goniometry indicated that limb conformation did not significantly correlate with protraction angles during the esbarrada (p = 0.27). The volta sobre patas demonstrated prolonged duration and increased thoracic limb suspension in the second turn. Also, the findings suggest that static conformation does not predict dynamic limb movement during the esbarrada.

Hydroxylbenyacarite, (H2O)2Mn2(Ti2Fe) (PO4)4 [O(OH)] (H2O)10·4H2O, is a new paulkerrite-group mineral from the El Criollo mine, Cordoba Province, Argentina (IMA2023-079). It was found in specimens of altered triplite, in association with bermanite, phosphosiderite, quartz, strengite and manganese oxides. Hydroxylbenyacarite occurs as light greenish-yellow rhombic tablets with dimensions of typically 20 to 50 µm, occasionally to 400 µm. The crystals are flattened on {010}, slightly elongated on [001] and bounded by the {111} and {010} forms. The calculated density is 2.32 g cm-3. Optically, hydroxylbenyacarite crystals are biaxial (+), with α=1.608(3), β=1.624(3), γ=1.642(3) (measured in white light) and 2V(meas.)=88(2)°. The calculated 2V is 87.5°. The empirical formula is Ca0.06A[K0.46(H2O)0.88[]0.66]Σ2.00 M1(Mn1.52Mg0.02Fe2+0.35[]0.11)Σ2.00 M2+M3(Fe3+1.21Al0.02Ti1.77)Σ3.00(PO4)4 X[F0.16(OH X[F0.16(OH)0.70O1.14]Σ2.00(H2O)10·3.77H2O. The average crystal structure for hydroxylbenyacarite has space group Pbca and unit cell parameters a=10.5500(3) Å, b=20.7248(5) Å, c=12.5023(3) Å, V=2733.58(12) Å3 and Z=4. It was refined using single-crystal data to wRobs=0.074 for 2611 reflections with I>3σ(I). The crystal structure contains corner-connected linear trimers of Ti-centred octahedra that share corners with PO4 tetrahedra to form 10-member rings parallel to (010). K+ cations and water molecules are located in interstitial sites within the rings. Additional corner-sharing of the PO4 tetrahedra with MnO2(H2O)4 octahedra occurs along [010] to complete the 3D framework structure. A new eight-coordinated interstitial site, previously unreported for paulkerrite-group minerals, is occupied by Ca2+ cations. Weak diffuse diffraction spots in reconstructed precession images for hydroxylbenyacarite violate the a and b glide plane extinctions for Pbca and are consistent with local, unit-cell-scale regions of monoclinic, P21/c structure, in which ordering of the interstitial K+ and Ca2+ cations occurs.

Cocoa bean shell (CBS) is a by-product from cocoa processing which is abundant in Indonesia, one of the largest cocoa-producing countries. It has a great potential for being processed into food ingredients due to its comparable composition to cocoa nibs. The present study was conducted to identify the proximate composition and bioactive compounds in CBS produced at several cocoa industries in Indonesia utilizing different cocoa varieties (Criollo and Forastero) and processing techniques (fermented, non-fermented, pulp washing, and drying), which remain unknown. The results showed that the CBS derived from roasted Criollo cocoa pods in the Kendeng Lembu cocoa industry had ash and protein content of about 8.21% and 18.79%, respectively, which was higher than other industries. Additionally, the concentration of bioactive substances was higher here than it was elsewhere. This included total phenolic (136.2 mg GAE g−1) and theobromine (22.50 mg g−1). The lowest ash and protein concentration found in CBS was from Forastero cocoa pods, non-fermented like Sulawesi cocoa. These values were 6.48% and 15.70%, respectively. The concentration of theobromine (15.40 mg g−1) was also lower compared to other industries.