Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population

A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance components for the partitioning of additive and non-additive effects. Heritabilities of yield over time ranged from 0.085 to 0.576, from 0.127 to 0.399 for vigor, and 0.141 to 0.146 for disease resistance traits. Significant (p < 0.001) general combining abilities were observed for ICS-43 and LcTeen-37 with negative effect on average yield (−0.674, −0.690), respectively. Specific combining abilities for yield had significant (p < 0.001) positive effect from the cross GU-154-L x UF-273 Type 2 (0.703) and strong negative interaction between ICS-43 and LF-1 (−0.975). A weighted index was used to select the top performers while providing the corresponding genetic gains. At an 1% selection intensity, yield component gains ranged from 17.8 to 331.9%. Agronomic traits such as branch angle, trunk diameter and jorquette height had lower genetic gains and lower heritabilities. In addition, the parents in this study were genotyped with a 96-SNP marker off-typing set and a significant positive correlation of 0.39 (p = 0.019) was found between genetic distance and specific combining abilities for yield. Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao

Caracterización pomológica y fisicoquímica de Tamarindus indica (tamarindo) en la Estación de Investigaciones en Horticultura Subtropical en Miami, Florida

Tamarind (Tamarindus indica L.) is a large evergreen tree belonging to the family Fabaceae (Leguminosae). Its fruits are eaten fresh, processed into a paste, used as a spice, made into a beverage, and used for tanning hides. Although this commercially important species has a wide geographical distribution, research on tamarind is sparse. Hence, the purpose of our research was to characterize 13 genotypes of tamarind at the Subtropical Horticultural Research Station in Miami, FL, USA, and to determine whether physical and pomological traits of this collection in fact reflect the genetic diversity within this fruit tree species. This work was conducted at SHRS in Miami, Florida. The pomological diversity of 13 tamarind genotypes was analyzed based on 18 qualitative and quantitative traits. Principal components analysis (PCA) conducted on quantitative traits showed an important degree of variability of about 72% for the first three principal components. A dendrogram was constructed based on average distances. Cluster analysis grouped all tamarind genotypes into three major clusters ('A', 'B' and 'C'). Cluster 'B' includes the genotypes predominantly with brown to dark brown sweet and semi-sweet pulp and from South East Asia (Thailand and Philippines); the B cluster individuals were then grouped into sub-clusters 'B1', 'B2', 'B3' and 'B4'. Semi-sour genotypes were grouped in cluster 'A' and the sour genotype in cluster 'C' Cluster 'B' contained genotypes predominantly characterized by sweet, dark pulp, and smaller fruit size, while the sour genotypes were characterized by trees of sour pulp and from other regions (Australia, Brazil, India and the Caribbean). We detected moderate genetic diversity among these tamarind genotypes. This information could be used as a basis for selection during genetic improvement of tamarind genotypes.El tamarindo (Tamarindus indica L.) es un árbol perenne de tamaño grande que pertenece a la familia Fabaceae (Leguminosae). Sus frutos se consumen frescos, procesados en una pasta, que se utiliza como especia, hecho en una bebida, y se utilizan para el curtido de pieles. A pesar de que estas especies comercialmente importantes tienen una amplia distribución geográfica, la investigación sobre el tamarindo es escasa. Por lo tanto, el propósito de nuestra investigación fue caracterizar 13 genotipos de tamarindo en el Repositorio Nacional de Germoplasma (SHRS, por sus siglas en inglés) en Miami, Florida, EE.UU., y determinar si los rasgos físicos y pomológicos de esta colección, de hecho, reflejan la diversidad genética dentro de esta especie de árboles frutales. Este trabajo se realizó en SHRS en Miami, Florida. La diversidad pomológica de 13 genotipos de tamarindo se analizó basado en 18 rasgos cualitativos y cuantitativos. Análisis de componentes principales realizados en los rasgos cuantitativos mostraron un importante grado de variabilidad de alrededor del 72% para los tres primeros componentes principales. Se construyó un dendrograma basado en distancias medias. El análisis de conglomerados agrupa todos los genotipos de tamarindo en tres grupos principales ('A', 'B' y 'C'). El grupo 'B' incluye los genotipos predominantemente de color marrón con pulpa dulce y semidulce marrón oscuro y del Sudeste de Asia (Tailandia y Filipinas); los individuos del grupo B fueron entonces agrupados en subgrupos 'B1', B2', 'B3', y 'B4'. Genotipos semi-agrio se agruparon en el grupo 'A' y el genotipo agrio en el grupo C. El grupo 'B' contenía una colección de genotipos predominantemente caracterizados por pulpa dulce y oscura, y el tamaño de los frutos más pequeños. Mientras que los genotipos agrios se caracterizan por árboles de pulpa ácida y de otras regiones (Australia, Brasil, India y el Caribe). Detectamos la diversidad genética moderada entre estos genotipos de tamarindo. Esta información podría ser utilizada como base para la selección durante el mejoramiento genético de los genotipos de tamarindo

Supplemental and synchronized pollination may increase yield in cacao

Artificial pollination management strategies are a potential solution to improving the livelihoods of smallholder cacao farmers by increasing crop productivity in situations when pollination services are limiting. However, field-based research trials evaluating the yield benefits of artificial pollination management strategies within intensified cacao systems are lacking. Thus, in an intensively managed cacao system, we evaluated the effects of artificial pollination condition (i.e., pollen genotype, pollination intensity, and pollination synchrony) on fruit development and yield in three high-yielding cacao clones. Artificial pollination, regardless of intensity, significantly increased fruit set and yield. Pollination synchrony had a significant effect on cherelle survivorship; older cherelles had greater survival rates across all developmental stages than younger cherelles. Yield differed between genotype crosses and varied according to the pollen donor used, highlighting the importance of understanding self- and cross-compatibility when selecting clones for cultivation. Pollination intensity had no significant effect on harvested yield, indicating that more rigorous research is needed to identify the pollination intensity required for optimized yield under artificial pollination conditions. We conclude that strategies to enhance flowering, pollination rates, and pollination synchrony while ensuring adequate tree nutrition may increase productivity in cacao. Future research evaluating numerous cacao clones across multiple years and locations may help us to understand the region-specific effects of intensive management strategies on the long-term sustainability of enhancing cacao tree productivity

Mapping of a Major QTL for Ceratocystis Wilt Disease in an F1 Population of Theobroma cacao

Cacao is an important crop, its beans are key raw materials for the chocolate and cosmetic industries. Ceratocystis wilt of cacao (CWC) caused by Ceratocystis cacaofunesta is a lethal disease for the crop. Therefore, the selection of resistant cacao varieties is one of the viable ways to minimize losses in cacao production. In this paper, we described the identification of a major QTL associated with CWC in an F1 mapping population from a cross between a resistant, “TSH 1188,” and a susceptible genotype, “CCN 51.” A set of 266 trees were genotyped using 3,526 single nucleotide polymorphic markers and then multiple QTL mapping analyses were performed. Two QTLs were identified on chromosomes IV and VI. The major QTL was located at 20 cM from the top position of chromosome VI, accounting for more than 60% of the phenotypic variation. The favorable allele T1, with haplotype GTT, came from the “TSH 1188” parent. It was evident that the haplotype combination T1C2 on chromosome VI was the most significant for resistance, since 93% of resistant trees had this haplotype. The major QTL converged to a genomic region of 739.4 kb that harbored nine candidate genes, including two major classes of resistance genes, which would make them the primary candidates involved in the resistance to CWC. The haplotypes detected are now used to improve the efficiency and precision of the selection of resistant trees in cacao breeding

Genetic Parameters and the Impact of Off-Types for Theobroma cacao L. in a Breeding Program in Brazil

Breeding programs of cacao (Theobroma cacao L.) trees share the many challenges of breeding long-living perennial crops, and genetic progress is further constrained by both the limited understanding of the inheritance of complex traits and the prevalence of technical issues, such as mislabeled individuals (off-types). To better understand the genetic architecture of cacao, in this study, 13 years of phenotypic data collected from four progeny trials in Bahia, Brazil were analyzed jointly in a multisite analysis. Three separate analyses (multisite, single site with and without off-types) were performed to estimate genetic parameters from statistical models fitted on nine important agronomic traits (yield, seed index, pod index, % healthy pods, % pods infected with witches broom, % of pods other loss, vegetative brooms, diameter, and tree height). Genetic parameters were estimated along with variance components and heritabilities from the multisite analysis, and a trial was fingerprinted with low-density SNP markers to determine the impact of off-types on estimations. Heritabilities ranged from 0.37 to 0.64 for yield and its components and from 0.03 to 0.16 for disease resistance traits. A weighted index was used to make selections for clonal evaluation, and breeding values estimated for the parental selection and estimation of genetic gain. The impact of off-types to breeding progress in cacao was assessed for the first time. Even when present at <5% of the total population, off-types altered selections by 48%, and impacted heritability estimations for all nine of the traits analyzed, including a 41% difference in estimated heritability for yield. These results show that in a mixed model analysis, even a low level of pedigree error can significantly alter estimations of genetic parameters and selections in a breeding program

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of \u3ci\u3eTheobroma cacao\u3c/i\u3e L. Beans

The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate’s characteristic texture and mouthfeel. Here, we used a linkage mapping population and phenotypic data of 3,292 samples from 420 progeny which led to the identification of 27 quantitative trait loci (QTLs) for fatty acid composition and six QTLs for fat content. Progeny showed extensive variation in fat levels and composition, with the level of palmitic acid negatively correlated to the sum of stearic acid, oleic acid, and linoleic acid. A major QTL explaining 24% of the relative level of palmitic acid was mapped to the distal end of chromosome 4, and those higher levels of palmitic acid were associated with the presence of a haplotype from the “TSH 1188” parent in the progeny. Within this region of chromosome 4 is the Thecc1EG017405 gene, an orthologue and isoform of the stearoyl-acyl carrier protein (ACP) desaturase (SAD) gene in plants, which is involved in fatty acid biosynthesis. Besides allelic differences, we also show that climate factors can change the fatty acid composition in the beans, including a significant positive correlation between higher temperatures and the higher level of palmitic acid. Moreover, we found a significant pollen donor effect from the variety “SIAL 70” which was associated with decreased palmitic acid levels

Data_Sheet_3_Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population.XLSX

<p>A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance components for the partitioning of additive and non-additive effects. Heritabilities of yield over time ranged from 0.085 to 0.576, from 0.127 to 0.399 for vigor, and 0.141 to 0.146 for disease resistance traits. Significant (p < 0.001) general combining abilities were observed for ICS-43 and LcTeen-37 with negative effect on average yield (−0.674, −0.690), respectively. Specific combining abilities for yield had significant (p < 0.001) positive effect from the cross GU-154-L x UF-273 Type 2 (0.703) and strong negative interaction between ICS-43 and LF-1 (−0.975). A weighted index was used to select the top performers while providing the corresponding genetic gains. At an 1% selection intensity, yield component gains ranged from 17.8 to 331.9%. Agronomic traits such as branch angle, trunk diameter and jorquette height had lower genetic gains and lower heritabilities. In addition, the parents in this study were genotyped with a 96-SNP marker off-typing set and a significant positive correlation of 0.39 (p = 0.019) was found between genetic distance and specific combining abilities for yield. Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao.</p

Data_Sheet_6_Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population.XLSX

<p>A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance components for the partitioning of additive and non-additive effects. Heritabilities of yield over time ranged from 0.085 to 0.576, from 0.127 to 0.399 for vigor, and 0.141 to 0.146 for disease resistance traits. Significant (p < 0.001) general combining abilities were observed for ICS-43 and LcTeen-37 with negative effect on average yield (−0.674, −0.690), respectively. Specific combining abilities for yield had significant (p < 0.001) positive effect from the cross GU-154-L x UF-273 Type 2 (0.703) and strong negative interaction between ICS-43 and LF-1 (−0.975). A weighted index was used to select the top performers while providing the corresponding genetic gains. At an 1% selection intensity, yield component gains ranged from 17.8 to 331.9%. Agronomic traits such as branch angle, trunk diameter and jorquette height had lower genetic gains and lower heritabilities. In addition, the parents in this study were genotyped with a 96-SNP marker off-typing set and a significant positive correlation of 0.39 (p = 0.019) was found between genetic distance and specific combining abilities for yield. Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao.</p