Location: Sustainable Perennial Crops Laboratory
2023 Annual Report
Objectives
Objective 1: With NPGS and international cooperators, elucidate the geospatial patterns of genetic diversity for the primary gene pool of cacao; strategically acquire cacao genetic resources to fill gaps in NPGS and other genebank collections; and incorporate genetic diversity data into this project’s website, international cacao genetic resources databases, and GRIN-Global. [NP301, C2, PS2A; C4, PS4]
Sub-Objective 1A: Elucidate geospatial patterns of genetic diversity for the primary gene pool of cacao.
Sub-Objective 1B: Assess whether the genetic diversity in ex situ collections is representative of cacao’s primary gene pool. Fill genetic gaps in those collections by strategically collecting new accessions from natural populations and farmer fields.
Sub-Objective 1C: Incorporate genetic diversity data into the project’s website, international cacao genetic resources databases and GRIN-Global.
Objective 2: With domestic and international cooperators, characterize and evaluate cacao genetic resources for tolerance to abiotic stresses, for adaptation to growth under different environments and horticultural management regimens, and for other priority horticultural traits. [NP301, C2, PS2A; C1, PS1A]
Sub-Objective 2A: Evaluate cacao germplasm for tolerance of soil moisture deficits to identify tolerant clones for breeding drought-tolerant varieties.
Sub-Objective 2B: Evaluate cacao germplasm for accumulation and translocation of heavy metals, such as cadmium; assess nutrient use efficiency in different environments to identify superior clones for breeding varieties with high nutrient use efficiency and low concentration of toxic heavy metals.
Objective 3: Develop and apply genomic tools for improving the efficiency and effectiveness of managing and utilizing genetic resources of other priority tropical crops, such as tea, guava, longan, rambutan, pitaya, star fruit, mangosteen, peach palm and macadamia nut. [NP301, C2, PS2A] With support from this budgetary increase, more effective coffee genetic resource evaluation, and characterization methods will be developed and applied, focusing on germplasm to be incorporated into the new USDA/ARS coffee genetic resource collection.
Approach
Firstly, the project will elucidate geospatial patterns of genetic diversity in the primary gene pool of Theobroma cacao using genomics, spatial genetics and bioinformatics. Wild cacao trees originated from Colombia, Peru, Ecuador, Bolivia, Brazil and French Guiana will be genotyped using Next Generation Sequencing. The NGS data, in conjunction with GIS and ecological information, will be analyzed to reveal distribution of Theobroma cacao in the Amazon. The resulting information will serve as a scientific baseline to support rational decision-making for future germplasm conservation and utilization. Diversity gaps in ex situ collections will be identified and filled through new collection expeditions to increase representation from the geographical centers of diversity and collect landraces and traditional varieties to support in situ/on-farm conservation. In collaboration with USDA’s GRIN-Global team and international partners, this project will also improve the genetic integrity of the genebank holdings and allow us to significantly improve the accuracy of information in the public databases.
Secondly, this project will evaluate cacao germplasm for tolerance to key abiotic stresses and horticultural traits, with the emphasis on drought tolerance and lower uptake and transport of Cd to improve the productivity and quality of cacao beans. Research will be conducted with research institutes and universities in Peru, Brazil, Puerto Rico and Ecuador. Cacao genetic resources will be characterized and evaluated in different agricultural ecologies in the Americas for tolerance to abiotic stresses. Field studies will be implemented with drought-tolerant genotypes identified to assess their growth performance and yield potentials under different cacao growing regions of South America. Interntional germplasm will be evaluated to identify genotypes that are tolerant to toxic levels of Cd. New parental genotypes with superior ability to establish under abiotic stresses and superior tolerance to drought and low uptake of soil Cd conditions, will be incorporated in breeding programs.
A third objective is to assess the diversity of other less studied tropical fruit and nut species. Genomic tools will be developed for improving the efficiency and effectiveness of managing and utilizing genetic resources of tropical fruits and nuts, such as tea, coffee, guava, longan, rambutan, pitaya, star fruit, mangosteen, peach palm and macadamia. SNP markers will be developed through data mining and/or NGS technology for these species. These putative SNP markers will be validated and evaluated for suitability in germplasm identification and genetic diversity assessment. High quality SNPs will be selected to form a genotyping panel for each species, which will be applied for SNP fingerpritting of germplasm of tropical specialty crops maintained USDA tropical fruits and nuts germplasm collections in Hilo, Hawaii and Mayagüez, Puerto Rico.
Progress Report
Sub-Objective 1A, significant progress was made in understanding the origin and evolution of wild cacao populations in the Amazon basin. ARS scientists, in collaboration with scientists at the University of Nebraska-Lincoln conducted comparative genomics analysis of five de novo cacao genome assemblies and revealed large genomic variations, repeats, and gene contents differences. The result showed that the time of divergence among cacao populations started approximately 1.8 million years ago. This new finding underscores the hypothesis that the Last Glacial Maximum (between 26,500 to 20,000 years ago) is the main cause of cacao population differentiation in the Amazon basin. These results provide new insights into genomic variations and the mechanisms behind the origin of cacao genetic diversity and evolutionary history.
Significant progress was made in comparative diversity analysis of wild populations and cultivated cacao in Peru. In collaboration with scientists in the Institute of Tropical Crops (ICT) Peru, Bioversity International, National University of the Peruvian Amazon, the Peruvian National Institute of Agriculture Research (INIA), ARS scientists analyzed a total of 520 wild cacao accessions collected during previous expeditions and 2,100 cultivated cacao trees sampled from 563 farms in 35 provinces, covering 90% of the cacao producing areas in Peru. The genotyping result established an association between wild population and cultivated cacao germplasm in Peru, enables explicit differentiation of indigenous populations from introduced germplasm, and supports authentication of fine flavored cacao beans from indigenous Peruvian varieties. This research provides essential scientific information to support future gap-filling collecting expeditions in the Amazon.
Sub-Objective 1B, progress was made in understanding parentage and population membership of enhanced cacao germplasm with resistance to frosty pod disease (caused by Moniliophthora roreri). In collaboration with scientists in the Center for Tropical Agricultural Research and Education (CATIE), Costa Rica, ARS scientists clarified the parentage of 184 germplasm accessions and breeding lines that are resistant to frosty pod disease. These resistant clones represent the breeding effort of CATIE over the last 30 years. M. roreri is currently confined to fifteen countries in tropical America and there is increasing concern that this pathogen will spread to other cacao producing countries. These genetically characterized resistant clones provide much-needed information to support cacao breeding programs worldwide.
Sub-Objective 1C, considerable progress was made in improving the information accuracy of USDA cacao repository in Puerto Rico. In collaboration with ARS scientists in Tropical Agricultural Station in Mayaguez, Puerto Rico, scientists in ARS Beltsville, Maryland, performed genotyping on 210 cacao accessions, representing the entire USDA cacao collection maintained in Mayagüez, Puerto Rico. Based on the genetic profiles the genetic integrity and population structure of the collection was analyzed. Genetic diversity gaps were identified by comparing the genetic diversity in USDA’s cacao collection with the international cacao germplasm collection, in Trinidad (ICG, T). The results improve the information accuracy and provide guidance for the introduction of international clones to fill the genetic diversity gaps in USDA-NPGS (National Plant Germplasm System) cacao collection. Under the same objective, progress was made to improving the accuracy of the cacao germplasm maintained in the International Cacao Quarantine Center (ICQC) in Reading, United Kingdom. In collaboration with scientists in the University of Reading, United Kingdom, ARS scientists genotyped 380 international clones, representing the entire ICQC collection. Based on the genotyping results of 400 single nucleotide polymorphism (SNP) markers, genetic integrity, and population membership of the ICQC international clones were verified, which improved the information accuracy of the international clones maintained in ICQC. The genotyping data, as well as the analytical results were submitted to the ICGD, Reading, U.K. ensuring that true-to type international clones will be distributed around the world.
Sub-Objective 2A Substantial progress was made to evaluation of cacao germplasm for tolerance to abiotic stresses. At the Institute of Tropical Crops (ICT) Peru, sixty cacao genotypes from diverse geographic origins were evaluated in greenhouse studies to identify acidity-tolerant cacao clones. The results showed significant difference among genotypes grown on acid soil, which enabled the selection of ten acidity-tolerant cacao clones. These genotypes are potentially useful as parental clones for breeding programs or as rootstock in cacao production. Substantial progress was made at the State University of Santa Cruz (UESC), Bahia, Brazil, where field experiments were conducted to evaluate the effect of soil physiographic features on cacao tree mortality during drought. The result showed that the edaphic or soil attributes related to cacao tree mortality were physical and mineralogical, and mainly in the soil subsurface layers. The result showed that it is possible to establish optimum edaphic attributes that increase the survival rate of cacao trees suffering drought.
Substantial progress was made at the State University of Santa Cruz (UESC), Bahia, Brazil, where field experiments were conducted to evaluate the effects of cacao scion-rootstock combinations for Cadmium (Cd) accumulation. The result revealed significant difference among the tested scion-rootstock combinations. The two best combinations (CCN 51/BN 34 and CCN 51/PH 16) demonstrated tolerance to Cd toxicity with higher carbon assimilation, higher water use efficiency, and higher physiological parameters. The selected low Cd scion-rootstock combinations can be potentially used by cacao farmers to mitigate Cd accumulation.
Objective 3. Significant progress was made in collaboration with scientists from the University of Nebraska-Lincoln, where the draft genome of peach palm (Bactris gasipaes), an economically important species of palm tree native to the tropical forests of Central and South America, was developed. The genome assembly has a size of 6,909 Mb and consists of 3,495 scaffolds with a scaffold N50 = 42.2Mb. Peach palm is one of the most important domesticated palm species of the Neotropics and its genome, is the first sequenced genome of a palm tree native to the neotropics. This genome will be a valuable resource to study the genetic diversity and evolution of palms.
Significant progress was made in collaboration with researchers from Federal University of Lavras, Brazil, an ARS scientist used DNA markers to assess the within-cultivar variation and progeny selection in a traditional Arabica coffee cultivar 'Mundo Novo'. The cup quality attributes, agronomic characteristics of 14 progenies were evaluated and their genetic identities were verified. The top three progenies with superior sensory quality and agronomic performance were selected as promising genotypes for future genetic improvement or for direct use in the production of specialty coffee. This research provides a viable option to select new materials by exploring intra-cultivar variation.
Significant progress was made in genotyping Robusta coffee germplasm in Ivory Coast. In collaboration with scientists from National Agriculture Research Institute, Ivory Coast and the French Agricultural Research Centre for International Development, an ARS scientist from Beltsville, Maryland, used DNA markers to assess population structure in the Guinean and Congolese germplasm of Robusta coffee. The analysis confirmed the classification of Robusta coffee into two main groups (Guineans and Congoleses) and showed the Congolese group can be further partitioned into four subgroups (SG1, SG2, B and C). Morphological traits, disease resistance and agronomic traits were evaluated and used to compute combining abilities among parental clones. The crosses between selected Guinean clones and SG1 or SG2 Congolese testers were found to be the best combination for producing hybrid progenies. This research provides useful information for improving the effective use of Robusta germplasm for coffee genetic improvement.
Significant progress was made in genotyping Jujube germplasm in the U.S. In collaboration with scientists from the New Mexico State University, ARS scientists genotype 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. The genotyping results revealed a significant rate of genetic redundancy among these jujube samples resulting in a total of 14 synonymous groups, comprising 48 accessions. A new hybrid population with a unique genetic profile was discovered in Fabens/Tornillo, Texas, and a semi-naturalized population was identified in Tucumcari, New Mexico. These findings provide valuable guidance to jujube growers and researchers for improving the utilization of jujube germplasm.
Significant progress was made in genotyping the USDA sugarcane germplasm repository. In collaboration with ARS scientists in Miami, Florida, and ARS scientists in Beltsville, Maryland, genotyped 900 sugarcane accessions maintained in World Sugarcane Collection in Florida. The DNA fingerprints revealed a high rate of genetic redundancy in the collection with 17% of the accessions having at least one duplicate, and 42% of the accessions displaying a near-matched genotype. The analyses of population structure detected 128 mislabelings within the recorded Saccharum species names. This study significantly improved the genetic integrity and provides valuable insight into sub-population structure in this collection. The results will significantly enhance the efficiency of conservation and utilization of sugarcane germplasm for crop improvement.
Accomplishments
1. Comparative genomics reveal new sights into the evolution of wild cacao populations in the Amazon basin. Scientists at USDA ARS in Beltsville, Maryland, with scientists at the University of Nebraska-Lincoln, conducted comparative genomics analysis of 5 new Theobroma cacao genomes from different Amazon River basin cacao populations. The results revealed large genomic variations, repeats, and variable gene contents among these diverse cacao genotypes. The genetic divergence among these cacao populations was calculated to have started approximately 1.8 million years ago, which supports the Last Glacial Maximum origin (between 26,500 to 20,000 years ago) of the current geographical distribution of cacao populations in the Amazon basin. These results are being used collaboratively with genebank curators and plant breeders in the U.S. and South America to improve cacao breeding programs.
2. Assessing the genetic origins and diversity of cultivated and wild cacao in Peru. Peru is within the center of diversity of cacao and establishing the genetic identity of Theobroma cacao trees is difficult requiring DNA based marker systems. A marker-based analysis system was used by ARS scientist in Beltsville, Maryland, to evaluate 2520 wild and cultivated cacao trees sampled from 563 farms and 15 rivers in 35 provinces, covering 90% of the cacao growing areas in Peru. This marker system enables unambiguous differentiation of the indigenous cacao population samples from the cultivated germplasm that has been introduced into Peru. Furthermore, these identities provide a way to authentication fine flavored indigenous Peruvian cacao varieties that is the bases to produce gourmet cacao. This research provides essential scientific information to support future gap-filling collecting expeditions in the Amazon, and on-farm conservation of cacao genetic resources in Peru and it will be used by researchers, collection curators and plant breeders to improve the conservation and utilization of Peruvian cacao germplasm.
3. New Coffea arabica breeding lines selected through intra-cultivar variation analysis. Coffea arabica is a highly homogenous crop, which make the identification of superior cultivars difficult. In collaboration with researchers from Federal University of Lavras, Minas Gerias, Brazil, scientists at USDA ARS in Beltsville, Maryland, accessed the genetic diverse of a traditional coffee cultivar 'Mundo Novo'. The genetic identities of selected progeny were verified and evaluated for their quality attributes, and agronomic characteristics. The top three progenies with superior sensory quality and agronomic performance were selected for future genetic improvement or for direct use in the production of specialty coffee. This research provides a viable option for selecting new materials by exploring intra-cultivar variations. This new selection approach is being used collaboratively by scientists in Brazil to improve production for the specialty coffee market.
4. Evaluating the genetic diversity of Jujube (Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas. Jujube or red dates is a highly adaptable fruit tree from China that is an emerging fruit crop for semi-arid regions of the USA. In collaboration with scientists from the New Mexico State University in Las Cruces, New Mexico, ARS scientists in Beltsville, Maryland, genotyped 204 jujube trees sampled from multiple locations in New Mexico, Texas, Missouri, and Kentucky. The genotyping results revealed a significant rate of genetic redundancy among these jujube samples resulting in a total of 14 synonymous groups, comprising 48 accessions. A new hybrid population with a unique genetic profile was discovered in Fabens/Tornillo, Texas, and a semi-naturalized population was identified in Tucumcari, New Mexico. These findings provide valuable guidance to jujube growers and researchers for improving the utilization of jujube germplasm.
Review Publications
Song, L., Meinhardt, L.W., Li, Z., Wan, Z., Zhang, D. 2022. Accurate cultivar authentication of fresh and dry jujube fruits using DNA fingerprints based on a nanofluidic SNP genotyping system. Journal of Agricultural and Food Chemistry. 8(9):792. https://doi.org/10.3390/horticulturae8090792.
D'Auria, J.C., Cohen, S.P., Leung, J., Glockzin, K., Glockzin, K., Gervay-Hague, J., Zhang, D., Meinhardt, L.W. 2022. USA Tea: A synopsis of ongoing tea research and USA production issues. Frontiers in Plant Science. 13:934651. https://doi.org/10.3389/fpls.2022.934651.
Ferraz, G., Lopez, M.E., Zhang, D., Rodrigues-Carvalho, G., Meinhardt, L.W., Chalfun-Junior, A. 2023. Selecting progenies of coffee variety “Mundo Novo” with potential for the specialty coffee market. Beverage Plant Research. 3(1):1-11. https://doi.org/10.48130/BPR-2023-0001.
Souza, J.J., Silveira, F.E., Silva Pereira, B., Mateus-Rodriguez, J., Ahnert, D., Baligar, V.C. 2022. Edaphic and physiographic attributes and their impact on death of cacao trees in drought years. Agronomy Journal. 115(3):1069-1084. https://doi.org/10.1002/agj2.21215.
Sapkota, D., Zhang, D., Park, S., Meinhardt, L.W., Yao, S. 2023. Genotyping of Jujube (Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas. Plants. 12:2405. https://doi.org/10.3390/plants12132405.
Arevalo-Hernandez, C., Arevalo-Ardini, E., Farfana, A., Amaringo-Gomez, M., Daymond, A., Zhang, D., Baligar, V. 2022. Growth and nutritional responses of juvenile wild and domesticated cacao genotypes to soil acidity. Agronomy. 12(12):3124. https://doi.org/10.3390/agronomy12123124.
Tosto, T., Almeida, A., Paiva, A., Ahnert, D., Baligar, V.C. 2022. Physiological, biochemical and molecular responses of young cacao plants grown in compacted and phosphorus-limited coastal plain soil. Journal of Plant Growth Regulation. 42:2389–2407. https://doi.org/10.1007/s00344-022-10712-3.
Shentu, J., He, Z., Xin, X., Zhang, T., Yang, X., Baligar, V.C. 2022. Sources, indicators, and assessment of soil contamination by potentially toxic metals. Sustainability. 14:15878. https://doi.org/10.3390/su142315878.
