Robert Krueger | USDA Agricultural Research Service (original) (raw)

Papers by Robert Krueger

Scientia Horticulturae, 2022

Citrus (Rutaceae) species have a relevant role in the culture of the Mediterranean countries, not... more Citrus (Rutaceae) species have a relevant role in the culture of the Mediterranean countries, not only for their gastronomic or medicinal value, but especially for their ornamental and symbolic importance. The interest on Citrus diversity led to collect and cultivate numerous cultivars around the Mediterranean Sea, at least since the Roman period. Their image is documented in mosaics, paintings, sculptures and coins since the first millennium BC. Among these, sweet and sour limettas Citrus × limon var. limetta (Risso) Ollitrault, Curk & R.Krueger stand for their history and conservation status. Presently sour limetta is cultivated in Morocco, especially in Marrakesh, and in the Valle de Ricote (Murcia, Spain). Our work has three main objectives: to characterize sour limetta on the basis of Spanish and Moroccan populations, as well as its cultural relevance throughout history, especially in painting, gastronomy, agriculture and gardening, to determine their relationships with limes and lemons and to evaluate the availability and state of conservation of that legacy. We analyze and illustrate the morphology of the plant, flowers and fruits of sour limetta and their differences with other related citrus species and cultivars: sweet limetta, lemon, common lime, Persian lime, bergamot, mellarosa, Meyer lemon, rough lemon, Pursha Romana lime, Palestine sweet lime, Pomum Adami lemon and Rangpur lime. The above species and cultivars were selected on the base of their known ancestry and pomological characters. The distinctive characters are useful for the identification of sour limetta in the field but also for the identifying images of this plant in paintings. We analyzed the ancestry of the different taxa involved and compared the classification based on phenotypes with the classification based on the proportion of ancestors' genomes in each individual taxa. The image of sour limetta appears in different paintings, from the van Eyck's Ghent Polyptych (early 15th century), and numerous still life works by Italian and Spanish authors of the 16th to 18th centuries. A peculiar type of evidence is provided by presence of limetta in the pictorial catalogues of the Medici's fruit collections displayed in a series of paintings by Bartolomeo Bimbi. This distinctly sour limetta is sold in the markets of Rabat (and other cities of Morocco), either fresh, candied or brined and canned. It is an important ingredient of traditional Moroccan cuisine. Although sour lime was a widely used ingredient in Italian cuisine during the 17th century, its state of preservation is deplorable outside of Morocco, and even there it is gradually replaced by lemons. We recommend its cultivation as a resource both for obtaining rootstocks as well as for its fruits, both for Moroccan cuisine and that of other parts of the world for the excellent aromas and flavors that they contribute to the dishes. In this way, by promoting its crop, we will prevent it from disappearing. It is also important to preserve sour lime in germplasm banks.

The Date Palm Genome, Vol. 1, 2021

The date palm (Phoenix dactylifera L.) is the type species for the genus Phoenix of the family Ar... more The date palm (Phoenix dactylifera L.) is the type species for the genus Phoenix of the family Arecaceae (Palmaceae). Phoenix species are native to tropical and subtropical areas of Asia and Africa. The date palm has been domesticated for several millennia in its centres of origin, diversity and domestication in the Middle East and North Africa. From there, date culture spread to other areas having a suitable climate (hot and arid or semiarid) with sufficient water available either as groundwater or irrigation. The date palm was introduced into the Western Hemisphere much later and has a more limited production area there. The date palm is a unique, arborescent monocotyledonous plant with distinctive anatomical features and environmental adaptations. It grows in arid, sandy environments but requires large volumes of water for growth and fruit production; it tolerates saline conditions but is not a true halophyte. Numerous labour-intensive cultural practices including pruning, pollination and bunch management are necessary for successful date production. Postharvest handling may include dehydration or hydration, depending upon the fruit moisture content at harvest. Date fruit is also processed into pastes, syrups, butters and other products. Production of dates has increased in recent decades and will likely continue to increase in the near-term future.

Genetic Resources and Crop Evolution

Citrus germplasm is conserved in genebanks at sites around the world to provide genetic resources... more Citrus germplasm is conserved in genebanks at sites around the world to provide genetic resources for breeding and research programs. The value of genebank collections is particularly evident as diseases and climate change threaten citrus production areas. We provide historical, inventory, and maintenance information about national citrus collections in Russia and in the United States. The Russian Research Institute of Floriculture and Subtropical Crops (RRIFSC) in Sochi, Russia maintains a collection of 132 citrus accessions representing 50 taxa. Southern Russia is one of the most northerly citrus growing areas in the world and many accessions in the RRIFSC collection were specifically selected for cold tolerance to facilitate citrus production in this region. Tree response data taken during the frequent severe winters in Sochi has provided an understanding of the relative cold tolerance of many RRIFSC accessions. Particularly noteworthy is the array of cold-tolerant lemon accessions maintained at the RRIFSC. The Aurantioideae collections at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS) National Clonal Germplasm Repository for Citrus and Dates (NCGRCD) and at the University of California Citrus Variety Collection in Riverside, California, maintain 1328 accessions of citrus cultivars and wild relatives. Because of federal and state quarantine regulations, accessions at this facility are tested for graft-transmissible pathogens and undergo therapy to eliminate known pathogens. In contrast to Sochi, desert-adapted lemon and grapefruit varieties are a major interest of the California-based collection. The collection of citrus and citrus relatives is being screened for resistance and/or tolerance genes to diseases such as huanglongbing which is currently threatening the US citrus industry. Through collaborative exchange efforts, the diversity in the two genebanks could be expanded to increase availability of desirable genetic resources to breeding and research communities throughout the world.

Economic Botany, 2014

The spring-fed mission oases of the Baja California peninsula, Mexico, hold several species, vari... more The spring-fed mission oases of the Baja California peninsula, Mexico, hold several species, varieties and unique hybrids of heritage citrus, which may represent valuable genetic resources. Citrus species first arrived to the peninsula with the Jesuit missionaries (1697-1768), and new varieties were introduced during the colonial and rancho periods following the mission era. These heritage trees are grown in field and house gardens as ornamental, fruit and shade trees. Commercial citrus varieties introduced from the United States have become a strong source of economic revenue for peninsula agriculturalists. A few of the peninsula oases support commercial citrus groves, though these are primarily found in the broader valleys of the peninsula where groundwater is tapped for irrigation. The isolated environments of the mission oases and surrounding ranches have facilitated propagation of unique citrus types, and these have stabilized through integration into the cultural practices of the region. We identify and document citrus of the peninsula oases to serve as a baseline for those interested in the cultural ecology of citrus and citrus genetic resources.ResumenLos oasis-misiones formados por manantiales en la península de Baja California, México, tienen especies, variedades e híbridos únicos de cítricos antiguos que pueden representar valiosos recursos genéticos. Las primeras especies de cítricos llegaron a la península con los misioneros jesuitas (1697-1768) y, posteriormente, las nuevas variedades se introdujeron durante los períodos colonial y ranchero después de la época misional. Estos árboles de genética antigua se cultivan en las huertas y los solares, como setos y como árboles ornamentales, frutales y de sombra. Las variedades de cítricos comerciales introducidas desde Estados Unidos se han convertido en una fuente importante de ingresos económicos para los agricultores de la península. Algunos de los oasis de la península tienen plantaciones comerciales de cítricos, aunque la mayoría de estas plantaciones comerciales se encuentran en los valles más extensos de la península dónde el agua subterránea es aprovechada para el riego. Los ambientes aislados de los oasis-misiones y de los ranchos circundantes han facilitado la propagación de tipos de cítricos únicos, y éstos se han estabilizado gracias a su integración en las prácticas culturales de la región. Identificamos y documentamos los cítricos de los oasis de la península lo que ha de servir como punto de referencia para los interesados en la ecología cultural y los recursos genéticos de los cítricos.

Genomics of Tree Crops, 2012

The palm family, consisting of over 2,500 species arrayed among ca. 200 genera, is the third most... more The palm family, consisting of over 2,500 species arrayed among ca. 200 genera, is the third most economically important family of plants after the grasses and legumes. Three palm species account for the large majority of the family’s economic importance: coconut (Cocos nucifera), African oil palm (Elaeis guineensis), and date palm (Phoenix dactylifera). Of the three, genomics has been least developed in the coconut, where molecular tools have largely been used to characterize germplasm, and, to a lesser extent, develop quantitative trait loci (QTL). Both date palm and oil palm have recently had their genomes sequenced. The application of genomic tools to these palm species will result in enormous advances in the genetic improvement of all three crops.

BMC Genomics

Background: The date palm is one of the oldest cultivated fruit trees. The tree can withstand hig... more Background: The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results: To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin. Conclusions: These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. We propose that earliest date palm cultivation occurred independently in at least 3 distinct locations. This discovery will further inform understanding of the history and origins of cultivated date palm.

Nature Communications

was incorrectly assigned as a present address and should have been listed as a full affiliation. ... more was incorrectly assigned as a present address and should have been listed as a full affiliation. This error has been corrected in both the PDF and HTML versions of the Article.

Plant Cell, Tissue and Organ Culture (PCTOC)

Agriculture

The objective of this study was to evaluate the effect of pollen source on the nutritional compos... more The objective of this study was to evaluate the effect of pollen source on the nutritional composition of seeds of the ‘Medjool’ date (Phoenix dactylifera L.) under conditions of northwest Mexico. The content of nutrients (protein, lipids, fiber, and ash), sugars (total, reducing, and non-reducing), and most abundant minerals, were evaluated, as well as antioxidant activities. The pollen of four cultivars (‘Deglet Noor’, ‘Khadrawy’, ‘Medjool’, and ‘Zahidi’) was selected. Four groups of three bunches were pollinated in each of the female palms. For the four treatments, the following ranges were obtained: Seeds had a weight of 1.32–1.41 g and low concentrations of protein (4.44–5.49 g/100 g) and lipids (9.62–10.19 g/100 g). The content of dietary fiber and ash was 59.65–72.59 g/100 g and 1.09–1.42 g/100 g, respectively. Total sugars content was 4.50–6.96 g/100 g, while the insoluble solids were 92.21–96.03 g/100 g. The predominant mineral was potassium with 399.97–459.79 mg/100 g dry ...

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms amon... more Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for speciWed Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Pon-cirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identiWed Wve populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.

Genetic Resources and Crop Evolution, 2005

... Ashraf M. El-Assar, Robert R. Krueger1, Pachanoor S. Devanand2 and Chih-Cheng T. Chao* Tropic... more ... Ashraf M. El-Assar, Robert R. Krueger1, Pachanoor S. Devanand2 and Chih-Cheng T. Chao* Tropical Fruit and Date Palm Research Department ... 72. Mokhtar T., AbdelAli B., Abdelmajid R., Andre´ R. and Mohamed M. 1998. ... Sharma DR, Dawra S. and Chowdhury JB 1984. ...

Journal of the American Society For Horticultural Science, Nov 1, 2003

New potential citrus germplasm accessions may be received as seed rather than budwood, thereby re... more New potential citrus germplasm accessions may be received as seed rather than budwood, thereby reducing phytosanitary risks. However, trueness-to-type may be an issue with seed materials because many varieties produce both apomictic (nucellar) and sexual (zygotic) embryos and most citrus is fairly heterozygous. To identify nucellar seedlings of polyembryonic types and to retain these as representing the type, we screened 1340 seedlings from 88 seed sources for markers amplified with two inter-simple sequence repeat (ISSR) primers. Sixteen seed sources produced no seedlings classified as being of nucellar origin. Among the remaining seed sources, seedlings classed as nucellar were identified for potential addition to the collection. In 37 accessions, both nucellar and zygotic seedlings were detected, and in some cases both types were retained. Inclusion of established accessions of the same cultivar group in the analysis allowed an initial assessment of similarity to existing accessions. This technique improved the efficiency of acquiring new germplasm of polyembryonic types by seed. The method identifies those seed sources that produce few or no nucellar seedlings, but it is not useful for determining which seedlings of monoembryonic types should be retained in collections.

ABSTRACT Citrus and citrus relatives are often hosts of pests and pathogens of quarantine signifi... more ABSTRACT Citrus and citrus relatives are often hosts of pests and pathogens of quarantine significance. Their fruits, leaves and propagative materials are also commonly smuggled into the United States, and this has caused grave economic harm to growers. As a complement to efforts to interdict smuggling, it can be useful to recognize when smuggling results from the unfilled demand for genotypes that are not readily available through conventional nurseries and clean plant programs. The Unforbidden Fruits project has identified several such species and varieties, and is seeking to ensure that safe pathogen-tested material is available to meet demand in California. The project’s initial focus has been on curry leaf (Bergera koenigii), used in South Asian cooking, and bael (Aegle marmelos), used for Hindu ritual purposes. In both cases the leaves are the primary plant part in demand; this makes them particularly dangerous because the leaves can host the Asian citrus psyllid (Diaphorina citri), the vector of Candidatus Liberibacter asiaticus, the bacterium associated with Huanglongbing (HLB), a devastating citrus disease. No established procedures exist for the grafting and indexing of such citrus relatives, so the project is first testing seed trees for seed-transmissible diseases, and then distributing seeds to cooperating licensed California citrus nurseries. In addition, the project has acquired germplasm of citron (C. medica) suitable for Jewish ritual purposes, which according to religious requirements must be derived from never-grafted stock; this poses challenges to conventional germplasm methods, which rely on collection of budwood and micro-shoot-tip grafting. The project has started distributing seeds of ‘Assads,’ a rare, prized citron of Moroccan origin, to interested nurseries.

Nature communications, 2015

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the M... more Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This anal...

G3: Genes|Genomes|Genetics, 2015

The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately ti... more The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors and sizes growing mainly in arid lands from the west of North Africa to India. The origin of date palm domestication is still uncertain and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm-growing regions, including four Phoenix species as outgroup. Here, for the first time we generate genome-wide genotyping data for 13,000 -65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm.

Theoretical and Applied Genetics, 2006

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms amon... more Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for specified Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor-joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Poncirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identified five populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.

Scientia Horticulturae, 2022

Citrus (Rutaceae) species have a relevant role in the culture of the Mediterranean countries, not... more Citrus (Rutaceae) species have a relevant role in the culture of the Mediterranean countries, not only for their gastronomic or medicinal value, but especially for their ornamental and symbolic importance. The interest on Citrus diversity led to collect and cultivate numerous cultivars around the Mediterranean Sea, at least since the Roman period. Their image is documented in mosaics, paintings, sculptures and coins since the first millennium BC. Among these, sweet and sour limettas Citrus × limon var. limetta (Risso) Ollitrault, Curk & R.Krueger stand for their history and conservation status. Presently sour limetta is cultivated in Morocco, especially in Marrakesh, and in the Valle de Ricote (Murcia, Spain). Our work has three main objectives: to characterize sour limetta on the basis of Spanish and Moroccan populations, as well as its cultural relevance throughout history, especially in painting, gastronomy, agriculture and gardening, to determine their relationships with limes and lemons and to evaluate the availability and state of conservation of that legacy. We analyze and illustrate the morphology of the plant, flowers and fruits of sour limetta and their differences with other related citrus species and cultivars: sweet limetta, lemon, common lime, Persian lime, bergamot, mellarosa, Meyer lemon, rough lemon, Pursha Romana lime, Palestine sweet lime, Pomum Adami lemon and Rangpur lime. The above species and cultivars were selected on the base of their known ancestry and pomological characters. The distinctive characters are useful for the identification of sour limetta in the field but also for the identifying images of this plant in paintings. We analyzed the ancestry of the different taxa involved and compared the classification based on phenotypes with the classification based on the proportion of ancestors' genomes in each individual taxa. The image of sour limetta appears in different paintings, from the van Eyck's Ghent Polyptych (early 15th century), and numerous still life works by Italian and Spanish authors of the 16th to 18th centuries. A peculiar type of evidence is provided by presence of limetta in the pictorial catalogues of the Medici's fruit collections displayed in a series of paintings by Bartolomeo Bimbi. This distinctly sour limetta is sold in the markets of Rabat (and other cities of Morocco), either fresh, candied or brined and canned. It is an important ingredient of traditional Moroccan cuisine. Although sour lime was a widely used ingredient in Italian cuisine during the 17th century, its state of preservation is deplorable outside of Morocco, and even there it is gradually replaced by lemons. We recommend its cultivation as a resource both for obtaining rootstocks as well as for its fruits, both for Moroccan cuisine and that of other parts of the world for the excellent aromas and flavors that they contribute to the dishes. In this way, by promoting its crop, we will prevent it from disappearing. It is also important to preserve sour lime in germplasm banks.

The Date Palm Genome, Vol. 1, 2021

The date palm (Phoenix dactylifera L.) is the type species for the genus Phoenix of the family Ar... more The date palm (Phoenix dactylifera L.) is the type species for the genus Phoenix of the family Arecaceae (Palmaceae). Phoenix species are native to tropical and subtropical areas of Asia and Africa. The date palm has been domesticated for several millennia in its centres of origin, diversity and domestication in the Middle East and North Africa. From there, date culture spread to other areas having a suitable climate (hot and arid or semiarid) with sufficient water available either as groundwater or irrigation. The date palm was introduced into the Western Hemisphere much later and has a more limited production area there. The date palm is a unique, arborescent monocotyledonous plant with distinctive anatomical features and environmental adaptations. It grows in arid, sandy environments but requires large volumes of water for growth and fruit production; it tolerates saline conditions but is not a true halophyte. Numerous labour-intensive cultural practices including pruning, pollination and bunch management are necessary for successful date production. Postharvest handling may include dehydration or hydration, depending upon the fruit moisture content at harvest. Date fruit is also processed into pastes, syrups, butters and other products. Production of dates has increased in recent decades and will likely continue to increase in the near-term future.

Genetic Resources and Crop Evolution

Citrus germplasm is conserved in genebanks at sites around the world to provide genetic resources... more Citrus germplasm is conserved in genebanks at sites around the world to provide genetic resources for breeding and research programs. The value of genebank collections is particularly evident as diseases and climate change threaten citrus production areas. We provide historical, inventory, and maintenance information about national citrus collections in Russia and in the United States. The Russian Research Institute of Floriculture and Subtropical Crops (RRIFSC) in Sochi, Russia maintains a collection of 132 citrus accessions representing 50 taxa. Southern Russia is one of the most northerly citrus growing areas in the world and many accessions in the RRIFSC collection were specifically selected for cold tolerance to facilitate citrus production in this region. Tree response data taken during the frequent severe winters in Sochi has provided an understanding of the relative cold tolerance of many RRIFSC accessions. Particularly noteworthy is the array of cold-tolerant lemon accessions maintained at the RRIFSC. The Aurantioideae collections at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS) National Clonal Germplasm Repository for Citrus and Dates (NCGRCD) and at the University of California Citrus Variety Collection in Riverside, California, maintain 1328 accessions of citrus cultivars and wild relatives. Because of federal and state quarantine regulations, accessions at this facility are tested for graft-transmissible pathogens and undergo therapy to eliminate known pathogens. In contrast to Sochi, desert-adapted lemon and grapefruit varieties are a major interest of the California-based collection. The collection of citrus and citrus relatives is being screened for resistance and/or tolerance genes to diseases such as huanglongbing which is currently threatening the US citrus industry. Through collaborative exchange efforts, the diversity in the two genebanks could be expanded to increase availability of desirable genetic resources to breeding and research communities throughout the world.

Economic Botany, 2014

The spring-fed mission oases of the Baja California peninsula, Mexico, hold several species, vari... more The spring-fed mission oases of the Baja California peninsula, Mexico, hold several species, varieties and unique hybrids of heritage citrus, which may represent valuable genetic resources. Citrus species first arrived to the peninsula with the Jesuit missionaries (1697-1768), and new varieties were introduced during the colonial and rancho periods following the mission era. These heritage trees are grown in field and house gardens as ornamental, fruit and shade trees. Commercial citrus varieties introduced from the United States have become a strong source of economic revenue for peninsula agriculturalists. A few of the peninsula oases support commercial citrus groves, though these are primarily found in the broader valleys of the peninsula where groundwater is tapped for irrigation. The isolated environments of the mission oases and surrounding ranches have facilitated propagation of unique citrus types, and these have stabilized through integration into the cultural practices of the region. We identify and document citrus of the peninsula oases to serve as a baseline for those interested in the cultural ecology of citrus and citrus genetic resources.ResumenLos oasis-misiones formados por manantiales en la península de Baja California, México, tienen especies, variedades e híbridos únicos de cítricos antiguos que pueden representar valiosos recursos genéticos. Las primeras especies de cítricos llegaron a la península con los misioneros jesuitas (1697-1768) y, posteriormente, las nuevas variedades se introdujeron durante los períodos colonial y ranchero después de la época misional. Estos árboles de genética antigua se cultivan en las huertas y los solares, como setos y como árboles ornamentales, frutales y de sombra. Las variedades de cítricos comerciales introducidas desde Estados Unidos se han convertido en una fuente importante de ingresos económicos para los agricultores de la península. Algunos de los oasis de la península tienen plantaciones comerciales de cítricos, aunque la mayoría de estas plantaciones comerciales se encuentran en los valles más extensos de la península dónde el agua subterránea es aprovechada para el riego. Los ambientes aislados de los oasis-misiones y de los ranchos circundantes han facilitado la propagación de tipos de cítricos únicos, y éstos se han estabilizado gracias a su integración en las prácticas culturales de la región. Identificamos y documentamos los cítricos de los oasis de la península lo que ha de servir como punto de referencia para los interesados en la ecología cultural y los recursos genéticos de los cítricos.

Genomics of Tree Crops, 2012

The palm family, consisting of over 2,500 species arrayed among ca. 200 genera, is the third most... more The palm family, consisting of over 2,500 species arrayed among ca. 200 genera, is the third most economically important family of plants after the grasses and legumes. Three palm species account for the large majority of the family’s economic importance: coconut (Cocos nucifera), African oil palm (Elaeis guineensis), and date palm (Phoenix dactylifera). Of the three, genomics has been least developed in the coconut, where molecular tools have largely been used to characterize germplasm, and, to a lesser extent, develop quantitative trait loci (QTL). Both date palm and oil palm have recently had their genomes sequenced. The application of genomic tools to these palm species will result in enormous advances in the genetic improvement of all three crops.

BMC Genomics

Background: The date palm is one of the oldest cultivated fruit trees. The tree can withstand hig... more Background: The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results: To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin. Conclusions: These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. We propose that earliest date palm cultivation occurred independently in at least 3 distinct locations. This discovery will further inform understanding of the history and origins of cultivated date palm.

Nature Communications

was incorrectly assigned as a present address and should have been listed as a full affiliation. ... more was incorrectly assigned as a present address and should have been listed as a full affiliation. This error has been corrected in both the PDF and HTML versions of the Article.

Plant Cell, Tissue and Organ Culture (PCTOC)

Agriculture

The objective of this study was to evaluate the effect of pollen source on the nutritional compos... more The objective of this study was to evaluate the effect of pollen source on the nutritional composition of seeds of the ‘Medjool’ date (Phoenix dactylifera L.) under conditions of northwest Mexico. The content of nutrients (protein, lipids, fiber, and ash), sugars (total, reducing, and non-reducing), and most abundant minerals, were evaluated, as well as antioxidant activities. The pollen of four cultivars (‘Deglet Noor’, ‘Khadrawy’, ‘Medjool’, and ‘Zahidi’) was selected. Four groups of three bunches were pollinated in each of the female palms. For the four treatments, the following ranges were obtained: Seeds had a weight of 1.32–1.41 g and low concentrations of protein (4.44–5.49 g/100 g) and lipids (9.62–10.19 g/100 g). The content of dietary fiber and ash was 59.65–72.59 g/100 g and 1.09–1.42 g/100 g, respectively. Total sugars content was 4.50–6.96 g/100 g, while the insoluble solids were 92.21–96.03 g/100 g. The predominant mineral was potassium with 399.97–459.79 mg/100 g dry ...

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms amon... more Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for speciWed Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Pon-cirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identiWed Wve populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.

Genetic Resources and Crop Evolution, 2005

... Ashraf M. El-Assar, Robert R. Krueger1, Pachanoor S. Devanand2 and Chih-Cheng T. Chao* Tropic... more ... Ashraf M. El-Assar, Robert R. Krueger1, Pachanoor S. Devanand2 and Chih-Cheng T. Chao* Tropical Fruit and Date Palm Research Department ... 72. Mokhtar T., AbdelAli B., Abdelmajid R., Andre´ R. and Mohamed M. 1998. ... Sharma DR, Dawra S. and Chowdhury JB 1984. ...

Journal of the American Society For Horticultural Science, Nov 1, 2003

New potential citrus germplasm accessions may be received as seed rather than budwood, thereby re... more New potential citrus germplasm accessions may be received as seed rather than budwood, thereby reducing phytosanitary risks. However, trueness-to-type may be an issue with seed materials because many varieties produce both apomictic (nucellar) and sexual (zygotic) embryos and most citrus is fairly heterozygous. To identify nucellar seedlings of polyembryonic types and to retain these as representing the type, we screened 1340 seedlings from 88 seed sources for markers amplified with two inter-simple sequence repeat (ISSR) primers. Sixteen seed sources produced no seedlings classified as being of nucellar origin. Among the remaining seed sources, seedlings classed as nucellar were identified for potential addition to the collection. In 37 accessions, both nucellar and zygotic seedlings were detected, and in some cases both types were retained. Inclusion of established accessions of the same cultivar group in the analysis allowed an initial assessment of similarity to existing accessions. This technique improved the efficiency of acquiring new germplasm of polyembryonic types by seed. The method identifies those seed sources that produce few or no nucellar seedlings, but it is not useful for determining which seedlings of monoembryonic types should be retained in collections.

ABSTRACT Citrus and citrus relatives are often hosts of pests and pathogens of quarantine signifi... more ABSTRACT Citrus and citrus relatives are often hosts of pests and pathogens of quarantine significance. Their fruits, leaves and propagative materials are also commonly smuggled into the United States, and this has caused grave economic harm to growers. As a complement to efforts to interdict smuggling, it can be useful to recognize when smuggling results from the unfilled demand for genotypes that are not readily available through conventional nurseries and clean plant programs. The Unforbidden Fruits project has identified several such species and varieties, and is seeking to ensure that safe pathogen-tested material is available to meet demand in California. The project’s initial focus has been on curry leaf (Bergera koenigii), used in South Asian cooking, and bael (Aegle marmelos), used for Hindu ritual purposes. In both cases the leaves are the primary plant part in demand; this makes them particularly dangerous because the leaves can host the Asian citrus psyllid (Diaphorina citri), the vector of Candidatus Liberibacter asiaticus, the bacterium associated with Huanglongbing (HLB), a devastating citrus disease. No established procedures exist for the grafting and indexing of such citrus relatives, so the project is first testing seed trees for seed-transmissible diseases, and then distributing seeds to cooperating licensed California citrus nurseries. In addition, the project has acquired germplasm of citron (C. medica) suitable for Jewish ritual purposes, which according to religious requirements must be derived from never-grafted stock; this poses challenges to conventional germplasm methods, which rely on collection of budwood and micro-shoot-tip grafting. The project has started distributing seeds of ‘Assads,’ a rare, prized citron of Moroccan origin, to interested nurseries.

Nature communications, 2015

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the M... more Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This anal...

G3: Genes|Genomes|Genetics, 2015

The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately ti... more The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors and sizes growing mainly in arid lands from the west of North Africa to India. The origin of date palm domestication is still uncertain and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm-growing regions, including four Phoenix species as outgroup. Here, for the first time we generate genome-wide genotyping data for 13,000 -65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm.

Theoretical and Applied Genetics, 2006

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms amon... more Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for specified Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor-joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Poncirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identified five populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.