Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n=32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community. Yaodong Yang et al. report a chromosome-scale genome assembly of the coconut and transcriptome analysis of coconut leaves. Their analysis reveals important steps along the evolutionary trajectory of palms and identifies genes that may play a key role in tolerance to salt stress.

Pour confirmer la ségrégation de l’un des deux loci codant pour la couleur du germe chez les cocotiers nains, le Back cross 1 : NJM x (NJM x GOA+) a été réalisé dans le cadre d’un projet de cartographie du génome du cocotier. Un donneur NJM x GOA+ (Nain jaune de Malaisie x Grand Ouest Africain+) et une receveuse NJM (Nain jaune de Malaisie) ont été impliqués dans le BC1. Les statistiques descriptives, le test U de Mann-Withney et le test du Khi-deux de conformité ont été appliqués. Pour un total de 1034 noix semences germées, les résultats ont montré que sur 5 ségrégations testées, seule la 1:1 vérifie la conformité des données observées à celles théoriques au seuil de risque de 5 %. Ceci suggère que le couple d’allèles Vert/Jaune codant pour l’expression phénotypique y afférente ségrége selon les lois de la génétique classique. Ces résultats s’apparentent à ceux de Bourdeix. Fort malheureusement, son analyse génétique était sous-tendue par de nombreuses hypothèses. De plus, les semences de noix étaient issues de pollinisations libres de pieds d’hybrides F1. Dans les deux cas, ce sont les germes issus des noix F2 germées qui ont été analysées. La ségrégation 1 : 1 issu du BC1 : NJM x (NJM x GOA+) suggère un contrôle monofactoriel du marqueur vert/jaune. Ce marqueur pourrait être introgressé dans les génotypes d’intérêt avant d’être utilisé, par la suite, pour la sélection précoce en germoir. To confirm the segregation of one of the two loci coding for the color of the germ in dwarf coconut palms, back cross 1: MYD x (MYD x WAT+) was carried out as part of a coconut genome mapping project. An MYD x WAT+ (Malayan Yellow Dwarf x West African Tall+) donor and an MYD (Malayan Yellow Dwarf) recipient were involved in BC1. Descriptive statistics, the Mann-Withney U test and the Chi-two conformance test were applied. For a total of 1034 seed nuts germinated, the results showed that out of 5 segregations tested, only the 1: 1 verifies the compliance of the observed data with the theoretical ones at the risk threshold of 5%. This suggests that the pair of Green / Yellow alleles encoding the related phenotypic expression segregates according to the laws of classical genetics. Those results are similar to those of Bourdeix. Unfortunately, his genetic analysis was underpinned by many hypotheses. In addition, the nut seeds were obtained from free pollination of F1 hybrid feet. In both cases, only germs from the germinated F2 nuts were analyzed. The 1:1 segregation from BC1: MYD x (MYD x WAT+) suggests a monofactorial control of the green / yellow marker. This marker could be moved into the interest of the genotypes before being used, thereafter, for early selection in the germinator.

Coconut is an integral part of the livelihood of millions of farmers in the coastal tropical areas and is facing an important mutation. While its place as a major cheap oil crop on the international market is slowly declining, promising markets are emerging, such as coconut water, virgin coconut oil, and sugar among others. Coconut is regaining its tradition role of multi-usage crop, leading to new opportunities. It is however facing serious threats such as widespread lethal diseases and insect pests. To meet these challenges, coconut genetic improvement should renew its practices and objectives. But it is a difficult task due to long generation duration, low planting densities and low prolificacy. Advances in coconut genomic studies will improve its efficiency in several ways: Neutral markers allow broadening the genetic base of selection; QTLs based on mapping populations or on whole genome association studies (GWAS) will reduce the time and the areas needed to establish a breeding program. Comparative genomics and transcriptomics provide an in-depth understanding of metabolic pathways involved in production, product quality and adaptation to biotic and abiotic stress. A coconut genome draft was published recently and will be converted into a reference sequence thanks to high-density linkage mapping. Other sequencing efforts have been undertaken, whose combined results will provide a preliminary basis for characterizing coconut genetic diversity at the gene level to be completed by more resequencing. A revival of coconut genetic improvement will depend, among other elements, on high quality phenotyping, in conjunction with large SNP sets, transcriptomics and comparative genomics. (Resume d'auteur)

The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).

Abstract Coconut palm (Cocos nucifera,2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific Islands, with a total growth area of more than 12 million hectares [1]. Coconut palm is generally classified into 2 main categories: “Tall” (flowering 8–10 years after planting) and “Dwarf” (flowering 4–6 years after planting), based on morphological characteristics and breeding habits. This Palmae species has a long growth period before reproductive years, which hinders conventional breeding progress. In spite of initial successes, improvements made by conventional breeding have been very slow. In the present study, we obtained de novo sequences of the Cocos nucifera genome: a major genomic resource that could be used to facilitate molecular breeding in Cocos nucifera and accelerate the breeding process in this important crop. A total of 419.67 gigabases (Gb) of raw reads were generated by the Illumina HiSeq 2000 platform using a series of paired-end and mate-pair libraries, covering the predicted Cocos nucifera genome length (2.42 Gb, variety “Hainan Tall”) to an estimated ×173.32 read depth. A total scaffold length of 2.20 Gb was generated (N50 = 418 Kb), representing 90.91% of the genome. The coconut genome was predicted to harbor 28 039 protein-coding genes, which is less than in Phoenix dactylifera (PDK30: 28 889), Phoenix dactylifera (DPV01: 41 660), and Elaeis guineensis (EG5: 34 802). BUSCO evaluation demonstrated that the obtained scaffold sequences covered 90.8% of the coconut genome and that the genome annotation was 74.1% complete. Genome annotation results revealed that 72.75% of the coconut genome consisted of transposable elements, of which long-terminal repeat retrotransposons elements (LTRs) accounted for the largest proportion (92.23%). Comparative analysis of the antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species.

The commercial cultivation of dwarf coconut is rare in the world, representing about 5% of global population. However, Dwarfs are currently receiving more attention, particularly for the harvest of tender nut water. Dwarfs are distinguished from tall coconuts primarily by their short height with an absence of a bole at the base of the stem, their early setting of nuts, their predominantly self fertilizing mating system and by large numbers of relatively small nuts. To date, the origin and domestication of Dwarfs has not been established. This study investigates the origin and domestication of dwarf coconut using molecular markers, mainly microsatellite (SSR) data. The inheritance of height and the presence of a bole was investigated in the F-2 of a cross between Dwarf and Tall palms. The data suggest that the presence of a bole results from a single codominant locus. There was no strong association between the presence of a bole and height, with height also depending on a single codominant gene. However genetic and environmental factors make it difficult to assign individuals a definite genotype. SSR allele frequency differences between dwarf and tall accessions, ethno botanical and geographic information indicate that dwarf coconut originated from a typical domestication event in Southeast Asia. (C) 2016 Elsevier B.V. All rights reserved.

The additive genetic value for oil yield of 135 parents from several African populations tested in the first cycle of Indonesian Oil Palm Research Institute (IOPRI) breeding programme were estimated by best linear unbiased prediction (BLUP) using an unbalanced data set. These values were used to evaluate the possibility of reduction in generation selection time in an oil palm breeding programme. The ranks of parental additive genetic values obtained with early yield period and whole cycle was found to be consistent. These make that highly potential parents could be selected and recombined at a more precocious time in order to reduce the period between cycle. Since oil yield trait is mainly controlled under additive gene effect, the recombination should be done carefully for retaining as highly as possible this character in a parent to be improved.

PREMISE OF THE STUDY: The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe.METHODS: Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci.KEY RESULTS: The coconut genome is large-averaging 5.966 pg-and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes.CONCLUSIONS: Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.

BACKGROUND:The pre-Columbian presence of coconut on the Pacific coast of Panama is attested by a number of independent written accounts. However, recent papers question their accuracy and conclude that coconut was introduced to the region by the Spaniards after their conquests. Scope In order to examine the value of such claims, an extensive search was conducted of the relevant historical accounts of coconut in America and in the Orient.KEY RESULTS:The Spanish chronicler Oviedo (1478-1557) is found to have effectively used fruit and seed size to distinguish coconut from other palms. In addition, it is shown that he has been inaccurately faulted with incorrectly representing a cluster of coconuts. The original drawing, a cluster of a native Bactris, was in the marginalia and was only assigned to coconut after Oviedo's death. Finally, the location is identified of a coastal Panamanian site described by Pedro Mártir de Anglería and where tidal dispersal of coconuts was observed.CONCLUSIONS:This previously overlooked evidence confirms the pre-historical presence of coconut in Panama. Genetic data indicate that it must have been brought there directly or indirectly from the Philippines. But when, where and by whom remains a subject of research. Further molecular marker studies, computer simulation of natural drift and archaeological research could contribute to this research.

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the presentstudy was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples werecollected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles perlocus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per populationranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populationsof Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia doForte. These results reveal a high level of genetic diversity in the Brazilian populations.

Coconut is cultivated throughout the tropical coasts and is integral part of the way of life of many human communities. There is no related wild species. Many coconut varieties were identified. Stature and mating system distinguish selfpollinating Dwarfs and cross-pollinating Talls. Within these types, varieties differ in terms of fruit color, size and morphology. Our work aimed to identify the genetic relationships between these varieties as well as the region where cultivation was initiated. It was also to elucidate its dissemination pathways. DNA was collected from 1322 individuals representing more than 100 populations from most of the producing countries. It was analyzed using a microsatellite kit. Results were interpreted in the light of historical information on human population movements. Software Structure identified two major groups. The largest and most diverse group (A) extended from South-east Asia to the whole Pacific. The other group (B) was present in India and on the Atlantic coasts. East Africa and the Western Indian Ocean showed evidence of introgression among groups. The frequency of group A alleles was higher in Madagascar and in the Comoros than in East Africa, reflecting austronesian migrations and arab trade in the region. Attempts to subdivide further diversity preserved group B but split group A into 4 populations. Three of them were centered on South-East Asia, Papua New Guinea (PNG) and the South Pacific without definite limit between them. Virtually all self-pollinating Dwarf coconuts were in the South-East Asian group suggesting that this region was the place of origin of dwarfism. The last population was found on the Pacific coast of Central America and was brought from the Philippines, probably at pre- Columbian times. Our results suggest that coconut cultivation was initiated separately in South Asia and in a region extending from South-East Asian and PNG. The high level of molecular differentiation between groups A and B suggests that gene exchange between India and Pacific was interrupted for a long period. Identifying QT alleles that were fixed during this period would provide breeders with efficient improvement strategies. (Texte integral)

The evolutionary history of the monotypic coconut (Cocos nucifera L.) is intriguing and its geographical origin remains unknown. The coconut is the quintessential strand plant, colonizing sandy coastal beaches and islands in the humid tropics and is well adapted for flotation and natural dispersal by oceanic currents. This palm has also been disseminated by humans for millennia through voyages of exploration and establishment of trade routes across the Indian and Pacific Oceans. This long-term human interaction with the coconut has altered its phenotype and the lack of a universal domestication trait has obscured the putative wild phenotype. Developments in molecular techniques such as next generation sequencing may well prove useful in elucidation of the coconut's origin. Here we propose to apply NGS to multi-loci molecular markers for 20 populations (188 individuals), sampled worldwide to examine the phylogeography, phylogeny, lineage sorting and discovery of polymorphisms for understanding the evolutionary history of the coconut. We will perform parallel tagged sequencing (PTS) for barcoding multiple samples and use the Illumina platform for high throughput sequencing. (Texte integral)

As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L.) played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and "niu vai" fruit morphology) arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent.

The coconut (Cocos nucifera L.) is a pantropical strand plant, colonizing sandy insular beaches in the humid tropics. Cocos is a monotypic genus in the Cocoseae tribe (18/ca. 200 spp.) within the Arecaceae family. Phylogenetic studies support its sister relationship to Syagrus, a Neotropical genus, sharing a common ancestor about 35 MYBP, though the crown group age of Cocos is about 11 MYBP. Fossil evidence indicates that members of the Cocos lineage were present in South America, India, New Zealand and Australia. Coconuts are adapted to drift-dispersal by ocean currents; however, human activities both historically and today have also aided its spread and impacted its phenotypic and genetic structure. Coconuts are traditionally classified as 'Talls' or 'Dwarfs' based on tree habit. Morphological examination reveal two predominant fruit types, attributed to Polynesian terminology: niu kafa are characterized by their elongated, triangular fruits with large proportion of fibrous husk and niu vai, whose fruits are rounded with large proportion of liquid endosperm. The niu kafa form is interpreted as the naturally evolved coconut, under natural selection for dissemination by sea currents whilst the niu vai form evolved from domestication under human selection for greater volume of delicious coconut water. Here we investigate the genetic diversity of coconuts, the impact of domestication, introgression and the taxonomic implications for this species. We used polymorphic microsatellite markers on 1322 coconut samples representing phenotypic and genetic variation worldwide to examine the geographical location of the center(s) of domestication and its progenitors. Bayesian analyses of population structure revealed two major subpopulations corresponding to the Pacific and Indo-Atlantic oceanic regions. Haplotype networks based on chloroplast and nuclear markers are used as a complementary dataset to examine the coconut's phylogeography. (Texte integral)

Coconut foliar decay (CFD) is a disease of coconut ( Cocos nucifera L.) associated with infection by coconut foliar decay virus (CFDV), which is endemic in Vanuatu, South Pacific. The local cultivar ‘Vanuatu Tall’ (VTT) is the only cultivar that is fully tolerant to CFD, whereas introduced cultivars and hybrids are affected to different degrees. From 1967 to 2008 a conventional breeding programme was conducted with the aim of creating hybrid planting material combining tolerance to CFD with improved copra yield and high copra weight per nut. This objective was achieved by crossing the progeny of selfed trees of ‘Rennell Island Tall’ (RIT) cultivar, selected for their low susceptibility to CFD in field screening tests, with VTT, improved by mass selection and intercrossing. An improved VTT × RIT hybrid was identified with a high degree of tolerance to CFD (less than 1% of diseased trees after 11 years of exposure to high disease pressure). The annual production of the improved VTT × RIT hybrid ranged from 21.9 to 28.6 kg of copra per tree, depending on the RIT parent, and was, on average, 34% higher than that of ‘VTT Elite’ an advanced cultivar obtained after four selection cycles of local VTT. However, the production of the hybrid in Vanuatu involves constraints such as frequent replanting and isolation of the seed garden and CFD control for the RIT parents. The importance of conducting research on the genetic determinism and the mechanism of tolerance to CFD for better control of the disease in the event that it spreads outside Vanuatu is discussed.

Coconut palms of the Tall group were introduced to Brazil from the Cape Verde Islands in 1553. The present study sought to evaluate the genetic diversity among and within Brazilian Tall coconut populations. Samples were collected of 195 trees from 10 populations. Genetic diversity was accessed by investigating 13 simple sequence repeats (SSR) loci. This provided a total of 68 alleles, ranging from 2 to 13 alleles per locus, with an average of 5.23. The mean values of gene diversity (He ) and observed heterozygosity (Ho ) were 0.459 and 0.443, respectively. The genetic differentiation among populations was estimated at θ^P=0.1600and the estimated apparent outcrossing rate was ta = 0.92. Estimates of genetic distances between the populations varied from 0.034 to 0.390. Genetic distance and the corresponding clustering analysis indicate the formation of two groups. The first consists of the Baía Formosa, Georgino Avelino, and São José do Mipibu populations and the second consists of the Japoatã, Pacatuba, and Praia do Forte populations. The correlation matrix between genetic and geographic distances was positive and significant at a 1% probability. Taken together, our results suggest a spatial structuring of the genetic variability among the populations. Geographically closer populations exhibited greater similarities.