The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Genome-wide admixture mapping identifies wild ancestry-of-origin segments in cultivated Robusta coffee

Humans have had a major influence on the dissemination of crops beyond their native range, thereby offering new hybridization opportunities. Characterizing admixed genomes with mosaic origins generates valuable insight into the adaptive history of crops and the impact on current varietial diversity. We applied the ELAI tool-an efficient local ancestry inference method based on a two-layer hidden Markov model to track segments of wild origin in cultivated accessions in the case of multiway admixtures. Source populations-which may actually be limited and partially admixed-must be generally specified when using such inference models. We thus developed a framework to identify local ancestry with admixed source populations. Using sequencing data for wild and cultivated Coffea canephora (commonly called Robusta), our approach was found to be highly efficient and accurate on simulated hybrids. Application of the method to assess elite Robusta varieties from Vietnam led to the identification of an accession derived from a likely backcross between two genetic groups from the Congo Basin and the western coastal region of Central Africa. Admixtures resulting from crop hybridization and diffusion could thus lead to the generation of elite high-yielding varieties. Our methods should be widely applicable to gain insight into the role of hybridization during plant and animal evolutionary history.

Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites

BACKGROUND AND AIMS

The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated.

METHODS

Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species.

KEY RESULTS

Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity.

CONCLUSIONS

Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.

Physical mapping of rDNA and heterochromatin in chromosomes of 16 Coffea species: a revised view of species differentiation

The chromosome organization among 15 wild diploid Coffea species and cultivated tetraploid C. arabica was determined by fluorochrome banding (CMA, DAPI) and double fluorescence in-situ hybridization (FISH) of 5S and 18S rDNA achieved on the same chromosome plates. Two to five chromosome pairs (plus one putative chromosome B) are marked. Overall, there are two SAT-chromosome pairs for East African species and one for the Malagasy and the West and Central African species. 18S rDNA loci are telomeric and strongly marked the SAT-chromosome pairs. Generally, only one pericentromeric 5S rDNA locus characterized East African species, while an additional minor locus co-localized with the 18S rDNA-SAT locus for the Malagasy species and West and Central African species. A combination of rDNA FISH plus CMA and DAPI banding patterns enables identification of almost all the species, even those for which the genetic or botanical status is still being discussed. C. arabica clearly appears to be an allotetraploid species, including one genome from East Africa and one from West and Central Africa. However, since the minor 5S rDNA-SAT locus present in West/Central African genomes is not detected, two evolutionary hypotheses could be put forward for C. arabica. Considering only the diploid species, global trends are obvious in rDNA signal patterns, genome size variations, and geographic distribution of the species, but there are no clear evolutionary trends. However, complex interactions between these factors and environmental growing conditions exist, which have resulted in loss and gain of rDNA loci and probably also in copy repeat number variations in each rDNA family.

Terminal 14q32.33 deletion: genotype-phenotype correlation

We report on a female infant presenting with psychomotor retardation and facial dysmorphism. Cytogenetic studies showed an abnormal chromosome 14 with ectopic NOR sequences at the extremity of the long arm with a terminal 14q32.33 deletion. Review of the eight cases with pure terminal 14q32.3 deletions described to date documented that our observation is the smallest terminal 14q deletion ever reported. Thus, genotype-phenotype correlation allows us to delimit the critical region for mental retardation, hypotonia, epi-telecanthus, short bulbous nose, long philtrum, thin upper lip, and small mouth observed in 14 qter deletions to the subtelomeric 1.6 Mb of chromosome 14.

SSR cross-amplification and variation within coffee trees (Coffea spp.)

Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was -11% for PSE and -9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.

Base Composition of Coffea AFLP Sequences and Their Conservation Within the Genus

Amplified fragment length polymorphism (AFLP) is often used for genetic mapping and diversity analysis, but very little information is currently available on their sequence characteristics. Species-specific sequences were analyzed from a single Coffea genome (Coffea pseudozanguebariae) associated with clustered or nonclustered AFLP loci of known genetic position. Compared with the expressed sequence tag (EST) sequence composition, their AT content exhibited a bimodal distribution with AT-poor sequences corresponding mainly to putative coding sequences. AT-rich sequences, apart from the EST distribution, were usually clustered on the genetic map and might correspond to noncoding sequences. Conversion of these AFLP markers into sequence-characterized amplified region (SCAR) anchor markers allowed us to assess sequence conservation within Coffea species with respect to species relatedness.

Genome size variations in diploid African Coffea species

Flow cytometry was conducted to evaluate genome size diversity among African diploid species of the Coffea genus. The study included 15 species and six new taxa from Congolese and Cameroonian forest regions which have yet to be botanically characterized. Between-population differences were also recorded in some cases. These evaluations using an internal standard were highly correlated with previous results obtained with an external standard, but differences of up to 18 % existed for some species, involving stoichiometric errors. Consequently, genome size variation between species and within species are discussed as true genome size differences or stoichiometric errors. Environmental and phenotypic correlations with genome size are also discussed.

AFLP and SSR polymorphism in a Coffea interspecific backcross progeny [( C. heterocalyx x C. canephora) x C. canephora]

An interspecific cross (BC 1) involving a species with one of the largest genomes in the Coffea genus [ Coffea heterocalyx (HET), qDNA = 1.74 pg] and a species with a medium-sized genome [ Coffea canephora (CAN), qDNA = 1.43 pg] was studied using two types of molecular markers, AFLP and SSR. One hundred and eighty eight AFLP bands and 34 SSR primer pairs were suitable for mapping. The total map length was 1,360 cM with 190 loci distributed in 15 linkage groups. The results were compared to those obtained previously on an interspecific BC 1 progeny involving a species with a medium-sized genome ( Coffea liberica var dewevrei, DEW) and a species with one of the smallest genomes ( Coffea pseudozanguebariae, PSE). They are discussed relative to three main points: (1) the relevance of the different marker types, (2) the genomic distribution of AFLP and SSR markers, and (3) the relation between AFLP polymorphism and genome size.

Comparative analysis of QTLs affecting domestication traits between two domesticated x wild pearl millet ( Pennisetum glaucum L., Poaceae) crosses

Comparative mapping of Quantitative trait loci (QTLs) involved in domestication of adaptative syndrome traits of pearl millet was realized at the intra-specific level using two F(2) populations derived from domesticated ( Pennisetum glaucum ssp. glaucum) x wild ( Pennisetum glaucum ssp. monodii) crosses. The two domesticated parents analyzed differ in their geographical origins, agronomic characteristics and life cycles. In both populations, two regions of the genome were identified on linkage groups 6 and 7, that controlled most of the key morphological differences. The importance of these two linkage groups reveals their central role both in the developmental control of spikelet structure and in the domestication process of this crop. In contrast, QTLs involved in traits that are components of yield and measure differences in resource allocation (such as the shape of the spike, the number of spikes per plant and plant height) show a low level of correspondence among our two crosses. The results of the comparative mapping between cereals, although preliminary, reveal that genes involved in seed-shattering could correspond in maize, rice and sorghum. The evolutionary significance of our results, and especially the relationships between genome organization and cereal domestication, are discussed. The potential use of these results in pearl millet genetic-resources enhancement are presented.

Incidence of AZF (azoospermia factor) deletions and familial forms of infertility among patients requiring intracytoplasmic spermatozoa injection (ICSI)

PURPOSE

The aim of our study was to determine the incidence of AZF deletions and familial forms of infertility suggesting autosomal mutations among patients requiring intracytoplasmic sperm injection with ejaculated sperm.

METHODS

Cases with obstructive pathologies were excluded; 81 patients were classified according to the numeration of spermatozoa. The distribution was as follows: 10 cases with normal numeration (greater than 20 million/ml) (group 1), 10 cases with between 10 and 20 million/ml (group 2), 6 cases with between 5 and 10 million/ml (group 3), 15 cases with between 1 and 5 million/ml (group 4), 29 cases with less than 1 million/ml (group 5), and 11 azoospermic patients (group 6). The infertility of 11 of the 81 patients might be explained by testicular ectopy.

RESULTS

We found two deletions limited to the AZFc region among our 81 infertile patients--one deletion in group 5 and one deletion in group 4 (both groups of oligozoospermic patients)--and no deletion in the groups with normal or subnormal numerations. We found six familial forms of infertility. We did not find any AZF deletion, neither in these 6 patients nor in the 11 with testicular ectopy. The identification of these families of infertile men will allow research of autosomal genes involved in male infertilities.

CONCLUSIONS

It is important to test deletions of the AZFc region for oligozoospermic patients, and familial forms of infertility do not seem to concern the same individuals.

Chloride channels in apical membrane of primary cultures of rabbit distal bright convoluted tubule

Using the patch clamp technique on the apical membrane of primary cultures of rabbit distal bright convoluted tubule cells (DCTb), two types of Cl- channel were identified. A small channel of 9 pS was observed in 9% of the patches. Cells pretreated with 1 mM 8-bromoadenosine 3',5'-cyclic monophosphate (8-BrcAMP) or 5 microM forskolin increased the expression of Cl- channels by 26 and 37%, respectively. In cell-attached and excised inside-out patches, the current-voltage (I-V) relationships of the 9-pS channel were linear. In only 1 out of 47 active patches was the small-conductance Cl- channel still active 1 h after membrane excision. The addition of 0.1 microM of the catalytic subunit protein kinase A with 2 mM ATP to the cytoplasmic side restored channel activity in 8 out of 15 excised membrane patches. In 5 out of 467 patches of stimulated or nonstimulated cells, a larger Cl- conductance of 30 pS was also recorded. In excised inside-out patches this channel outwardly rectified and was activated by strong depolarization. In cultured DCTb cells, the small-conductance, cAMP-activated Cl- channel shares many properties with the cystic fibrosis transmembrane conductance regulator. Our results suggest that at least the small-conductance channel may participate in Cl- secretion across the apical membrane of DCTb in primary culture. This secretion may increase the rate of the apical Cl-/HCO3- exchange indirectly by enhancing the inwardly-directed Cl- gradient.

Toxin pharmacology of the large-conductance Ca(2+)-activated K+ channel in the apical membrane of rabbit proximal convoluted tubule in primary culture

The patch-clamp technique was used to study the toxin pharmacology of the large-conductance Ca(2+)-activated K+ channel (BKCa) present in the apical membrane of rabbit proximal convoluted tubules (PCT) in primary culture. Experiments were performed with the inside-out configuration. This channel was very selective for K+ against Na+ and had a conductance of 180 pS with 140 mmol/l in the pipette and the bath. The action of toxins was studied on the extracellular side of the channel by using the pipette perfusion technique. Experimental conditions were 140 mmol/l KCl in the pipette and 140 mmol/l NaCl in the bath. Pipette potential was maintained at 0 mV. Perfusion of crude venom from Leiurus quinquestriatus hebraeus inhibited reversibly the open probability (Po) in a concentration-dependent fashion (IC50 = 0.8 mg/l; n = 3). The following synthetic or purified toxins were tested: synthetic charybdotoxin (ChTX) IC50 = 7.3 x 10(-9) M (n = 5); iberiotoxin (IbTX) IC50 = 5.5 x 10(-7) mol/l (n = 3); and kaliotoxin (KTX) IC50 = 4.8 x 10(-7) mol/l (n = 3). The suppression of the six first N-terminal amino-acids slightly reduced the affinity of ChTX (IC50 = 1.2 x 10(-8) mol/l, n = 4). Neither Dendroaspis polylepis venom nor purified alpha dendrotoxin modified Po even at high concentrations (20 mg/l and 10(-6) mol/l respectively). Apamin, which blocked the small-conductance K+ channel in cultured PCT, did not act on BKCa. These results indicate that ChTX is the most efficient known toxin against the epithelial BKCa in primary cultures of PCT.(ABSTRACT TRUNCATED AT 250 WORDS)

A calcium-permeable channel in the apical membrane of primary cultures of the rabbit distal bright convoluted tubule

Calcium is actively reabsorbed in the distal nephron segments and recent studies have demonstrated the presence of Ca2+ channels in these epithelial cells, which could be involved in transepithelial transport. To test this possibility, single-channel currents were recorded by the patch-clamp technique in the apical membrane of primary cultures of the rabbit distal bright convoluted tubule cells (DCTb). In the cell-attached mode with 100 mmol/l BaCl2 in the pipette and 145 mmol/l NaCl in the bath, inward negative currents, consistent with Ba2+ currents, were recorded. In these conditions, the single-channel conductance was 15 pS. In excised inside-out patches, the single-channel conductance was 13 pS and the current reversal potential of +60 mV was close to the Nernst equilibrium potential for Ba2+ (> +58 mV). Similar experiments conducted with Ca2+ as the main charge carrier showed that this ion was less permeant through the channel than Ba2+ (PBa/PCa approximately 1.4). We also showed that the Ca(2+)-channel blocker, lanthanum (1 mumol/l La3+), added on the cytosolic side of the membrane, reversibly blocked the channel activity. On the other hand, verapamil (0.1 mmol/l) and nifedipine (10 mumol/l), perfused on the cytosolic side of the membrane, abolished the channel activity but this effect was not reversible. Another type of channel was also identified in the apical membrane of cultured DCTb cells. Ion-substitution experiments showed that this 21-pS conductance channel did not discriminate between Na+ and K+ and did not conduct Ba2+.(ABSTRACT TRUNCATED AT 250 WORDS)

Apical membrane ionic channels in the rabbit cortical thick ascending limb in primary culture

Cortical thick ascending limbs of Henle's loop (cTAL) were microdissected from rabbit kidneys and cultured in a hormonally-defined medium. The cultured cells grew as a monolayer and retained the morphological and biochemical characteristics of the original tubule. Cyclic AMP production of the cultured cells was increased by human calcitonin (x13) and parathyroid hormone (x2). The cultured epithelial developed a transepithelial potential of 4.1 +/- 1.3 mV that was orientated positively towards the apical compartment. The basolateral membrane of the cells exhibited a chloride conductance sensitive to diphenylamine 2-carboxylate (DPC) and the apical membrane a barium-sensitive K+ permeability. Patch clamp analysis conducted on the apical membrane of the cells revealed the presence of three types of ionic channel. The first is a large conductance Ca(2+)-activated K+ channel (95 pS). The second K+ channel has a much smaller conductance (18.3 pS) and is insensitive to Ca2+. It may represent the conductive pathway for K+ recycling into the lumen in the original tubule. The last channel is cation selective, does not discriminate between Na+ and K+ and was found to have a conductance of 20.5 pS. Channel activity required a high cytoplasmic calcium concentration (1 mM), and was blocked by ATP (10 microM) applied on its cytoplasmic face.