André Charrier

Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L.

Abstract The aim of this study was to develop a cultivar identification tool based on molecular analysis and a statistical approach. From the PIC parameter we defined the D parameter, which evaluates the efficiency of a primer for the purpose of identification of varieties; i.e. the probability that two randomly chosen individuals have different patterns. D can be used to compare different types of markers even if only the allelic frequencies are known. We used this parameter to develop an algorithm for selecting the optimal combination of primers necessary to identify a set of varieties. The optimal combination of primers determined for a small elite group of varieties applied on a larger set induces a risk of confusion involving 1 of the elite varieties. We estimated the risk of confusion using the D value of each primer of the combination. We applied this methodology on a set of 224 varieties of Vitis vinifera screened with 21 RAPD primers and two microsatellite loci. The discriminating power of the primers did not only depend on the number of patterns it generates but also on the frequencies of the different patterns. A combination of 8 primers (6 RAPD and two microsatellite) was found to be optimum for the discrimination of these 224 varieties. A subset of 38 elite varieties was also investigated. The determined optimal combination of 4 primers (3 RAPD and one microsatellite) applied on the 224 varieties gave 9 risks of confusion involving 1 of the elite varieties. Confusion can happen between varieties with the same origin as well as between varieties of very diverse geographical origins.

Several QTLs involved in osmotic-adjustment trait variation in barley (Hordeum vulgare L.)

Abstract Osmotic adjustment (OA) was previously demonstrated to be an important adaptive mechanism of drought tolerance in cereals. In order to determine which genomic regions are involved in OA variation, 187 barley (Hordeum vulgare L.) recombinant inbred lines (RILs) derived from a cross between Tadmor (drought tolerant) and Er/Apm (susceptible) were studied in a growth chamber for their OA capacity (through correlated traits and by calculation), at an early growth stage and under two water treatments (soil moisture of 14% and 100% of field capacity). The continuous distribution of the traits and their broad-sense line heritabilities, ranging from 0.04 to 0.44, indicated that OA and related traits should have a polygenic nature. A subset of 167 RILs were also genotyped using 78 RFLP, 32 RAPD and three morphological markers and a linkage map was constructed. Despite strong environmental effects acting on the traits, interval mapping and single-marker ANOVA allowed the detection of three QTLs for relative water content (RWC), four QTLs for osmotic potential (ψπ), two QTLs of osmotic potential at full turgor (ψπ100) and one QTL for osmotic adjustment at a soil moisture of 14% field capacity. For the irrigated treatment, only two QTLs were detected: one for RWC and one for ψπ100. Two chromosomal regions were involved in several OA-related trait variations and could be considered as regions controlling OA; these were present on chromosome 1 (7H) and chromosome 6 (6H), whereas other regions were specific for one trait. No major QTL was found. However, the genomic region involved in OA-related traits on chromosome 1 (7H) in barley seemed to be conserved for OA variation among cereals. Epistatic effects, with or without additive effects, acted on the traits.

Botanical Classification of Coffee

While the international coffee trade is concerned with only two coffee species — Coffea arabica and C. canephora — botanists regard as coffee trees all tropical plants of the Rubiaceae family, which produce seed resembling coffee beans. During botanical explorations of the tropical regions, from the sixteenth century onwards, wild coffees also attracted the attention of explorers and botanists. Their specimens are found in the herbaria and the names of the most famous explorers have been commemorated in both specific and generic epithets. Hundreds of species have been described, but the taxonomic classification of the genus Coffea has become very complex and rather confused.

Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica and Bourbon, spread in the 18th century, which gave rise to the most currently grown cultivars. Twenty-nine polymorphic fragments were used to calculate a similarity index and construct dendrograms. The Ethiopian material was separated from the Typica- and Bourbon-derived accessions and classified in four groups: one with most of the collected material from southwestern Ethiopia and three from southern and southeastern Ethiopia. Almost all detected diversity was found in the southwestern group while the southern and southeastern groups presented only 59% of identified markers. The genetic distances were low between the southwestern group and the southern and southeastern groups, and between the southwestern group and the Typica- and Bourbon-derived accessions. The cultivated coffee derived from the genetic populations Typica and Bourbon appeared little differentiated from wild coffee growing in the southwest. The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast. A separate analysis of the 80accessions classified in the southwestern group allowed identifying particular spontaneous- and subspontaneous-derived accessions and redundancies in the collected material from southwestern Ethiopia. RAPD markers did not detect any within-collection polymorphism except for two trees that were identified as off-types in the CATIE field genebank.

Phylogenetic relationships of coffee-tree species ( Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA

Abstract Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica.

Inheritance and restriction fragment length polymorphism of chloroplast DNA in the.genus Coffea L.

CpDNA variation among 52 tree samples belonging to 25 different taxa of Coffea and two species of Psilanthus was assessed by RFLP analysis on both the total chloroplast genome and the atpB-rbcL intergenic region. Twelve variable characters were distinguished allowing the identification of 12 different plastomes. The low sequence divergence observed might suggest that Coffea is a young genus. The results were in contradiction with the present classification into two genera. Additionally, cpDNA inheritance was studied in interspecific hybrids between C. arabica and C. canephora, and in an intraspecific progeny of C. canephora, using PCR-based markers. Both studies showed exclusively maternal inheritance of cpDNA.

Isozyme diversity within African Manihot germplasm

SummaryIsozyme diversity is described among a collection of 365 Manihot esculenta cultivars plus 109 accessions from wild relatives (M. glaziovii and spontaneous hybrids) from Africa. The study is based on 17 polymorphic loci. A natural hybrid swarm is detected between the two species. Although they were recently introduced, M. esculenta and M. glaziovii show high levels of polymorphism: heterozygosity estimates are 0.225 and 0.252 respectively. For the wild species, diversity is structured at the unilocus level, and the multilocus approach reveals a geographical pattern. The organization of the diversity is not so clear for the cultivated cassava, but a multilocus approach, based on both common and rare alleles, led us to identify different groups of clones with many intermediate genotypes between them. Elements of the secondary diversification process of Manihot in Ivory Coast are discussed.

#Coffea arabica# hybrid performance for yield, fertility and bean weight

The performance of F1 hybrid plants derived from crosses between traditional varieties of Coffea arabica of Latin America with a “wild” collection of Sudan–Ethiopian origin were studied for yield, fertility and bean weight. Sudan–Ethiopian material possesses resistance to certain diseases, and possibly, better beverage quality. The objective of this breeding programme is to widen the very narrow genetic base of Central American coffee, even while increasing quality and productivity. The hybrid plants were obtained from two factorial crosses made and evaluated in two locations. They were compared in the two field trials using the six maternal lines as controls. Observations were taken on vegetative characters, annual and cumulated yield, dry weight of 100 beans, extent of early abortion as measured by the fraction of ‘peaberries’ and post-zygotic ovule fertility as measured by the fraction of mature no-floating berries in water (FF). The F1 hybrid population were compared to the populations of maternal lines for the aforementioned variables. An index-based selection was done in the hybrid populations employing three traits, yield, 100-bean weight and the post-zygotic fertility (FF). The performance of the selected hybrids was then compared to those of the best parental ‘control’ lines in each trial. The hybrid populations yielded 22–47% more than the maternal lines, but hybrids showed significantly more sterility than the parental control lines. Selection in the hybrid populations using the three selected traits led to significant genetic gain for yield and dry weight of 100 beans, and insignificant gain for fertility (FF). When selected on the basis of fertility alone, increase in yield and 100-bean weight were not obtained within the hybrid populations. By applying selection on yield and 100-bean weight, the selected hybrids produced 11–47% higher yields than the best line along with significantly higher or identical 100-bean weight and performed identically for fertility. The yield performance of hybrids between the Latin American material and the “wild’’ Sudan–Ethiopian material calls for further selection effort for improving beverage quality.

Selection for bean and liquor qualities within related hybrids of Arabica coffee in multilocal field trials

The success of a new variety of Arabica coffee (Coffea arabica L.) depends to an important extent on its liquor and bean qualities. Selection for these traits is however constrained by the prevalence of large genotype-by-environment (G×E)interactions in conjunction with the low genetic variability characteristic of this species. The aim of this study was to assess the extent to which key bean and liquor traits are affected by the environments and could be combined in order to improve the efficiency of selection for coffee quality in a narrow genetic basis set of hybrids obtained from a set of related lines and collectively representing the Ruiru 11 cultivar. Twenty-one full-sib families representative of this hybrid cultivar grown in Kenya in five sites exhibiting strong edaphic and climatic differences were used for the study. Rainfall amounts during various phases of berry development were used to explain the differences observed in the discriminating abilities of the locations for bean and liquor traits. The results showed that these families were best differentiated for bean sizes in the site where moisture supply was optimal throughout berry expansion and filling stages, whereas discrimination on the basis of liquor traits were best observed in the site where moderate moisture stress occurred during bean filling stage. The overall precision in prediction of family values was low for liquor qualities; but a much more efficient selection for large bold beans, optimally based on the AA grade was shown to be possible. Selection indices for family selection were computed to realize a trade-off between genetic gains in bean size and liquor flavour.

Heredity of seventeen isozyme loci in cassava (Manihot esculenta Crantz)

SummaryStarch gel electrophoresis was used to assess isozyme polymorphism in two Manihot species. Crude extracts were obtained from leaves and pollen. Ten enzymes were examined for their polymorphism in a germplasm collection of 365 cultivated plus 109 wild accessions, mainly from Africa. The inheritance of these enzymes was examined using 13 intra and interspecific progenies. Seventeen polymorphic loci were found for the ten enzyme systems, with 59 alleles. All the markers showed disomic heredity and three linkage groups were identified.