José Quero-García

Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry.

The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3–8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.

Nature of taro (Colocasia esculenta (L.) Schott) genetic diversity prevalent in a Pacific Ocean island, Vanua Lava, Vanuatu

Taro (Colocasia esculenta (L.) Schott), cultivated in Vêtuboso, a village of northern Vanuatu, Melanesia, was surveyed to: (1) assess the extent of morphological and molecular variation being maintained by growers at the village level and, (2) compare this diversity with the diversity found in the crops in Vanuatu. Ethnobotanical data were combined with AFLP analysis to elucidate possible sources of variation. Folk assessment of variation is based on: (a) morphological characteristics (11 characters), (b) names and (c) classification according to habitat, uses, origin and agronomic adaptation. This 3-fold approach allowed growers to differentiate 96 morphotypes, all of which are given distinct vernacular names. AFLP fingerprints successfully differentiated all these 96 morphotypes which do not present a significant intra-clonal variation. But genetic results showed no clear groupings according to geographic origin or habitat of morphotypes and stated that the diversity found within the village was comparable with the overall diversity found in Vanuatu. Local nomenclature and stories associated with each cultivar suggested three sources of diversity: introductions (38%), somatic mutations (15%) and sexual recombinations (48%). AFLP results confirm folk beliefs about origin at least for three pairs of mutants. The 11 so-called wild forms analysed by AFLP were suggested to be feral, escapes from domestication. A dynamic in situ conservation strategy (DISC), favouring a broadening of the national genetic base, was discussed for taro.

Construction and Comparative Analyses of Highly Dense Linkage Maps of Two Sweet Cherry Intra-Specific Progenies of Commercial Cultivars

Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between ‘Black Tartarian’ × ‘Kordia’ (BT×K) and ‘Regina’ × ‘Lapins’(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1–LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.

A germplasm stratification of taro (Colocasia esculenta) based on agro-morphological descriptors, validation by AFLP markers

This paper presents a simple and practical method for stratifying taro germplasm based on morpho-agronomical characters. More than 450 accessions of taro collected throughout Vanuatu and established in a field collection were described using 19 descriptors. A hierarchical approach was used to stratify the agro-morphological variation. Three sampling strategies were tested and the variation captured within each sample was compared for the frequencies of characters. The first sample (S1) was randomly selected; the second sample (S2) was conducted within the subgroups produced by the stratification method, and the third sample (S3) was based on UPGMA clustering within each subgroup. AFLP markers were used to compare the diversity between S3 and a fourth sample (S4) that included the parents of the Vanuatu breeding programme, and more diversity was found in S3. AFLPs were found to be useful to validate the hierarchical approach used for stratification. These studies have confirmed the narrow genetic base of the Vanuatu taro germplasm. They have been useful for detecting duplicates and fingerprinting of accessions.

Rosaceae conserved orthologous sequences marker polymorphism in sweet cherry germplasm and construction of a SNP-based map

The Rosaceae Conserved Orthologous Set (RosCOS) provides a gene-based genome-wide set of markers that have been used in comparative analyses of peach (Prunus persica), apple (Malus × domestica), and strawberry (Fragaria spp.). In order to extend the use of these RosCOS to sweet cherry (Prunus avium L.), we identified markers that are polymorphic in breeding germplasm. Ninety-five percent (595/627) of previously designed RosCOS primer pairs amplified a product in six sweet cherry cultivars predicted to represent the range of genetic diversity in breeding germplasm. A total of 45% (282/627) RosCOS were polymorphic among the six cultivars, and allele number ranged from 2 to 6, with a genome-wide mean of 2.35. A subset of 92 genome-wide single nucleotide polymorphisms (SNPs) corresponding to 76 RosCOS was analyzed in 36 founder accessions and progeny. The expected and observed heterozygosity suggested that 83% of the RosCOS were in Hardy–Weinberg equilibrium, implying that most RosCOS behave as neutral markers. Principal coordinate analysis (PCO) identified one wild accession and two Spanish landraces that clustered differently from the other accessions. The relatively high number of unique alleles found in the three differentially clustered selections suggested that their use as parents has potential to increase the genetic diversity in future US-bred cultivars. Of the 92 RosCOS SNPs, 81 SNPs that represented 68 genome-wide RosCOS segregated in four mapping populations. These RosCOS were mapped in four F1 populations, thereby greatly improving the genetic linkage map of sweet cherry.

Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium).

The timing of flowering in perennial plants is crucial for their survival in temperate climates and is regulated by the duration of bud dormancy. Bud dormancy release and bud break depend on the perception of cumulative chilling during endodormancy and heat during the bud development. The objectives of this work were to identify candidate genes involved in dormancy and flowering processes in sweet cherry, their mapping in two mapping progenies ‘Regina’ × ‘Garnet’ and ‘Regina’ × ‘Lapins’, and to select those candidate genes which co-localized with quantitative trait loci (QTLs) associated with temperature requirements for bud dormancy release and flowering. Based on available data on flowering processes in various species, a list of 79 candidate genes was established. The peach and sweet cherry orthologs were identified and primers were designed to amplify sweet cherry candidate gene fragments. Based on the amplified sequences of the three parents of the mapping progenies, SNPs segregations in the progenies were identified. Thirty five candidate genes were genetically mapped in at least one of the two progenies and all were in silico mapped. Co-localization between candidate genes and QTLs associated with temperature requirements and flowering date were identified for the first time in sweet cherry. The allelic composition of the candidate genes located in the major QTL for heat requirements and flowering date located on linkage group 4 have a significant effect on these two traits indicating their potential use for breeding programs in sweet cherry to select new varieties adapted to putative future climatic conditions.

Cracking in sweet cherries: A comprehensive review from a physiological, molecular, and genomic perspective

Rain-induced cracking in fruits of sweet cherry (Prunus avium L.) is a problem in most producing areas of the world and causes significant economic losses. Different orchard management practices have been employed to reduce the severity of this problem, although a complete solution is not yet available. Fruit cracking is a complex phenomenon and there are many factors that seem to be involved in its development. During the last decade, genomic and biochemical approaches have provided new insights on the different mechanisms that could be involved in the differential susceptibility shown by commercial cultivars. For instance, sweet cherry genome and transcriptome sequencing information have provided new opportunities to study the expression and structure of genes involved in cracking, which may help in the development of new tolerant cultivars. The present review summarizes, discuss, and integrate most of the recently generated information in cultural practices, physiology, biochemistry, and genetics in relation to cracking in sweet cherries.

New Insights into Fruit Firmness and Weight Control in Sweet Cherry

Fruit firmness and weight are among the most important fruit quality traits in fruit species. Understanding the control of fruit firmness and weight is essential for the development of domestication research approaches and for the implementation of new breeding strategies. A forward genetic study for these traits was performed using two F1 sweet cherry (Prunus avium) progenies derived from modern cultivars. Quantitative trait locus (QTL) analysis allowed the identification of genomic regions accounting for most of the phenotypic variation in both families. In addition, screening the Prunus persica genome v1.0 permitted the identification of putative candidate genes underlying the QTL with the major effect for fruit weight (LG5) and the one for firmness (LG6). A colocalization of QTLs and candidate genes was found in peach, apple, and tomato. These results give new insights of the interaction between fruit firmness and fruit weight and provide new cues for the identification of genes implicated in the control of these traits. The colocalization of genomic regions between progenies issued from modern cultivars and from modern cultivars × wild individuals suggests the absence of allele fixation within genes controlling fruit firmness and size, two traits potentially involved in domestication/diversification in sweet cherry.

Taro and cocoyam

Aroids are an economically important source of food for numerous tropical countries. They are mostly consumed for their corms and cormels but leaves and petioles can also be part of the diet. According to FAO databases (www.fao.org 2007) taro (Colocasia esculenta (L.) Schott) and cocoyam (Xanthosoma sagittifolium (L.) Schott) produce the lowest average yields (6.5 tons/ha) of all root crops. World production in 2006 was approximately 11.9 million fresh tons from 1.8 million hectares but significant taro producers such as India, Bangladesh, Burma, Indonesia, Papua New Guinea, and Cuba do not supply production figures. Since taro production was around 4 million tons in 1961, its cultivation is stable or even growing and follows the global trend of demographic growth. Aroids are considered minor crops but they are a staple food for numerous poor populations from tropical countries.

Hybrid performance in taro (Colocasia esculenta) in relation to genetic dissimilarity of parents

Taro (Colocasia esculenta) breeding, as other root crop breeding, is based on the production and evaluation of large numbers of hybrids. The selection of parents is based on their phenotypic value in the absence of information concerning general combining ability (GCA), specific combining ability (SCA), or genetic distances between varieties. By combining data from heritability trials and from genetic diversity studies conducted with AFLP and SSR markers, we aimed at studying the relationship between hybrid vigour and genetic dissimilarity between parents. The traits studied included number of suckers, corm weight, corm dimensions, and dry matter content. Correlation coefficients between hybrid gain and dissimilarity values were calculated. The prediction of hybrid performance based on the mid-parent value was compared to the prediction based on a modified expression that takes into account the genetic relationships between parents. Correlations were all but one positive but not statistically significant for all traits, with the exception of the number of suckers, when using SSR markers for dissimilarity calculations. Accordingly, the genetic dissimilarities in the prediction of hybrid performances did not increase the correlation between predicted and observed hybrid vigour values. However, large differences were observed among the residual means from the regression between predicted and observed values when using AFLP or SSR markers, mainly due to the much higher polymorphism revealed by the latter. Models need to be further adapted to the type of molecular marker used, since their ability to reveal different rates of polymorphism will have a direct incidence on the calculation of genetic dissimilarities between genotypes. Nevertheless, since SSR markers are more polymorphic and more informative than AFLP markers, they should be preferentially used for these studies. Low genetic dissimilarity of parents yielded weak heterosis effects and future studies need to be conducted by using a broader genetic base. This is the first study assessing the relationship of hybrid vigour with the genetic distances between parents, conducted on a tropical root crop.