Showing papers in "Tree Genetics & Genomes in 2011"

Genomic selection in forest tree breeding

Abstract: Genomic selection (GS) involves selection decisions based on genomic breeding values estimated as the sum of the effects of genome-wide markers capturing most quantitative trait loci (QTL) for the target trait(s). GS is revolutionizing breeding practice in domestic animals. The same approach and concepts can be readily applied to forest tree breeding where long generation times and late expressing complex traits are also a challenge. GS in forest trees would have additional advantages: large training populations can be easily assembled and accurately phenotyped for several traits, and the extent of linkage disequilibrium (LD) can be high in elite populations with small effective population size (N e) frequently used in advanced forest tree breeding programs. Deterministic equations were used to assess the impact of LD (modeled by N e and intermarker distance), the size of the training set, trait heritability, and the number of QTL on the predicted accuracy of GS. Results indicate that GS has the potential to radically improve the efficiency of tree breeding. The benchmark accuracy of conventional BLUP selection is reached by GS even at a marker density ~2 markers/cM when N e ≤ 30, while up to 20 markers/cM are necessary for larger N e. Shortening the breeding cycle by 50% with GS provides an increase ≥100% in selection efficiency. With the rapid technological advances and declining costs of genotyping, our cautiously optimistic outlook is that GS has great potential to accelerate tree breeding. However, further simulation studies and proof-of-concept experiments of GS are needed before recommending it for operational implementation.

QTL analysis of fruit quality traits in two peach intraspecific populations and importance of maturity date pleiotropic effect

Abstract: Two intraspecific peach breeding populations have been used to conduct a quantitative trait locus (QTL) analysis of fruit quality traits: an F1 from the cross Bolero (B) x OroA (O) and an F2 from the cross Contender (C) x Ambra (A). A total of 344 Prunus simple sequence repeats (SSRs) were analyzed in B, O, C, A parents and CxA F1 hybrid. Eight SSR were mapped for the first time in peach. A multiplex-ready polymerase chain reaction (PCR) protocol has allowed considerable time and cost saving during genotyping steps. Two maps (B map and O map) were produced for BxO population following the pseudo-test cross strategy and one for CxA. No marker could be mapped on G6 for the B map, on G4 and G8 for the O map and on G5 for the CxA map. Both populations were phenotyped over 2 years for maturity date (MD), fruit weight, external fruit skin overcolor, juice total soluble solids (SSC, Brix degree), juice titrable acidity and juice pH. Data for blooming time and flower type were scored only for BxO in 2007. All traits had a normal distribution, except for MD which was bimodal in BxO and trimodal in CxA, where it was scored as a co-dominant trait. Up to two QTLs per trait were detected in each population, and most of them were located in the same region forming clusters of QTLs, especially on G4. This is likely due to a major pleiotropic effect of MD masking the identification of other QTLs for different traits.

Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

Abstract: Cinnamyl alcohol dehydrogenase (CAD) is involved in the biosynthesis of lignin, a component of plant cell wall which negatively impacts paper pulp processing and biomass fermentation to ethanol. Transgenic poplars with depressed CAD activity show structural alterations of lignin. Natural CAD mutants have been identified in several plants; however, no natural CAD mutants have been identified in poplar. We surveyed the natural genetic variation in CAD4, a gene coding for CAD, in 360 poplar trees from Western Europe. We measured linkage disequilibrium (LD) between single-nucleotide polymorphisms (SNPs), performed neutrality tests and estimated diversity indexes, and investigated their dependence from sample size. We identified 45 SNPs, six of which caused an amino acid substitution. Our results suggest a short span of LD in Populus nigra CAD4 gene. We identified carriers of different nonsynonymous SNPs in CAD4; those subjects are candidate to be used in classical breeding programs to obtain carriers of different combinations of functional polymorphisms. We showed that use of small sample size might lead to biased estimates of LD, neutrality tests, and diversity indexes.

New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny

Abstract: The aim of this work was to provide a set of mitochondrial markers to reveal polymorphism and to study the maternal phylogeny in citrus. We first used 44 universal markers previously described in the literature: nine of these markers produced amplification products but only one revealed polymorphism in citrus. We then designed six conserved pairs of primers using the complete mitochondrial DNA sequences of Arabidopsis thaliana and Beta vulgaris to amplify polymorphic intergenic and intronic regions. From these six pairs of primers, three from introns of genes coding for NADH dehydrogenase subunits 2, 5, and 7, revealed polymorphism in citrus. First, we confirmed that citrus have a maternal mitochondrial inheritance in two populations of 250 and 120 individuals. We then conducted a phylogenic study using four polymorphic primers on 77 genotypes representing the diversity of Citrus and two related genera. Seven mitotypes were identified. Six mitotypes (Poncirus, Fortunella, Citrus medica, Citrus micrantha, Citrus reticulata, and Citrus maxima) were congruent with previous taxonomic investigations. The seventh mitotype enabled us to distinguish an acidic mandarin group (‘Cleopatra’, ‘Sunki’ and ‘Shekwasha’) from other mandarins and revealed a maternal relationship with Citrus limonia (‘Rangpur’ lime, ‘Volkamer’ lemon) and Citrus jambhiri (‘Rough’ lemon). This mitotype contained only cultivated species used as rootstocks due to their good tolerances to abiotic stress. Our results also suggest that two species classified by Swingle and Reece, Citrus limon, and Citrus aurantifolia, have multiple maternal cytoplasmic origins.

EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera

Abstract: A total of 12,080 sequences, including 5,851 transcriptome contigs developed at NBRI and 5,002 singlets and 1,227 contigs assembled from 13,201 expressed sequence tags (ESTs) of Jatropha curcas from National Center for Biotechnology Information database were used to search for simple sequence repeats (SSRs). Seven hundred and two sequences containing 786 SSRs with 93.4% simple and 7.6% compound repeat motifs were identified. Dinucleotide repeats (DNRs) were most abundant, followed by trinucleotide and tetranucleotide repeats. AG/CT was the most common motif (50.0%) followed by AT/AT (38.8%) and AC/GT (10.0%) among the DNRs. Four hundred and six primer pairs were designed out of the 702 SSR-containing sequences. Fifty randomly selected EST-SSR markers were amplified in 25 accessions collected from different geographical regions of India. Twenty-one SSR markers were polymorphic and with allele variation from two to four. Polymorphic information content value ranged between 0.04 and 0.61 with an average of 0.25 ± 0.16, indicating low to moderate level of informativeness within these EST-SSRs. The polymorphic markers showed 57.0% to 95.6% transferability among five species of Jatropha and 47.0% transferability across genera in Ricinus communis. Fifty-one alleles detected by the 21 polymorphic EST-SSRs were used to determine genetic relationships among 25 J. curcas accessions. Genetic similarity coefficient ranged from 0.44 to 0.94. The 25 accessions got grouped to three main clusters, comprising 10, 11, and four accessions. This is the first report of development of EST-SSRs in J. curcas and will be valuable resource for future genetical studies, like construction of linkage maps, diversity analysis, quantitative trait locus/association mapping, and molecular breeding of J. curcas.

Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica

Abstract: Genomic selection (GS) can be a powerful technology in conifer breeding because conifers have long generation intervals, protracted evaluation times, and high costs of breeding inputs. To elucidate the potential of GS for conifer breeding, we simulated 60-year breeding programs in Cryptomeria japonica with and without GS. In conifers, the rapid decay of linkage disequilibrium (LD) can constitute a severe barrier to application of GS. For overcoming that barrier, we proposed an idea to leverage a seed orchard system, which has been used commonly in conifers, because some degree of LD exists in progenies derived from the limited number of elite trees in a seed orchard. The base population used for simulations consisted of progenies from 25 elite trees. Results show that GS breeding (GSB) done without model updating outperformed phenotypic selection breeding (PSB) during the first 30 years, but the genetic gain achieved over the 60 years was smaller in GSB than in PSB. However, GSB with model updating outperformed PSB over the 60 years. The genetic gain achieved over the 60 years of GSB with model updating was nearly twice that of PSB. Advantages of GSB over PSB prevailed, even for a low heritability polygenic trait. The number of markers necessary for efficient GS was a realistic level (e.g., one in every 1 cM), although higher marker density engendered higher accuracy of selection. These results suggest that GS can be useful in C. japonica breeding. Updating of the prediction model was, however, indispensable for attaining the large genetic gain.

Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea

Abstract: The phylogeny of the genus Picea was investigated by sequencing three loci from the paternally inherited chloroplast genome (trnK, rbcL and trnTLF) and the intron 2 of the maternally transmitted mitochondrial gene nad1 for 35 species. Significant topological differences were found between the trnK tree and the rbcL and trnTLF phylogenetic trees, and between cpDNA and mtDNA phylogenies. None of the phylogenies matched morphological classifications. The mtDNA phylogeny was geographically more structured than cpDNA phylogenies, reflecting the different inheritance of the two cytoplasmic genomes in the Pinaceae and their differential dispersion by seed only and seed and pollen, respectively. Most North American taxa formed a monophyletic group on the mtDNA tree, with topological patterns suggesting geographic speciation by range fragmentation or by dispersal and isolation. Similar patterns were also found among Asian taxa. Such a trend towards geographic speciation is anticipated in other Pinaceae genera with similar life history, autecology and reproductive system. Incongruences between organelle phylogenies suggested the occurrence of mtDNA capture by invading cpDNA. Incongruences between cpDNA partitions further suggested heterologous recombination presumably also linked to ancient reticulate evolution. Whilst cpDNA appears potentially valuable for molecular taxonomy and systematics purposes, these results emphasize the reduced value of cpDNA to infer vertical descent and the speciation history for plants with paternal transmission and high dispersal of their chloroplast genome.

Genetic linkage maps of two interspecific grape crosses (Vitis spp.) used to localize quantitative trait loci for downy mildew resistance.

Abstract: Two populations (Pop) segregating quantitatively for resistance to downy mildew (DM), caused by Plasmopara viticola, were used to construct genetic maps and to carry out quantitative trait locus (QTL) analysis. Pop1 comprised of 174 F1 individuals from a cross of ‘Moscato Bianco’, a susceptible Vitis vinifera cultivar, and a resistant individual of Vitis riparia. Pop2 consisted of 94 progeny from a cross of two interspecific hybrids, ‘VRH3082 1-42’ and ‘SK77 5/3’, with resistance traits inherited from Vitis rotundifolia and Vitis amurensis, respectively. Resistance of progeny was measured in field and greenhouse conditions by visual evaluation of disease symptoms on leaves. Linkage maps of 1037.2 and 651 cM were built essentially with simple sequence repeat markers and were enriched with gene-derived single-strand conformational polymorphism and single-nucleotide polymorphism markers. Simple interval mapping and Kruskall–Wallis analysis detected a stable QTL involved in field resistance to DM on linkage group (LG) 7 of the Pop1 integrated map co-localized with a putative Caffeoyl-CoA O-methyltransferase-derived marker. Additional QTLs were detected on LGs 8, 12 and 17. We were able to identify genetic factors correlated with resistance to P. viticola with lower statistical significance on LGs 1, 6 and 7 of the Pop2 map. Finally, no common QTLs were found between the two crosses analyzed. A search of the grapevine genome sequence revealed either homologues to non-host-, host- or defense-signalling genes within the QTL intervals. These positional candidate genes may provide new information about chromosomal regions hosting phenotypic loci.

Developing seed zones and transfer guidelines with multivariate regression trees

Abstract: Managing seed movement is an important component of forest resource management to minimize maladaptation of planting stock in forest plantations. Here, we describe a new approach to analyze geographic patterns of adaptive and neutral genetic variation in forest trees and to link this genetic information to geographic variables for the delineation of seed zones and the development of seed transfer guidelines. We apply multivariate regression trees to partition genetic variation, using a set of environmental or geographic predictor variables as partitioning criteria in a series of dichotomous splits of the genetic dataset. The method can be applied to any type of genetic data (growth, adaptive, or marker traits) and can simultaneously evaluate multiple traits observed over several environments. The predictor variables can be categorical (e.g., ecosystem of seed source), continuous (e.g., geographic or climate variables), or a combination of both. Different sets of predictor variables can be used for different purposes: In two case studies for aspen and red alder, we show (1) how latitude, longitude, and elevation of seed sources in a provenance trial can be used to develop simple seed transfer guidelines; (2) how ecosystem classes and elevation as predictor variables can be used to delineate seed zones and breeding regions; and (3) how climate variables as predictors can reveal adaptation of genotypes to the environments in which they occur. Partitioning of genetic variation appears very robust regarding the choice of predictor variables, and we find that the method is a powerful aid for interpreting complex genetic datasets.

The sucrose synthase gene family in Populus: structure, expression, and evolution

Abstract: Sucrose synthase is a key enzyme in sucrose metabolism in plant cells, and it is involved in the synthesis of cell wall cellulose. Although the sucrose synthase gene (SUS) family in the model plants Arabidopsis thaliana has been characterized, little is known about this gene family in trees. This study reports the identification of two novel SUS genes in the economically important poplar tree. These genes were expressed predominantly in mature xylem. Using molecular cloning and bioinformatics analysis of the Populus genome, we demonstrated that SUS is a multigene family with seven members that each exhibit distinct but partially overlapping expression patterns. Of particular interest, three SUS genes were preferentially expressed in the stem xylem, suggesting that poplar SUSs are involved in the formation of the secondary cell wall. Gene structural and phylogenetic analyses revealed that the Populus SUS family is composed of four main subgroups that arose before the separation of monocots and dicots. Phylogenetic analyses associated with the tissue- and organ-specific expression patterns. The high intraspecific nucleotide diversity of two SUS genes was detected in the natural population, and the πnonsyn/πsyn ratio was significantly less than 1; therefore, SUS genes appear to be evolving in Populus, primarily under purifying selection. This is the first comprehensive study of the SUS gene family in woody plants; the analysis includes genome organization, gene structure, and phylogeny across land plant lineages, as well as expression profiling in Populus.

Analysis of the NAC transcription factor gene family in citrus reveals a novel member involved in multiple abiotic stress responses

Abstract: The NAC (NAM, ATAF1, -2, and CUC2) gene family encodes a large family of plant-specific transcription factors that play diverse roles in plant development and stress regulation. In this study, we performed a survey of citrus NAC transcription factors in the HarvEST: Citrus database, in which 45 NAC domain-containing proteins were identified and phylogenetically classified into 13 different subfamilies. The results suggest the existence of a structurally diversified family of NAC transcription factors in citrus, which has not been previously characterized. One of these NAC genes, CsNAC1 was found to be a member of the stress-NAC subfamily, whose homologs from other plant species function in pathways of environmental stress response and tolerance, and was further characterized. The CsNAC1 deduced protein was shown to contain the five N-terminal A through E NAC subdomains, a C-terminal region containing three transcriptional activation motifs, and a predicted NAC nuclear localization signal, consistent with its putative role as a NAC transcription factor. In silico analysis indicated that CsNAC1 was primarily expressed in leaves and shoot meristems, and was involved in general stress responses. Quantitative real-time reverse transcription PCR analysis revealed that CsNAC1 was strongly induced by drought stress in leaves of Citrus reshni and Citrus limonia, and also by salt stress, cold, and ABA in leaves and roots of C. reshni. Collectively, these results suggest that CsNAC1 encodes a novel stress-responsive NAC transcription factor that is potentially useful for engineering tolerance to multiple abiotic stresses in citrus.

Factors affecting cork oak growth under dry conditions: local adaptation and contrasting additive genetic variance within populations

Abstract: Increased drought severity is expected in the Mediterranean Basin over the twenty-first century, but our understanding of the potential of most forest tree species to cope with it remains uncertain. In this study, (1) we examined the potential effects of long-term selection and the capacity to respond to future changes in selective pressures in three populations of cork oak (Quercus suber L.). For this purpose, we evaluated the response to dry conditions of 45 open-pollinated trees originating from populations in Morocco, Portugal, and Spain. Growth, leaf size, specific leaf area (SLA), carbon isotope discrimination (Δ13C), leaf nitrogen content (Nmass), and total chlorophyll content (Chlmass) were measured in 9-year-old plants. (2) We also investigated the relationships between functional traits and aboveground growth by regression models. Plants presenting larger and more sclerophyllous leaves (low SLA and high leaf thickness) exhibited higher growths, with results suggesting that these traits are subjected to divergent selection in this species. Heritability estimates were moderately high for Δ13C (0.43 ± 0.25–0.83 ± 0.31) and stem diameter (0.40 ± 0.15–0.71 ± 0.28) for the tree populations. For the rest of the traits (except for annual growth), heritability values varied among populations, particularly for height, leaf size, leaf thickness, and Nmass. Our results suggest that natural selection has led to local adaptations and has also affected the genetic variance intrapopulation in these cork oak populations, although studies with a higher number of populations should be carried out across different years. Additionally, the absence of significant genetic correlations and the fact that correlated traits did not undergo opposing selection provided little evidence for constraints on evolution caused by genetic correlations.

Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests

Abstract: Eucalypts are keystone species in their natural ranges and are extensively planted worldwide for high-quality woody biomass. A novel set of 21 polymorphic and interspecifically transferable microsatellite markers based on tetra-, penta- and hexanucleotide repeats were developed and tested for high-precision genotyping of species of Eucalyptus. These microsatellites were characterized in population samples of four species, Eucalyptus grandis, Eucalyptus globulus, Eucalyptus urophylla, and Eucalyptus camaldulensis, representing three phylogenetic sections of subgenus Symphyomyrtus. These markers provide a clear advantage for accurate allele calling due to their larger allele size difference. Two multiplexed microsatellite combinations, a 14-locus/four-dye and an 18-locus/five-dye set, analyzable in single lanes were designed, providing resolution and throughput analogous to those routinely used in human DNA profiling. This set of microsatellites was shown to have high resolution for clone fingerprinting, inter-individual genetic distance estimation, species distinction, and assignment of hybrid individuals to their most likely ancestral species. These systems will be particularly useful for comparative population genetics and molecular breeding applications that require consistent allele calling across different points in time or laboratories.

Genetic diversity of the genus Malus and implications for linkage mapping with SNPs

Abstract: Knowledge about the sequence-based genetic diversity of a crop species is important in order to develop highly informative genotyping assays, which will eventually positively impact breeding practice Diversity data were obtained from two pools of 185 and 75 accessions each, representing most of the species belonging to the genus Malus, by re-sequencing 27 gene-specific amplicons and by screening 237 Malus × domestica SNPs using the multiplex genotyping technology SNPlex™ Nucleotide diversity and insertion/deletion rates in M × domestica were estimated as π = 00037 and 1/333 bp, respectively The SNP frequency was estimated as 00194 (1 SNP/52 bp) while within a single apple cultivar an average of one SNP in every 455 bp was found We also investigated transferability (T SNP) of the heterozygous state of SNPs across the species M × domestica and the genus Malus Raw re-sequencing showed that 12–15% of M × domestica SNPs are transferable to a second M × domestica cultivar, however T SNP rose to ∼41% with SNPs selected for high minor allele frequency T SNP of chosen SNPs averaged ∼27% in the two M × domestica-related species, Malus sieversii and Malus sylvestris, but was much lower in more distantly related species On the basis of T SNP, simulations, and empirical results, we calculated that a close-design, multiplexed genotyping array with at least 2,000 SNPs is required for building a highly saturated linkage maps within any M × domestica cross The same array would gradually lose informativeness in increasingly phylogenetically distant Malus species

Effects of seed dispersal, adult tree and seedling density on the spatial genetic structure of regeneration at fine temporal and spatial scales

Abstract: Several demographic factors can produce family structured patches within natural plant populations, particularly limited seed and pollen dispersal and small effective density. In this paper, we used computer simulations to examine how seed dispersal, density, and spatial distribution of adult trees and seedlings can explain the spatial genetic structure (SGS) of natural regeneration after a single reproductive event in a small population. We then illustrated the results of our simulations using genetic (isozymes and chloroplast microsatellites) and demographic experimental data from an Abies alba (silver fir) intensive study plot located in the Southern French Alps (Mont Ventoux). Simulations showed that the structuring effect of limited dispersal on seedling SGS can largely be counterbalanced by high effective density or a clumped spatial distribution of adult trees. In addition, the clumping of natural regeneration far from adult trees, which is common in temperate forest communities where gap dynamics are predominant, further decreases SGS intensity. Contrary to our simulation results, low adult tree density, aggregated spatial distribution of seedlings, and limited seed dispersal did not generate a significant SGS in our A. alba experimental plot. Although some level of long distance pollen and seed flow could explain this lack of SGS, our experimental data confirm the role of spatial aggregation (both in adult trees and in seedlings far from adult trees) in reducing SGS in natural populations.

Important processes during differentiation and early development of somatic embryos of Norway spruce as revealed by changes in global gene expression

Abstract: The aim of this study has been to identify important processes that regulate early stages of embryo development in conifers. Somatic embryogenesis in Picea abies has become a model system for studying embryology in conifers, providing a well-characterized sequence of developmental stages, resembling zygotic embryogeny, which can be synchronized by specific treatments, making it possible to collect a large number of somatic embryos at specific developmental stages. We have used this model to analyze global changes in gene expression during early stages of embryo development by generating an expression profile of 12,536 complementary DNA clones. This has allowed us to identify molecular events regulating putative processes associated with pattern formation during the earliest stages of embryogenesis which have not been identified on the molecular level in conifers before. We recognize notable changes in the expression of genes involved in regulating auxin biosynthesis and auxin response, gibberellin-mediated signaling, signaling between the embryo and the female gametophyte, tissue specification including the formation of boundary regions, and the switch from embryonic to vegetative development. In addition, our results confirm the involvement of previously described processes, including stress, differentiation of a protoderm, and programmed cell death.

Comparative mapping in Pinus: sugar pine (Pinus lambertiana Dougl.) and loblolly pine (Pinus taeda L.)

Abstract: The majority of genomic research in conifers has been conducted in the Pinus subgenus Pinus mostly due to the high economic importance of the species within this taxon. Genetic maps have been constructed for several of these pines and comparative mapping analyses have consistently revealed notable synteny. In contrast, little genomic research has been conducted on the Pinus subgenus Strobus, even though these pines have strong ecological relevance. We report a consensus genetic linkage map for sugar pine (Pinus lambertiana Dougl.) constructed with 399 single nucleotide polymorphisms markers derived from annotated genes. The map is 1,231 cM in length and organized into 19 linkage groups. Two of the mapping populations were derived from trees that were segregating for the major gene of resistance (Cr1 )t oCronartium ribicola, the fungal pathogen responsible for white pine blister rust. The third mapping population was derived from a full-sib cross segregating for partial resistance to white pine blister rust. In addition, we report the first comparative mapping study between subgenera Strobus and Pinus. Sixty mapped markers were found in common between sugar pine and the loblolly pine reference map with 56 of them (93%) showing collinearity. All 19 linkage groups of the sugar pine consensus map coaligned to the 12 linkage groups of the loblolly pine reference map. The syntenic relationship observed between these two clades of pines provides a foundation for advancing genomic research and genetic resources in subgenus Strobus.

Long-term human impacts on genetic structure of Italian walnut inferred by SSR markers

Abstract: Life history traits, historic factors, and human activities can all shape the genetic diversity of a species. In Italy, walnut (Juglans regia L.) has a long history of cultivation both for wood and edible nuts. To better understand the genetic variability of current Italian walnut resources, we analyzed the relationships among the genetic structure of local walnut populations (inferred by SSR markers) and human migrations along ancient routes, using the territory of Royal Tratturo Candela-Pescasseroli (RT) as a case study. Sixteen J. regia provenances were collected along RT and compared with 13 Italian provenances and the landrace Sorrento. Although the level of SSR polymorphism we observed was moderately high, AMOVA revealed that most of the diversity was located within individuals (92.58%), and geographical differentiation was low (Dest = 0.076). Evidence for human-mediated domestication bottleneck events was detected in about 95% of walnut provenances. A Bayesian approach divided 456 walnut samples into three clusters: (1) Sorrento genotypes, (2) trees from the island of Sicily, and (3) the remaining germplasm. The UPGMA tree based on Nei's distances distinguished northeastern provenances and weakly grouped 12 of 16 provenances of RT. The observed genetic differences derived mainly from gradations in allele frequencies. Separation of the Sicilian provenance from the mainland may be explained in terms of founder effects and prolonged geographic isolation. Two contrasting forces, selection, and frequent inter-regional transfer of propagules, appear to drive the patterns of genetic variability for J. regia.

DNA markers identify hybrids between butternut ( Juglans cinerea L.) and Japanese walnut ( Juglans ailantifolia Carr.)

Abstract: Butternut (Juglans cinerea L.) is a temperate deciduous hardwood native to the eastern USA and southern Canada valued for its nuts and wood. Butternut’s survival is threatened by butternut canker, a disease caused by the exotic fungus Sirococcus clavigignenti-juglandacearum Nair, Kostichka & Kuntz. Field observations indicate that trees commonly called buartnut (a hybrid of butternut and its close congener Japanese walnut (Juglans ailantifolia × J. cinerea)) may be more resistant to butternut canker than is either parental species. Hybrids are difficult to distinguish morphologically from butternuts, and scientists have expressed concern over the possibility of range-wide genetic invasion by Japanese walnut via hybridization with butternut. We used pair-wise combinations of 40 random primers to screen bulked DNA pools of butternut, Japanese walnut, and buartnuts to identify genomic regions unique to Japanese walnut. We ultimately identified one ITS region marker, one chloroplast marker, one mitochondrial marker, and six nuclear markers. The utility of the markers for identifying hybrids was tested and verified using more than 190 genotypes. The markers will be used to identify buartnut hybrids based on the presence of introgressed genomic fragments inherited from Japanese walnut. We confirmed that hybrids have a complex genetic history and present features of the parental species in all possible combinations. These results will assist in the identification and testing of (non-hybrid) butternut for breeding and reintroduction of the species to its former habitats.

A rubber tree’s durable resistance to Microcyclus ulei is conferred by a qualitative gene and a major quantitative resistance factor

Abstract: The components of genetic resistance from the Hevea brasiliensis cultivar MDF 180 against South American Leaf Blight (SALB) caused by Microcyclus ulei were investigated by QTL mapping. MDF 180 has already been described as a cultivar with a high level of partial and long-lasting resistance. The resistance of progeny individuals from a cross between a susceptible cultivar and MDF 180 was assessed both under controlled conditions of inoculation by three M. ulei isolates and under natural infection in a field trial. Genetic maps of the two parents of this progeny were mainly established based on microsatellites and AFLP markers. No resistance QTL were found in the susceptible parent. In the resistant parent, we identified a qualitative gene responsible for the resistance against isolates from French Guiana and a major quantitative resistance factor determining the resistance against isolates from the state of Bahia (Brazil). The qualitative resistance gene was denominated M15md and was located in the linkage group g15. Four minor resistance QTLs were also identified, two of which showed an epistatic interaction with M15md. The durability of the resistance of MDF 180 is discussed in light of these data.

Genetic variability and diversification process in local pear cultivars from northwestern Spain using microsatellites

Abstract: This is the first known large-scale molecular study of simple sequence repeats loci based on pear cultivars from the northwestern Iberian Peninsula. Most of the Spanish pear crop (one of the largest in Europe) is based on the Spanish cultivar Blanquilla and various other foreign cultivars. However, local cultivars can still be found in old orchards in northwestern Spain. Between 1978 and 1981, the Centro de Investigaciones Agrarias de Mabegondo (Xunta de Galicia) established a Germplasm Bank of local pear cultivars containing 221 accessions. In the current study, these were analysed and compared with 20 commercial cultivars of Pyrus spp. using 19 microsatellites. We identified 127 genotypes out of 221 accessions with an average of 43% clonality in this collection. Genotypes were analysed using a model-based Bayesian procedure (Structure), factorial correspondence analysis and molecular variance analysis, and Jaccard coefficients were estimated. Four reconstructed populations were identified by Structure, one related to Asian cultivars, two to French and English cultivars and one to Galician cultivars. The four identified groups of pears had evolved independently. This study explains the diversification process in pear cultivars from northwestern cultivars based on hybridization (16%), selection of triploids (38%) and the introgression of commercial cultivars in the collection (4%).

Quantitative trait loci for foliar terpenes in a global eucalypt species

Abstract: Terpenes are a diverse group of plant secondary metabolites that mediate a plethora of ecological interactions in many plant species. Despite increasing research into the genetic control of important adaptive traits in some plant species, the genetic control of terpenes in forest tree species is still relatively poorly studied. In this study, we use quantitative genetic and quantitative trait loci (QTL) analysis to investigate the genetic control of foliar terpenes in an ecologically and commercially important eucalypt species, Eucalyptus globulus. We show a moderate to high within-family broad-sense heritability and significant genetic basis to the variation in 14 of the 16 terpenes assayed. This is the first report of QTL for terpenes in this species. Eleven QTL influenced the terpenes overall. One QTL on linkage group 6 affected six of the seven different sesquiterpenes assayed (plus one monoterpene), which, in combination with highly significant correlations between these compounds, argues that their variation is influenced by a QTL with pleiotropic effect early in the biosynthetic pathway. We examine the homology of these QTL to those found in a closely related eucalypt, Eucalyptus nitens, and provide evidence that both common and unique QTL influence terpene levels.

Improving the quality of African robustas: QTLs for yield- and quality-related traits in Coffea canephora

Abstract: Coffea canephora breeding requires combining sustainable productivity with improved technological and cup quality characteristics. Beverage quality is a complex and subjective trait, and breeding for this trait is time consuming and depends on knowledge of the genetics of its components. A highly variable C. canephora progeny resulting from an intraspecific cross was assessed for 63 traits over 5 years. To identify quantitative trait loci (QTLs) controlling agronomic, technological, and quality-related traits, a genetic map comprising 236 molecular markers was constructed, and composite interval mapping was performed. Beverage quality was evaluated in relation to biochemical and cup tasting traits. QTLs were identified for almost half of the traits evaluated, with effects ranging from 6% to 80% of phenotypic variation. Most of them present a consistent detection over years. The strongest QTLs explained a high percentage of the variation for yield in 2006 (34% to 57%), bean size (25% to 35%), content of chlorogenic acids (22% to 35%), sucrose and trigonelline content (29% to 81%), and acidity and bitterness of coffee beverages (30% to 55%). Regions of the C. canephora genome influencing beverage quality were identified. Five QTL zones were co-localized with candidate genes related to the biosynthesis of the analyzed traits: two genes coding for caffeine biosynthesis, one gene implicated in the biosynthesis of chlorogenic acids, and two genes implicated in sugar metabolism. This is one of the first studies on the identification of QTLs combining agronomic and quality traits in coffee. The high variability of quality traits within C. canephora and the presence of consistent QTLs offer breeders a promising tool to improve coffee cup quality.

Activation tagging is an effective gene tagging system in Populus

Abstract: Knowledge of the functional relationship between genes and organismal phenotypes in perennial plants is extremely limited. Using a population of 627 independent events, we assessed the feasibility of activation tagging as a forward genetics tool for Populus. Mutant identification after 2 years of field testing was nearly sevenfold (6.5%) higher than in greenhouse studies that employed Arabidopsis and identical transformation vectors. Approximately two thirds of all mutant phenotypes were not seen in vitro and in the greenhouse; they were discovered only after the second year of field assessment. The trees’ large size (5-10 m in height), perennial growth, and interactions with the natural environment are factors that are thought to have contributed to the high rate of observable phenotypes in the field. The mutant phenotypes affected a variety of morphological and physiological traits, including leaf size and morphology, crown architecture, stature, vegetative dormancy, and tropic responses. Characterization of the insertion in more than 100 events with and without mutant phenotypes showed that tags predominantly (70%) inserted in a 13-Kbp region up- and downstream of the genes’ coding regions with approximately even distribution among the 19 chromosomes. Transcriptional activation was observed in many proximal genes studied. Successful phenotype recapitulation was observed in 10 of 12 retransformed genes tested, indicating true tagging and a functional relationship between the genes and observed phenotypes for most activation lines. Our studies indicate that in addition to associating mapping and QTL approaches, activation tagging can be used successfully as an effective forward gene discovery tool in Populus.

SSR-based analysis of clonality, spatial genetic structure and introgression from the Lombardy poplar into a natural population of Populus nigra L. along the Loire River

Abstract: A scarcity of favourable habitats and introgression from exotic cultivars are two major threats to black poplars (Populus nigra L.) in Europe. Natural vegetative propagation contributes to maintenance of the species in areas where seedling recruitment is limited. Exhaustive sampling of all mature trees in a natural P. nigra stand (413 individuals at recorded positions), genotyping at 11 SSR loci, and a standardized analysis framework resulted in a precise description of clonality in terms of (a) frequency, (b) spatial growth form, and (c) impacts on the overall spatial genetic structure (SGS). The high proportion of replicated genotypes detected resulted in a genotypic richness (R) of 0.47. Up to 18 ramets were found per multilocus lineage (MLL), but 95% of MLLs contained fewer than five ramets (Pareto index β = 1.07). No significant difference in vegetative propagation potential was found between genders. Uneven spatial distribution of ramets, with clustering of clonal ramets (aggregation index Ac = 0.62) and near-zero intermingling between MLLs (clonal dominance index Dc = 0.99), resulted in a ‘phalanx’ clonal growth form, explaining most of the SGS observed over short distances (0–20 m, Sp = 0.0324). Although they did not exhibit the typical columnar shape of the Lombardy poplar (P. nigra var. italica), five trees were found to be probable F1 hybrids of this old and widely distributed cultivar.

High-density genetic mapping for coffee leaf rust resistance

Abstract: Coffee leaf rust caused by the fungus Hemileia vastatrix causes considerable economic losses for coffee producers. Although agrochemical products can provide sufficient disease control, the use of resistant cultivars is a safer alternative. This resistance may be constrained by one or a few genetic factors, mainly those found in material originating from interspecific hybrids. In this study, the genetic analysis of an F2 population consisting of 224 plants derived from a crossing of Hibrido de Timor UFV 427-15 (resistant) with Catuai Amarelo IAC 30 (susceptible) showed that a dominant gene confers the resistance of coffee to race II of H. vastatrix. From a genetic map saturated with 25 amplified fragment length polymorphism (AFLP) markers linked to the resistance gene, we developed a high-density genetic map with six sequence-characterized amplified region (SCAR) markers delimiting a chromosomal region of 9.45 cM and flanking the dominant gene at 0.7 and 0.9 cM. This is the first saturated and high-density genetic map obtained from this region containing the resistance gene. The results of this study are of great importance for the introduction of molecular markers for marker-assisted selection; they will also facilitate studies related to the cloning, structure, and function of race-specific genes involved in the resistance of coffee trees to H. vastatrix.

Relationships between early growth and Quambalaria shoot blight tolerance in Corymbia citriodora progeny trials established in Queensland, Australia

Abstract: The fungal pathogen Quambalaria pitereka can cause significant damage to spotted gum (Corymbia sp.) plantations in Australia. A series of seven progeny trials, involving seed from a range-wide collection from 527 individuals within 25 native populations of Corymbia citriodora sub-species variegata, were assessed for height growth and damage from Quambalaria around 1 year after planting. Infection at this young age has been found to detrimentally impact growth, form, and wood quality for many years. Genetic variance was found to be significant at both the provenance and family level. However, selection of families within provenances should lead to greater levels of genetic gain than what can be realized from selecting among provenances as estimates of additive genetic variance were consistently greater than estimates of variance among populations. Strong relationships between height and Quambalaria shoot blight (QSB) damage assessments in these trials were evidenced by very high genetic correlations between the traits; therefore, selection for any of these traits could be used to identify more productive and QSB-tolerant populations. While both provenances and families were found to interact with the trial environments at a similar level across traits, genetic correlations indicated that rankings for growth were be less stable than rankings for QSB tolerance across environments. Genetic parameter estimates derived from general and generalized linear models were very similar and either analytical method could be used to evaluate fungal damage.

Range shift and loss of genetic diversity under climate change in Caryocar brasiliense , a Neotropical tree species

Abstract: Many species have suffered reduction in habit- able area due to recent climate change, but few studies evaluated how these range collapses will impact genetic diversity. Here, we modeled shifts in the species' geograph- ical range to evaluate how genetic diversity of Caryocar brasiliense will change as a consequence of predicted climate change in the next 50 years. A total of 135 records of species occurrence were obtained to model species' distribution based on the current environment using MAXENT and forecasting future distribution using a combination of three coupled atmospheric-oceanic global circulation models. Genetic parameters were estimated based on the polymorphism at ten microsatellite loci for 466 individuals. Our results show that climatic suitable areas for C. brasiliense will be restricted to the southern- most distribution of savanna vegetation. Genetic diversity and the number of alleles may decrease slowly if populations persist in regions up to 0.5 of environmental suitability estimated by MAXENT, but will sharply de- crease above this level. Nevertheless, deviation from mutation-drift equilibrium is significant even if a small amount of local populations is lost. More climatic suitable areas in the future will be in the most disturbed regions in Brazil, and populations that will persist there are those with higher levels of inbreeding at present. This may impose several threats to the species, including the limited capacity to cope with ongoing climatic changes by adaptation and constraints to dispersal.

Mapping Rm2 gene conferring resistance to the green peach aphid ( Myzus persicae Sulzer) in the peach cultivar “Rubira®”

Abstract: The green peach aphid (GPA), Myzus persicae (Sulzer), is a widespread pest insect that significantly reduces yield in peach orchards [Prunus persica (L.) Batsch]. Chemical control of the GPA population in the orchards showed little efficiency because of the development of resistance to most classes of insecticides. Biological control partially gave convincing results. Breeding for resistant peach cultivars is therefore a serious option to take into account for the development of sustainable pest management. Among the few available resistance cultivars, the rootstock peach “Rubira®” shows a strong induced antixenosis-type GPA resistance. This was demonstrated segregating as a single dominant gene. In order to investigate the genetic basis of resistance and develop molecular tools useful in breeding programs, a F2 population derived from “Rubira®” also segregating for leaf color was grown and scored for GPA resistance under contrasted environmental conditions. An SSR-based genetic linkage map composed of 120 SSR loci spanned over a distance of 497.8 cM was then established. The GPA resistance mapped to a single locus at the bottom end of linkage group 1. We propose to name Rm2 the dominant allele of the underlying gene. Additionally, a reciprocal translocation was identified near the Gr gene controlling leaf color. The red-leaf parent “Rubira®” was demonstrated responsible for the translocation. This study provides the basis for future molecular analysis for the use of Rm2 in peach breeding programs against GPA in peach orchards.

Genotype by environment interactions for Pinus radiata in New South Wales, Australia

Abstract: Historical data from 26 progeny trials in the NSW breeding program was analyzed to determine the extent and practical importance of genotype by environment (G×E) interactions for a range of traits. Significant G×E interaction was present for diameter (DBH) with 75% of the 35 estimated between-site genetic correlations falling below the threshold value of 0.6 where regionalization should be considered. Estimated genetic correlations for stem straightness, branch quality, and outerwood density were much higher, indicating these traits are not as affected by G×E. Levels of G×E for DBH are sufficient to have serious impacts on the expression of genetic gain in deployed material. For DBH, altitude differences between sites appear to be the key factor driving the G×E with a difference of greater than 280 m in altitude leading to a breakdown in correlations. Two groups of sites were identified as having limited G×E within each group: one for sites above 900 m elevation plus a lower-altitude group. Sites included in the higher-altitude group were located across the entire north–south geographic range of NSW. Equations for prediction of site mean DBH indicate that altitude, prior land use, and underlying geology are key driving variables. A more complex model was developed for predicting the between-site genetic correlations for DBH with the model accounting for approximately 50% of the observed variation.