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Eastern black walnut, Juglans nigra L., is an economically important tree species valued for its high-quality timber and edible nuts. A regional industry for the species' nut and kernel products resides in Missouri, where over 9 million kg of hulled in-shell nuts are purchased in masting years. The crop is primarily based upon nuts harvested from wild trees, placing a ceiling on nut volume and quality (e.g. small nut size, dark pellicle color, and 10–14% kernel by weight). Orchards of named cultivars, like 'Kwik Krop' and 'Sparrow', supply up to 22,000 kg of nuts with a higher kernel percentage (> 26%) and improved quality. Such cultivars often represent chance wild or on-farm seedlings, clonally propagated since the late 1800's by enthusiasts. Today, continued improvement of eastern black walnut as an orchard crop is limited by a long generation time, delayed expression of important traits, and space requirements – creating a strong need for marker-trait association studies that inform progeny selection. The first linkage map for J. nigra was recently created using the 'Sparrow' × 'Schessler' F1 population and loci for phenology traits discovered. The objective of this study is to utilize these genetic resources to detect quantitative trait loci (QTL) and report associated DNA markers for the spur-bearing habit, which promotes precocity and high yield. Using single-year data from the 11-year-old population, we observe that segregation for the spur-bearing habit appears to be recessive and multigenic. Three QTLs (p > 0.99) were identified on linkage group (LG) 8, LG11, and LG16 that explain 7.2%, 8.7%, and 10% of trait variation, respectively. Regions between flanking DNA markers were 3.16 cM, 4.32 cM, and 9.69 cM, respectively. This study is the first to examine the genetic control of bearing habit and yield in eastern black walnut and informs breeders' approach for their future genetic improvement. [ABSTRACT FROM AUTHOR]

Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F1 full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping in J. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to the J. regia "Chandler" V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequent J. nigra maps and other Juglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut. [ABSTRACT FROM AUTHOR]

A factorial mating population between 10 Eucalyptus urophylla S. T. Blake and 10 E. tereticornis Smith parents tested at two sites was used to investigate the relationship of parental genetic variation to hybrid mean value (MV), specific hybridizing ability (SHA), and heterosis. Based on 184 polymorphic expressed sequence tag (EST) derived simple sequence repeats (SSR) markers, genetic distance (GD) between parents (GDAll) ranged from 0.293 to 0.783, averaging at 0.700. For tree height, breast-high diameter and wood density at age of 7.5 years, GDAll, GDs based on markers beyond 0.70 and 0.80 in polymorphism information content and GDs based on alleles within 0.10–0.90, 0.20–0.80, and 0.30–0.70 in allele frequency were not significantly correlated with MV, SHA, and the majority of heterosis types. GD based on effect-significant alleles was significantly correlated only with a few of traits or for certain site, while GDs based on effect-increasing (GDIA) and effect-decreasing alleles (GDDA) had significantly positive and negative correlations, respectively, with all the MV and SHA as well as across-site mid-parent heterosis. These results suggest the potential utility of GDIA and GDDA for molecular prediction of hybrid performance, SHA, and heterosis in Eucalyptus and may have implications for hybrid breeding in other plants. [ABSTRACT FROM AUTHOR]

Identification of markers associated with genes of interest and quantitative trait loci (QTLs), combined with high-density genetic linkage maps, can help reduce labor and costs by enabling marker-assisted selection (MAS). In this study, a dwarfing apple rootstock cultivar 'JM7' ( Malus prunifolia × Malus pumila 'Malling 9') and wild apple Malus sieboldii 'Sanashi 63' (section Sorbomalus) were used for constructing genetic linkage maps. Here, a species from section Sorbomalus was used for the first time as a target species in a genome-wide mapping study. We also developed and mapped 137 novel-expressed sequence tag-simple sequence repeat (EST-SSR) markers. The genetic linkage maps of 'JM7' and 'Sanashi 63' consisted of 415 and 310 loci and spanned 998.0 and 981.8 cM, respectively, comparable to the reference map of Malus × domestica 'Discovery'. A BLASTN search revealed that all of the EST-SSR sequences used in this study exhibited very high homology to one or more previously characterized apple genome contigs. Although the most homologous contigs of 89 EST-SSRs were located within the same linkage groups (LGs) identified by mapping analysis, the other 48 EST-SSRs were aligned into contigs positioned in different LGs than those identified by mapping. When search criteria were expanded to include the five most homologous contigs of each EST-SSR, at least one of the top five contigs for 15 of these 48 EST-SSRs corresponded to the LG obtained by mapping. The maps of 'JM7' and 'Sanashi 63' may be useful for analyzing important rootstock characteristics and identifying markers for MAS. [ABSTRACT FROM AUTHOR]

Eucalyptus globulus is the most commonly planted hardwood species for pulpwood in temperate regions. We aimed to develop and characterize functional molecular markers for population genetic analyses and molecular breeding in this model tree species. Public expressed sequence tag (EST) databases were screened for nonredundant sequences to predict putative gene functions and to discover simple sequence repeats (EST-SSRs), which were then validated in E. globulus and six other Eucalyptus species. A total of 4,924 nonredundant sequences were identified from 12,690 updated E. globulus ESTs. Approximately 19.3% (952) were unigenes and contained 1,140 EST-SSR markers, which were mainly trimeric (58.6%). A set of 979 primers for putative SSR markers was designed after bioinformatic analysis. The predicted functions of these ESTs containing SSR were classified according to their gene ontology (GO) categories (biological process, molecular function, and cellular component). GO categories were assigned to 226 ESTs (30.2%). Most ESTs containing SSR (78.7%) had significant matches ( E ≤ 10) with the nonredundant protein database using BLASTX. From a set of 56 random primer pairs, 37 could be validated in eight E. globulus genotypes and were also tested for cross-transferability to other six Eucalyptus species ( Eucalyptus grandis, Eucalyptus saligna, Eucalyptus dunnii, Eucalyptus viminalis, Eucalyptus camaldulensis, Eucalyptus tereticornis). Seventeen polymorphic EST-SSR markers for E. globulus were evaluated in 60 unrelated trees, being representative of the species' natural distribution. As a result, six highly informative markers were proposed for genetic diversity analyses, fingerprinting, and comparative population studies, between different species of E. globulus. [ABSTRACT FROM AUTHOR]

Tea plant ( Camellia sinensis (L.) O. Kuntze) originated from China, where distributed abundant genetic resources. It is of critical importance to well understanding of genetic diversity and population structure for effective collection, conservation, and utilization of tea germplasms. In this study, 96 new polymorphic EST-SSR markers were developed and used to analyze 450 tea accessions collected from 14 tea-producing regions across China. A total of 409 alleles were observed, and the gene diversity ( H) and polymorphic information content ( PIC) were estimated to be averagely 0.64 and 0.61, respectively, across all the tested samples. The higher level of genetic diversity was observed in original regions like Guangxi, Yunnan, and Guizhou provinces. The allele number, H, and PIC showed decreasing trend when the region was more and more away from origin center of tea plant, which gave us implications on the spreading route of tea plant in China. The clustering of 450 samples both showed a clear separation according to their geographic origin based on either model simulation or genetic distance. The genetic differentiation was further analyzed among five inferred populations represented different eco-geographic regions. The lowest F and the closest relationship were revealed between proximal populations, which indicated that gene exchanges occurred frequently between nearby regions than distance ones. The majority of genetic variation resulted from differentiation within population (81.36%) rather than among inferred (13.6%) and regional (5.04%) populations based on analysis of molecular variance. Our study also revealed that the lower diversity and simpler population structure were found in improved cultivars than wild teas and landraces, which indicated that genetic base of developed cultivars became narrow because of long-standing domestication and artificial selection. So more attentions should be focused to conserve and utilize the beneficial genes in wild teas and landraces to broaden genetic variation of new cultivars in future breeding of the tea plant. [ABSTRACT FROM AUTHOR]

Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine ( Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant EST and cDNA sequences (UniGenes) and designed SSR primer pairs from both sequence types. Overall SSR densities were 96 SSR/Mb in GSSs and 38 SSR/Mb in UniGenes. Loblolly pine had the lowest transcriptome SSR density when compared to 49 other species in the NCBI UniGene database. Among the five different GSS genome fractions of loblolly pine analyzed, methylation-filtered DNA had the highest SSR density at 145 SSR/Mb. The most abundant loblolly pine SSR motif was AT in both GSSs (34 SSR/Mb) and UniGenes (7.6 SSR/Mb). Among the trinucleotide SSR motifs, the most abundant was AAT (9.5 SSR/Mb) in GSSs and AGC (4.9 SSR/Mb) in UniGenes. We designed PCR primer pairs for 120 genomic SSRs and 315 EST-SSRs and evaluated PCR amplification for 108 (25%). We identified 21 primer pairs that reliably amplified polymorphic loci from 31 loblolly pine individuals and estimated that at least 60 additional polymorphic marker loci could be developed from available P. taeda GSS and UniGene resources. [ABSTRACT FROM AUTHOR]

Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function. A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function. Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3 cM was found, with approximately one SSR every 2 cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%, and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5′UTR and 3′UTR regions. This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out association mapping studies. [ABSTRACT FROM AUTHOR]