Uniform standards for genome databases in forest and fruit trees

TreeGenes and tree fruit Genome Database Resources serve the international forestry and fruit tree genomics research communities, respectively. These databases hold similar sequence data and provide resources for the submission and recovery of this information in order to enable comparative genomics research. Large-scale genotype and phenotype projects have recently spawned the development of independent tools and interfaces within these repositories to deliver information to both geneticists and breeders. The increase in next generation sequencing projects has increased the amount of data as well as the scale of analysis that can be performed. These two repositories are now working towards a similar goal of archiving the diverse, independent data sets generated from genotype/phenotype experiments. This is achieved through focused development on data input standards (templates), pipelines for the storage and automated curation, and consistent annotation efforts through the application of widely accepted ontologies to improve the extraction and exchange of the data for comparative analysis. Efforts towards standardization are not limited to genotype/phenotype experiments but are also being applied to other data types to improve gene prediction and annotation for de novo sequencing projects. The resources developed towards these goals represent the first large-scale coordinated effort in plant databases to add informatics value to diverse genotype/phenotype experiments.     

EST contig-based SSR linkage maps for Malus?×?domestica cv Royal Gala and an apple scab resistant accession of M. sieversii, the progenitor species of domestic apple

Malus sieversii is a progenitor species of domestic apple M. × domestica. Using population “GMAL 4595” of 188 individuals derived from a cross of Royal Gala × PI 613988 (apple scab resistant, M. sieversii), 287 SSR (simple sequence repeats) loci were mapped. Of these SSRs, 80 are published anchors and 207 are newly developed EST (expressed sequence tag) contig-based SSRs, representing 1,630 Malus EST accessions in GenBank. Putative gene functions of these EST contigs are diverse, including regulating plant growth, development and response to environmental stresses. Among the 80 published SSRs, 18 are PI 613988 specific, 38 are common and 24 are Royal Gala specific. Out of the 207 newly developed EST contig-based SSRs, 79 are PI 613988 specific, 45 are common and 83 are Royal Gala specific. These results led to the construction of a M. sieversii map (1,387.0 cM) of 180 SSR markers and a Royal Gala map (1,283.4 cM) of 190 SSR markers. Mapping of scab resistance was independently conducted in two subsets of population “GMAL 4595” that were inoculated with Ventura inaequalis races (1) and (2), respectively. In combination with the two major resistance reactions Chl (chlorotic lesions) and SN (stellate necrosis) to each race, four subsets of resistance data, i.e., Chl/race (1), SN/race (1), Chl/race (2) and SN/race (2), were constituted and analyzed, leading to four resistance loci mapped to the linkage group 2 of PI 613988; SNR1 (stellate necrosis resistance to race (1)) and SNR2 are tightly linked in a region of known scab resistance genes, and ChlR1 (Chlorotic lesion resistance to race (1)) and ChlR2 are also linked tightly but in a region without known scab resistance genes. The utility of the two linkage maps, the new EST contig-based markers and M. sieversii as sources of apple scab resistance are discussed.     

Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.     

Insecticidal activity of Brassica juncea seed meal to the fungus gnat Bradysia impatiens Johannsen (Diptera:Sciaridae)

Fungus gnats (Bradysia impatiens) can be a serious pest especially to plants grown in confined areas, and although various methods of control are available, safer and more effective control measures are desirable. Mustard seed meal, a by‐product remaining after oil removal for use as a biodiesel feedstock, contains compounds called glucosinolates that hydrolyse to insecticidal 2‐propenyl isothiocyanate. Our objective was to produce a dose‐response curve for making recommendations of Brassica juncea seed meal applications that will result in fungus gnat larvae control. Twenty colony‐raised fungus gnat larvae were added to 20 g (226 per cm³) of potting media, and adult emergence monitored during 2 weeks using yellow sticky cards. Treatments included without meal, detoxified meal and 19 doses ranging from 0.05 to 3.0 g seed meal. A logistic model was used to predict an LC50 of 0.18 and an LC90 of 0.38 g seed meal for the 20‐g pot. The amounts of seed meal required to produce the observed LC50 and LC90 were predicted to produce 0.08 and 0.17 μmol 2‐propenyl isothiocyanate per cm³ potting medium, respectively. B. juncea seed meal has potential utility for the control of B. impatiens, thus warranting additional studies to determine the seed meal's chronic impact on fungus gnats, phytotoxicity and plant fertility benefits.     

Genome-wide characterization and selection of expressed sequence tag simple sequence repeat primers for optimized marker distribution and reliability in peach

Simple sequence repeats (SSR) in Prunus expressed sequence tags (EST) were mined, and flanking primers designed and used for genome-wide characterization and selection of primers to optimize marker distribution and reliability in peach. A total of 4,770 and 9,029 SSRs were identified from 12,618 contigs and 34,238 singlets, from which 3,695 and 6,849 primers were designed, respectively. Alignment of the 10,544 forward and reverse primer sequences (21,088 queries) against the peach reference genome at 9e-03 resulted in 23,553 hits (96,621 alignments) with 16,885 queries, and “no hits found” (NHF) for the remaining 4,203 queries. A majority of aligned primers had only one hit/alignment on the peach scaffolds, and the distribution of the 5,500 singly aligned primers (pairs) on each 500-kb genome interval was determined. The average number of ESR-SSR primers per 500-kb interval was 10.8. The primers were categorized into eight subgroups based on the difference between the genome amplicon size and expressed amplicon size of each primer, with 288 primers of optimized distribution and reliability selected for genotype evaluation. Only 2 of the 288 primers failed in all 4 peach cultivars screened, with an overall successful primer/sample rate of 97.2 %. The average number of alleles detected in the four cultivars was 3.84. The polymorphism information content (PIC) values suggested that a majority of the 288 primers had a high rate of allele polymorphism among the four peach cultivars. The advantages of genome-wide analysis of EST-SSR primers and options to improve the polymorphism rate are discussed.     

Development of SCAR markers linked to <Emphasis Type="Italic">sin</Emphasis>-<Emphasis Type="Italic">2</Emphasis>, the stringless pod trait in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

With increasing consumer demand for vegetables, edible-podded peas have become more popular. Stringlessness is one of most important traits for snap peas. A single recessive gene, sin-2, controls this trait. Because pollen carrying the stringless gene is less competitive than pollen carrying the stringy gene, there are fewer than expected stringless plants recovered in segregating generations. Marker-assisted selection (MAS) is a valuable tool to identify plants with the traits of interest at an early stage in the breeding process. The objective of this study was to identify robust, user-friendly molecular markers tightly linked to sin-2. A total of 144 target region amplification polymorphism (TRAP) primer combinations were used to screen four DNA bulks, which were constructed from 32 pea breeding lines based on their phenotypes. Sixty polymorphic TRAP primer combinations were identified between bulks of stringless and stringy pods. Five primer combinations, F6_Trap03_168, F6_SA12_145, F10_ODD8_130, F11_GA5_850, and F12_SA12_190, showed more than 90 % association with the stringless phenotype in 32 pea breeding lines. Two of the TRAP markers, F10_ODD8_130 and F12_SA12_190, were cloned, sequenced, and successfully converted to sequence characterized amplified region (SCAR) markers. These two SCAR markers were validated using 20 F₅ recombinant inbred lines derived from a cross between Bohatyr (a dry pea variety with strings) and S1188 (a stringless snap pea variety) and showed strong marker-trait association. The results will have direct application in MAS of stringless edible-podded peas.     

Environmental effects on hormonal regulation of testicular descent

Regulation of testicular descent is hormonally regulated, but the reasons for maldescent remain unknown in most cases. The main regulatory hormones are Leydig cell-derived testosterone and insulin-like factor 3 (INSL3). Luteinizing hormone (LH) stimulates the secretion of these hormones, but the secretory responses to LH are different: INSL3 secretion increases slowly and may reflect the LH dependent differentiated status of Leydig cells, whereas testosterone response to LH is immediate. Testosterone contributes to the involution of the suspensory ligament and to the inguinoscrotal phase of the descent, while INSL3 acts mainly in transabdominal descent by stimulating the growth of the gubernaculum. INSL3 acts through a G-protein coupled receptor LGR8. In the absence of either INSL3 or LGR8 mice remain cryptorchid. In humans only few INSL3 mutations have been described, whereas LGR8 mutations may cause some cases of undescended testis. Similarly, androgen insensitivity or androgen deficiency can cause cryptorchidism. Estrogens have been shown to down regulate INSL3 and thereby cause maldescent. Thus, a reduced androgen–estrogen ratio may disturb testicular descent. Environmental effects changing the ratio can thereby influence cryptorchidism rate. Estrogens and anti-androgens cause cryptorchidism in experimental animals. In our cohort study we found higher LH/testosterone ratios in 3-month-old cryptorchid boys than in normal control boys, suggesting that cryptorchid testes are not cabable of normal hormone secretion without increased gonadotropin drive. This may be either the cause or consequence of cryptorchidism. Some phthalates act as anti-androgens and cause cryptorchidism in rodents. In our human material we found an association of a high phthalate exposure with a high LH/testosterone ratio. We hypothesize that an exposure to a mixture of chemicals with anti-androgenic or estrogenic properties (either their own activity or their effect on androgen–estrogen ratio) may be involved in cryptorchidism.     

Improved Agrobacterium-mediated transformation of three maize inbred lines using MS salts

Transformation technology as a research or breeding tool to improve maize is routinely used in most industrial and some specialized public laboratories. However, transformation of many inbred lines remains a challenging task, especially when using Agrobacterium tumefaciens as the delivery method. Here we report success in generating transgenic plants and progeny from three maize inbred lines using an Agrobacterium-mediated standard binary vector system to target maize immature embryos. Eleven maize inbred lines were pre-screened for transformation frequency using N6 salts. A subset of three maize inbred lines was then systematically evaluated for frequency of post-infection embryogenic callus induction and transformation on four media regimes: N6 or MS salts in each of two distinct media backgrounds. Transgenic plants recovered from inbred lines B104, B114, and Ky21 were analyzed for transgene integration, expression, and transmission. Average transformation frequencies of 6.4% (for B104), 2.8% (for B114), and 8% (for Ky21) were achieved using MS salts. Availability of Agrobacterium-mediated maize inbred line transformation will improve future opportunities for maize genetic and functional genomic studies.     

Notch induces cyclin-D1-dependent proliferation during a specific temporal window of neural differentiation in ES cells

The Notch signaling pathway controls cell fate choices at multiple steps during cell lineage progression. To produce the cell fate choice appropriate for a particular stage in the cell lineage, Notch signaling needs to interpret the cell context information for each stage and convert it into the appropriate cell fate instruction. The molecular basis for this temporal context-dependent Notch signaling output is poorly understood, and to study this, we have engineered a mouse embryonic stem (ES) cell line, in which short pulses of activated Notch can be produced at different stages of in vitro neural differentiation. Activation of Notch signaling for 6 h specifically at day 3 during neural induction in the ES cells led to significantly enhanced cell proliferation, accompanied by Notch-mediated activation of cyclin D1 expression. A reduction of cyclin-D1-expressing cells in the developing CNS of Notch signaling-deficient mouse embryos was also observed. Expression of a dominant negative form of cyclin D1 in the ES cells abrogated the Notch-induced proliferative response, and, conversely, a constitutively active form of cyclin D1 mimicked the effect of Notch on cell proliferation. In conclusion, the data define a novel temporal context-dependent function of Notch and a critical role for cyclin D1 in the Notch-induced proliferation in ES cells.