High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations

Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait “shell-thickness” (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species

Synthesis of 2,6-Di(pyrazol-1-yl)pyrazine derivatives and the spin-state behavior of their iron(II) complexes

Chlorination of 2,6-bis(pyrazol-1-yl)pyrazine (bppz) with Na- ClO in acetic acid afforded 2,6-bis(4-chloropyrazol-1-yl)pyrazine (LCl). 2,6-Bis(4-bromopyrazol-1-yl)pyrazine (LBr), 2,6-bis(4-iodopyrazol-1- yl)pyrazine (LI), 2,6-bis(4-methylpyrazol- 1-yl)pyrazine (L Me), and 2,6-bis(4-nitropyrazol-1- yl)pyrazine (LNO ) were also prepared by reactions of the preformed 4-substituted pyrazoles with 2,6-dichloropyrazine. The reduction of LNO with iron powder gave 2,6-bis(4- aminopyrazol-1-yl)pyrazine (L NH) and LI was converted into 2,6-bis[4-(phenylethynyl)pyrazol-1-yl]pyrazine (LCCPh) by a Sonogashira coupling reaction. The salts [Fe(LMe)]X (X- = BF - and ClO -) underwent thermal spin-crossover abruptly at around 200 K in one and two steps, respectively. The [Fe(LMe)]X salts exhibited dif- ferent light-induced excited spin-state trapping (LIESST) behavior; the BF - salt behaves classically [T(LIESST) = 93 K], but the ClO - salt undergoes a multistep LIESST relaxation. In contrast, solid [Fe(L Cl)][BF]2 adopts a fixed 2:1 high/ low-spin-state population that does not change with temperature below 300 K, whereas [Fe(LBr)][BF]2 and [Fe(L I)][BF]2 form low-spin solvated crystals that are transformed into high-spin powders on drying. The pyrazinyl group in the LR ligands slightly stabilizes the low-spin state of the complexes, as determined by solution-phase magnetic measurements. The crystal structure of [Fe(LCCPh)(OH)z]- [BF]2 contains a disordered mixture of six- (z = 3) and sevencoordinate (z = 4) iron centers

SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of Eucalyptus grandis

Simple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihood-based estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.Fil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; ArgentinaFil: Klápště, Jaroslav. Czech University Of Life Sciences Prague; República Checa. University of British Columbia; Canadá. New Zealand Forest Research Institute Ltd.; Nueva ZelandaFil: Garcia, Martín Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Investigación En Ciencias Veterinarias y Agronómicas; ArgentinaFil: Villalba, Pamela Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Investigación En Ciencias Veterinarias y Agronómicas; ArgentinaFil: Marcucci Poltri, Susana Noemí. Investigación En Ciencias Veterinarias y Agronómicas; Argentin