Molecular modeling of S-RNases involved in almond self-incompatibility

Gametophytic self-incompatibility (GSI) is a mechanism in flowering plants, to prevent inbreeding and promote outcrossing. GSI is under the control of a specific locus, known as the S-locus, which contains at least two genes, the RNase and the SFB. Active S-RNases in the style are essential for rejection of haploid pollen, when the pollen S-allele matches one of two S-alleles of the diploid pistil. However, the nature of their mutual interactions at genetic and biochemical levels remain unclear. Thus, detailed understanding of the protein structure involved in GSI may help in discovering how the proteins involved in GSI may function and how they fulfill their biological roles. To this end, 3D models of the SC (Sf) and two SI (S8 and S23) S-RNases of almond were constructed, using comparative modeling tools. The modeled structures consisted of mixed α and β folds, with six helices and six β-strands. However, the self-compatible (Sf) RNase contained an additional extended loop between the conserved domains RC4 and C5, which may be involved in the manifestation of self-compatibility in almond

Molecular modeling of RNases from almond involved in serlf-incompatibility

Gametophytic self-incompatibility (GSI) is a natural mechanism in flowering plants, including almond and other fruit tree species, to prevent inbreeding and promote outcrossing. It is typically under the control of a specific locus, known as the S-locus, which contains at least two genes. The first gene encodes glycoproteins with ribonuclease (S-RNase) activity in the pistils, and the second is a specific F-box gene (SFB) expressed in the pollen. In Solanaceae, Scrophulariaceae and Rosaceae, active S-RNases in the style are essential for rejection of haploid pollen, when the S-allele of pollen matches one of two S-alleles of the diploid pistil. The S-RNase was first identified in Prunus more than 20 years ago, whereas SFB was identified only recently. In spite of the knowledge of the genetic structure of the female and male determinants of GSI, the nature of their mutual interactions at genetic and biochemical levels remain unclear. Thus, detailed understanding of the protein structure involved in GSI may help in discovering how proteins involved in GSI function and fulfil their biological roles. To this aim, three-dimensional (3D) models of a self-compatible (Sf) and a self-incompatible (S8) S-RNase of almond have been constructed, using comparative modelling tools. The molecular models of Sf and S8 showed that 3D architectures of their folds had the same topology as typical members of the RNase T2 family. The modelled structures consisted of mixed α and β folds, with six helices and six beta-strands.Peer Reviewedalmondself-(in) compatibility3D modellingRNase T2Publishe

Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars "Nonpareil" and "Lauranne." Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.info:eu-repo/semantics/publishedVersio

Genotyping by sequencing in almond : SNP discovery, linkage mapping, and marker sesign

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars "Nonpareil" and "Lauranne." Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond

Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.info:eu-repo/semantics/publishedVersio

Transposons played a major role in the diversification between the closely related almond and peach genomes: Results from the almond genome sequence

We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long‐read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein‐coding genes and 6,747 non‐coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (P. persica) diverged around 5.88 Mya. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions/kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). TEs have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. TEs may also be at the origin of important phenotypic differences between both species, and in particular, for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.info:eu-repo/semantics/publishedVersio

Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

[ES]: Reducir la pérdida de variabilidad genética es un reto en los programas de mejora debido al repetido uso de un escaso número de genotipos. Para estudiar la variabilidad genética del almendro en su mejora a nivel mundial se utilizaron datos genealógicos de 222 variedades y selecciones provenientes de Argentina, Australia, Francia, Grecia, Israel, Italia, Rusia, España y EE. UU. Se calculó la consanguinidad, las relaciones por parejas y la contribución genética para todos los genotipos. Los resultados señalan dos principales líneas de mejora basadas en tres cultivares ‘Tuono’–‘Cristomorto’ y ‘Nonpareil’. Existen 75 descendientes directos (compartiendo 30) de ‘Tuono’ o ‘Cristomorto’ mientras que ‘Nonpareil’ tiene 72 descendientes directos. El coeficiente medio de consanguinidad de los genotipos analizados fue 0,036, con 13 presentando una elevada consanguinidad. Los programas de mejora de EE. UU. (0,06), Francia (0,05) y España (0,03) mostraron consanguinidad. De acuerdo con su contribución genética, las variedades modernas de Israel, Francia, EE. UU., España y Australia, se basan en seis, cinco, cuatro, cuatro y dos genotipos fundadores principales respectivamente. Entre el grupo de 65 genotipos con el alelo Sf de autocompatibilidad, el coeficiente medio de relación fue de 0,133, con ‘Tuono’ como principal fundador (23,75% de la contribución genética total).[EN]: Loss of genetic variability is a challenge increasing when breeding due to the repeated use of a reduced number of founders. Pedigree data of 222 almond cultivars and selections were used to study worldwide genetic variability in modern programs from Argentina, Australia, France, Greece, Israel, Italy, Russia, Spain and USA. Inbreeding coefficients, pairwise relatedness and genetic contribution were calculated. The results reveal two mainstream breeding lines based in three cultivars: ‘Tuono’–‘Cristomorto’ and ‘Nonpareil’. Direct descendants from ‘Tuono’ or ‘Cristomorto’ account to 75 (sharing 30 descendants), while ‘Nonpareil’ has 72 direct descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.036, with 13 genotypes presenting a high inbreeding coefficient. Breeding programs from USA (0.06), France (0.05) and Spain (0.03) showed inbreeding. According to their genetic contribution, modern cultivars from Israel, France, USA, Spain and Australia, trace back to six, five, four, four and two main founders respectively. Among the group of 65 genotypes with the Sf allele for self–compatibility, the mean relatedness coefficient was 0.133, with ‘Tuono’ as main founder (23.75% of total genetic contribution).Peer reviewe

Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

Background: Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results: Using an almond intraspecific cross between ‘Nonpareil’ and ‘Lauranne’ (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P < 0.05. Due to the large number of skewed markers in the linkage group 7, the potential existence of deleterious gene(s) was assessed in the group. Integrated maps produced by two different mapping methods using JoinMap® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions: We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.Iraj Tavassolian, Gholmereza Rabiei, Davina Gregory, Mourad Mnejja, Michelle G Wirthensohn, Peter W Hunt, John P Gibson, Christopher M Ford, Margaret Sedgley, and Shu-Biao W

The Almond Tree Genome

Editors: Raquel Sánchez-Pérez, Angel Fernandez i Marti, Pedro Martinez-GomezThis book brings together the latest information on almond genomics and transcriptomics, with a particular focus on cutting-edge findings, tools, and strategies employed in genome sequencing and analysis with regard to the most important agronomic traits. Cultivated almond [(Prunus dulcis (Miller) D. A. Webb, syn. Prunus amygdalus Batsch., Amygdalus communis L., Amygdalus dulcis Mill.)] is a tree crop producing seeds of great economic interest, and adapted to hot and dry climates. Domesticated in Southeast Asia, its small diploid genome and phenotypic diversity make it an ideal model to complement genomics studies on peach, generally considered to be the reference Prunus species. Both represent consanguineous species that evolved in two distinct environments: warmer and more humid in the case of peach, and colder and xerophytic for almond. The advent of affordable whole-genome sequencing, in combination with existing Prunus functional genomics data, has now made it possible to leverage the novel diversity found in almond, providing an unmatched resource for the genetic improvement of this speciesPeer reviewe

Genetic variability and leaf waxes of some Eucalyptus species with horticultural potential / Michelle Gabrielle Wirthensohn

Copies of author's previously published articles inserted.Bibliography: leaves 122-137.xiv, 158 leaves, [16] leaves of plates : ill. (chiefly col.) ; 30 cm.18 species of Eucalyptus were subjected to trials to investigate their suitability for floriculture and the effect of pruning for cut flower production. Post harvest trials were conducted to assess the vase life of cut stems, and the effect of pulsing and simulated transportation on vase life. Species of Eucalyptus were also studied for changes in wax morphology of juvenile foliage with leaf age and for variation in amount and composition of leaf epicuticular wax. Molecular markers were discovered which may facilitate the management of E. gunnii breeding and selection for the cut foliage industry, by providing an initial screen for glaucousness. 12 species were recommened for the cut foliage industry.Thesis (Ph.D.) -- University of Adelaide, Dept. of Horticulture, Viticulture and Oenology, 199