14 research outputs found
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
Linkage disequilibrium, genetic association mapping and gene localization in crop plants
A seed coat cyanohydrin glucosyltransferase is associated with bitterness in almond ('Prunus dulcis') kernels
The secondary metabolite amygdalin is a cyanogenic diglucoside that at high concentrations is associated with intense bitterness in seeds of the Rosaceae, including kernels of almond ('Prunus dulcis' (Mill.), syn. 'Prunus amygdalus' D.A. Webb Batsch). Amydalin is a glucoside of prunasin, itself a glucosider of 'R'-mandelonitrile (a cyanohydrin). Here we report the isolation of an almond enzyme (UGT85A19) that stereo-selectively gucosylates 'R'-mandelonitrile to produce prunasin. In a survey of developing kernels from seven bitter and 11 non-bitter genotypes with polyclonal antibody raised to UGT85A19, the enzyme was found to accumulate to higher levels in the bitter types in later development. This differential accumulation of UGT85A19 is associated with more than three-fold greater mandelonitrile glucosyltrajsferase activity in bitter kernels compared with non-bitter types, and transcriptional regulation was demonstrated using quantitative-PCR analysis. UGT85A19 and its encoding transcript were most concentrated in the testa (seed coat) of the kernel compared with the embryo, and prunasin and amygdalin were differentially compartmentalised in these tissues. Prunasin was confined to the testa and amygdalin was confined to the embryo. These results are consisted with the seed coat being an important site of synthesis of prunasin as a precursor of amygdalin accumulation in the kernel. The presence of UGT85A19 in the kernel and other tissues of both bitter and non-bitter types indicates that its expression is unlikely to be a control point for amygdalin accumulation and suggests additional roles for the enzyme in almond metabolism
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
Development and Evaluation of an Axiom<sup>TM</sup> 60K SNP Array for Almond (<i>Prunus dulcis</i>)
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits
A seed coat cyanohydrin glucosyltransferase is associated with bitterness in almond (Prunus dulcis) kernels
© CSIRO 2008The secondary metabolite amygdalin is a cyanogenic diglucoside that at high concentrations is associated with intense bitterness in seeds of the Rosaceae, including kernels of almond (Prunus dulcis (Mill.), syn. Prunus amygdalus D. A. Webb Batsch). Amygdalin is a glucoside of prunasin, itself a glucoside of R-mandelonitrile (a cyanohydrin). Here we report the isolation of an almond enzyme (UGT85A19) that stereo-selectively glucosylates R-mandelonitrile to produce prunasin. In a survey of developing kernels from seven bitter and 11 non-bitter genotypes with polyclonal antibody raised to UGT85A19, the enzyme was found to accumulate to higher levels in the bitter types in later development. This differential accumulation of UGT85A19 is associated with more than three-fold greater mandelonitrile glucosyltransferase activity in bitter kernels compared with non-bitter types, and transcriptional regulation was demonstrated using quantitative-PCR analysis. UGT85A19 and its encoding transcript were most concentrated in the testa (seed coat) of the kernel compared with the embryo, and prunasin and amygdalin were differentially compartmentalised in these tissues. Prunasin was confined to the testa and amygdalin was confined to the embryo. These results are consistent with the seed coat being an important site of synthesis of prunasin as a precursor of amygdalin accumulation in the kernel. The presence of UGT85A19 in the kernel and other tissues of both bitter and non-bitter types indicates that its expression is unlikely to be a control point for amygdalin accumulation and suggests additional roles for the enzyme in almond metabolism.Tricia K. Franks, Abbas Yadollahi, Michelle G. Wirthensohn, Jennifer R. Guerin, Brent N. Kaiser, Margaret Sedgley and Christopher M. For