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

A peach germplasm collection for increasing the genetic diversity in European breeding programs

Trabajo presentado al VIII International Peach Symposium, celebrado en Matera (Italia) del 17 al 20 de junio de 2013.European breeding programs are hampered by the low intraspecific genetic diversity, which is due to the self-compatibility of this homozygous species along with the low number of genotypes introduced and thus used for breeding. In 2009, four research institutions which carried out peach breeding programs in Aragon, Catalonia, Valencia and Murcia, started a new peach germplasm collection worldwide aimed at enlarging the peach genetic diversity available for breeding. The plant material was introduced from germplasm collections located in China, Central Asia, Iran and the USA (National Germplasm Repository of Davis). Sanitary status was assessed by molecular diagnosis of known diseases caused by virus, viroid, bacteria and phytoplasm pathogens. Healthy plant material was grafted and maintained in quarantine conditions. The new germplasm collection was established in two places: Zaragoza as high chilling and Murcia as low chilling requirements. Pomological and molecular data were gathered and a public database constructed. The descriptors used were from the National Center for Genetic Resources from the INIA. Introduced budwood and seeds resulted in more than 250 new genotypes from 15 countries. The molecular analysis of a subset of the collection with 21 SSR markers evenly distributed in the genome resulted in a high number of alleles per SSR (mean A=9.5) and low observed heterozygosity (mean Ho=0.38). Variability was further assessed by geographic origin. Population structure analysis revealed the existence of 8 subpopulations explained, in some cases, by the geographic origin of the genotypes. As a result of the project a new database containing 95 accessions and 38 variables is available.Peer reviewe

Over-expression of a tomato N-acetyl-L-glutamate synthase gene (SlNAGS1) in Arabidopsis thaliana results in high ornithine levels and increased tolerance in salt and drought stresses

A single copy of the N-acetyl-L-glutamate synthase gene (SlNAGS1) has been isolated from tomato. The deduced amino acid sequence consists of 604 amino acids and shows a high level of similarity to the predicted Arabidopsis NAGS1 and NAGS2 proteins. Furthermore, the N-terminus ArgB domain and the C-terminus ArgA domain found in SlNAGS1 are similar to the structural arrangements that have been reported for other predicted NAGS proteins. SlNAGS1 was expressed at high levels in all aerial organs, and at basic levels in seeds, whereas it was not detected at all in roots. SlNAGS1 transcript accumulation was noticed transiently in tomato fruit at the red-fruit stage. In addition, an increase of SlNAGS1 transcripts was detected in mature green tomato fruit within the first hour of exposure to low oxygen concentrations. Transgenic Arabidopsis plants have been generated expressing the SlNAGS1 gene under the control of the cauliflower mosaic virus (CaMV) 35S promoter. Three homozygous transgenic lines expressing the transgene (lines 1-7, 3-8, and 6-5) were evaluated further. All three transgenic lines showed a significant accumulation of ornithine in the leaves with line 3-8 exhibiting the highest concentration. The same lines demonstrated higher germination ability compared to wild-type (WT) plants when subjected to 250 mM NaCl. Similarly, mature plants of all three transgenic lines displayed a higher tolerance to salt and drought stress compared to WT plants. Under most experimental conditions, transgenic line 3-8 performed best, while the responses obtained from lines 1-7 and 6-5 depended on the applied stimulus. To our knowledge, this is the first plant NAGS gene to be isolated, characterized, and genetically modified

Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)

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.info:eu-repo/semantics/publishedVersio

Development and Evaluation of an Axiom^TM 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

Journal of Experimental Botany, Page 1 of 13

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A PEACH GERMPLASM COLLECTION FOR INCREASING THE GENETIC DIVERSITY IN EUROPEAN BREEDING PROGRAMS

Trabajo presentado al VIII International Peach Symposium, celebrado en Matera (Italia) del 17 al 20 de junio de 2013.European breeding programs are hampered by the low intraspecific genetic diversity, which is due to the self-compatibility of this homozygous species along with the low number of genotypes introduced and thus used for breeding. In 2009, four research institutions which carried out peach breeding programs in Aragon, Catalonia, Valencia and Murcia, started a new peach germplasm collection worldwide aimed at enlarging the peach genetic diversity available for breeding. The plant material was introduced from germplasm collections located in China, Central Asia, Iran and the USA (National Germplasm Repository of Davis). Sanitary status was assessed by molecular diagnosis of known diseases caused by virus, viroid, bacteria and phytoplasm pathogens. Healthy plant material was grafted and maintained in quarantine conditions. The new germplasm collection was established in two places: Zaragoza as high chilling and Murcia as low chilling requirements. Pomological and molecular data were gathered and a public database constructed. The descriptors used were from the National Center for Genetic Resources from the INIA. Introduced budwood and seeds resulted in more than 250 new genotypes from 15 countries. The molecular analysis of a subset of the collection with 21 SSR markers evenly distributed in the genome resulted in a high number of alleles per SSR (mean A=9.5) and low observed heterozygosity (mean Ho=0.38). Variability was further assessed by geographic origin. Population structure analysis revealed the existence of 8 subpopulations explained, in some cases, by the geographic origin of the genotypes. As a result of the project a new database containing 95 accessions and 38 variables is available.Peer reviewe

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

A draft assembly of the almond genome

Almond is one of the oldest cultivated nut crops with its origin in central and western Asia. The selection of the sweet type [i](Prunus dulcis[/i]) distinguishes the domesticated almond from its bitter wild relatives. It is economically important, especially in California with the highest worldwide production, followed by Australia and Spain. The almond belongs to the same subgenus as the peach, for which there already exists a reference genome. However, to fully understand the genetic underpinnings marking the key phenotypic differences between almond and peach, we have sequenced the genome of the ‘Texas’ almond, one of the traditional cultivars producing a sweet nut. Whole-genome shotgun sequencing of Illumina paired-end libraries gave an initial low-contiguity assembly of 512 Mbp, nearly double the estimated genome size. Counting of k-mers indicates a 275 Mbp genome with substantial heterozygosity as well as repetitive sequence. In order to tackle both problems, we constructed a fosmid library and sequenced 68 pools of ~500 clones per pool. We then assembled the pools, merged them and finished the assembly by scaffolding with paired end and mate pair libraries, which resulted in a 240 Mbp assembly with a scaffold N50 of 500 kbp, a contig N50 of 33.5 kbp and CEGMA completeness of 99%. Two thirds of the assembly was anchored to the peach-almond genetic map, and using re-sequencing data of peach-almond hybrids and their parents we inferred the two haplotypes of the sequenced almond tree. We performed additional validation of the assembly using Oxford Nanopore MinION sequencing