Diversity and Genetic structure of the Spanish collection of durum wheat (Triticum turgidum L) landraces

The objectives of this study were to assess diversity and genetic structure of a collection of Spanish durum wheat (Triticum turgidum L) landraces, using SSRs, DArTs and gliadin-markers, and to correlate the distribution of diversity with geographic and climatic features, as well as agro-morphological traits. A high level of diversity was detected in the genotypes analyzed, which were separated into nine populations with a moderate to great genetic divergence among them. The three subspecies taxa, dicoccon, turgidum and durum, present in the collection, largely determined the clustering of the populations. Genotype variation was lower in dicoccon (one major population) and turgidum (two major populations) than in durum (five major populations). Genetic differentiation by the agro-ecological zone of origin was greater in dicoccon and turgidum than in durum. DArT markers revealed two geographic substructures, east-west for dicoccon and northeast-southwest for turgidum. The ssp. durum had a more complex structure, consisting of seven populations with high intra-population variation. DArT markers allowed the detection of subgroups within some populations, with agro-morphological and gliadin differences, and distinct agro-ecological zones of origin. Two different phylogenetic groups were detected; revealing that some durum populations were more related to ssp. turgidum from northern Spain, while others seem to be more related to durum wheats from North Afric

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit f lesh color in Japanese plum

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the f lesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red f lesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the f lesh color natural variation in Japanese plum and provide a molecular marker for MAS.info:eu-repo/semantics/publishedVersio

Genetic Structure of Modern Durum Wheat Cultivars and Mediterranean Landraces Matches with Their Agronomic Performance

A collection of 172 durum wheat landraces from 21 Mediterranean countries and 20 modern cultivars were phenotyped in 6 environments for 14 traits including phenology, biomass, yield and yield components. The genetic structure of the collection was ascertained with 44 simple sequence repeat markers that identified 448 alleles, 226 of them with a frequency lower than 5%, and 10 alleles per locus on average. In the modern cultivars all the alleles were fixed in 59% of the markers. Total genetic diversity was HT = 0.7080 and the genetic differentiation value was GST = 0.1730. STRUCTURE software allocated 90.1% of the accessions in five subpopulations, one including all modern cultivars, and the four containing landrace related to their geographic origin: eastern Mediterranean, eastern Balkans and Turkey, western Balkans and Egypt, and western Mediterranean. Mean yield of subpopulations ranged from 2.6 t ha-1 for the western Balkan and Egyptian landraces to 4.0 t ha-1 for modern cultivars, with the remaining three subpopulations showing similar values of 3.1 t ha-1. Modern cultivars had the highest number of grains m-2 and harvest index, and the shortest cycle length. The diversity was lowest in modern cultivars (HT = 0.4835) and highest in landraces from the western Balkans and Egypt (HT = 0.6979). Genetic diversity and AMOVA indicated that variability between subpopulations was much lower (17%) than variability within them (83%), though all subpopulations had similar biomass values in all growth stages. A dendrogram based on simple sequence repeat data matched with the clusters obtained by STRUCTURE, improving this classification for some accessions that have a large admixture. landraces included in the subpopulation from the eastern Balkans and Turkey were separated into two branches in the dendrogram drawn with phenotypic data, suggesting a different origin for the landraces collected in Serbia and Macedonia. The current study shows a reliable relationship between genetic and phenotypic population structures, and the connection of both with the geographic origin of the landraces.The research was funded by the Ministerio de Economía y competitividad project AGL-2006-09226-C02-01, and Dr. Jose Miguel Soriano is funded by Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (http://www.mineco.gob.es/)

Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

Correction 21 Jun 2012: Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, et al. (2012) Correction: Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. PLOS ONE 7(6): 10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ~75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species

Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis

Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar “Skovfoged” and higher expression in the flat “Grand’mere.” The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.C.D. was supported by “DON CARLOS ANTONIO LOPEZ” Abroad Postgraduate Scholarship Program, BECAL-Paraguay. V.C.A. is a recipient of grant PRE2019-088780 funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future.” This research was supported by project PID2021-128885OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe.” This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 817970 (INVITE). We acknowledge support from the CERCA Programme (“Generalitat de Catalunya”), and the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-2015-0533) and 2020-2023 (CEX2019-000902-S) both funded by MCIN/AEI/10.13039/501100011033.info:eu-repo/semantics/publishedVersio

Diversity analysis

International audienc

Evaluation of hydroelectric potential through modeling in the Geographic Information System and algorithm in Matlab in the Department of Amazonas

La presente tesis busca evaluar el potencial hidroeléctrico mediante el uso del Sistema de Información Geográfica y algoritmo en Matlab en el departamento de Amazonas, con el fin de estimar ubicaciones potenciales para el desarrollo de centrales hidroeléctricas de pasada. Para llevar a cabo esta investigación, se realiza el desarrollo de un modelo de elevación digital del área de estudio haciendo uso del software ArcGIS. EL modelo de elevación digital comprende: la sectorización del departamento de Amazonas en base a las cuencas que este presenta, la red hídrica del departamento, los centros poblados, áreas protegidas y sitios arqueológicos. Por otro lado, el algoritmo en Matlab facilita la ubicación de sitios potenciales, empleando una serie de códigos, los cuales trabajan con características geográficas establecidas para las posibles ubicaciones. Después de haber estimado las ubicaciones potenciales, se hace uso del modelo de balance hídrico, estimando los caudales medios anuales. En la presente tesis se estiman dichos caudales con un 85% de persistencia, para obtener un resultado que se asemeje a la realidad de la zona. Una vez estimados los caudales, se pasó a realizar las restricciones: políticas, demográficas, ambientales y económicas, con el fin de obtener las opciones con mayor viabilidad. Se obtuvieron 21 posibles ubicaciones, las cuales producen entre 3 a 10 MW aproximadamente de energía hidroeléctrica. De las 21 ubicaciones obtenidas se escogieron 5 localidades las cuales generan 103.89 GW.h al año. Energia que satisface el consumo de la población, sobrepasando la energía generada por las estaciones existentes.Despite the fact that the department of Amazonas has one of the densest water networks, it is one of the departments with minimal hydroelectric energy production, demonstrating the lack of use of water resources. For this reason, an improvement is proposed in evaluation of the hydroelectric potential of department in order to increase the production of hydroelectric energy, and in turn reduce the production of thermal energy, avoiding gas emissions. The most important tool used in the optimization of evaluation is: the Geographic Information System and the Matlab coding. Similar to hydrometeorological information obtained from the PISCO product was used. The result of this study shows that with new evaluation of the hydroelectric potential it is possible to increase the production of hydroelectric energy and therefore satisfy the demand for hydroelectric energy of the population of Amazonas department.Tesi

An efcient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions. A case study in the Prunus salicina LG3-MYB10 genes cluster

Background: Genome complexity is largely linked to diversifcation and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In both duplicated and non‑dupli‑cated genes, much of the variability in agronomic traits is caused by large as well as small and middle scale structural variants (SVs), which highlights the relevance of the identifcation and characterization of complex variability between genomes for plant breeding. Results: Here we improve and demonstrate the use of CRISPR‑Cas9 enrichment combined with long‑read sequenc-ing technology to resolve the MYB10 region in the linkage group 3 (LG3) of Japanese plum (Prunus salicina). This region, which has a length from 90 to 271 kb according to the P. salicina genomes available, is associated with fruit color variability in Prunus species. We demonstrate the high complexity of this region, with homology levels between Japanese plum varieties comparable to those between Prunus species. We cleaved MYB10 genes in fve plum varieties using the Cas9 enzyme guided by a pool of crRNAs. The barcoded fragments were then pooled and sequenced in a single MinION Oxford Nanopore Technologies (ONT) run, yielding 194 Mb of sequence. The enrichment was confrmed by aligning the long reads to the plum reference genomes, with a mean read on‑target value of 4.5% and a depth per sample of 11.9x. From the alignment, 3261 SNPs and 287 SVs were called and phased. A de novo assembly was constructed for each variety, which also allowed detection, at the haplotype level, of the variability in this region. Conclusions: CRISPR‑Cas9 enrichment is a versatile and powerful tool for long‑read targeted sequencing even on highly duplicated and/or polymorphic genomic regions, being especially useful when a reference genome is not available. Potential uses of this methodology as well as its limitations are further discussed. Keywords: Cas9 enrichment, Complex regions, Long‑read, Targeted sequencing, Variability, Gene duplication, MYB10info:eu-repo/semantics/publishedVersio

Role of FRIGIDA and FLOWERING LOCUS C in Determining Variation in Flowering Time of Arabidopsis

Arabidopsis (Arabidopsis thaliana) accessions provide an excellent resource to dissect the molecular basis of adaptation. We have selected 192 Arabidopsis accessions collected to represent worldwide and local variation and analyzed two adaptively important traits, flowering time and vernalization response. There was huge variation in the flowering habit of the different accessions, with no simple relationship to latitude of collection site and considerable diversity occurring within local regions. We explored the contribution to this variation from the two genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), previously shown to be important determinants in natural variation of flowering time. A correlation of FLC expression with flowering time and vernalization was observed, but it was not as strong as anticipated due to many late-flowering/vernalization-requiring accessions being associated with low FLC expression and early-flowering accessions with high FLC expression. Sequence analysis of FRI revealed which accessions were likely to carry functional alleles, and, from comparison of flowering time with allelic type, we estimate that approximately 70% of flowering time variation can be accounted for by allelic variation of FRI. The maintenance and propagation of 20 independent nonfunctional FRI haplotypes suggest that the loss-of-function mutations can confer a strong selective advantage. Accessions with a common FRI haplotype were, in some cases, associated with very different FLC levels and wide variation in flowering time, suggesting additional variation at FLC itself or other genes regulating FLC. These data reveal how useful these Arabidopsis accessions will be in dissecting the complex molecular variation that has led to the adaptive phenotypic variation in flowering time