- Background: One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. - The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces.. - The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsp. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article Pascual et al. - of the daily protein and food calories of the human popula- tion. - Roughly 90 to 95% of the wheat produced in the world is common, or bread wheat (Triticum aestivum L.. - The remainder of the world’s wheat production includes about 35–40 million tons of durum wheat (T. - The successful genomics-assisted breeding of any crop will be enhanced by a thorough understanding of the species’ genetic diversity. - For GWAS analysis, the optimum diverse panel must be genotyped with a set of molecular markers covering as much of the genome of the species as possible [24], but the population structure needs to be investigated to avoid false associations between phenotypes and markers [25].. - The Spanish wheat landraces conserved at the Na- tional Plant Genetic Resources Center (CRF-INIA) and maintained in the national collection were collected in the first half of the twentieth century. - Several studies have shown the great variability of the Spanish durum wheat accessions compared to other germplasm collec- tions [26–29]. - However, no genetic description of the bread wheat landraces has been reported, and the high- throughput genomic characterization of the durum wheat landraces remains to be fully realized.. - The aim of the present study was to characterize two col- lections of durum and bread wheat landraces from CRF- INIA by using the DArTseq-GBS approach. - The specific objectives of the present investigation were: (1) to assess the genomic diversity of a set of durum wheat accessions comprising 191 Spanish landraces and 23 reference var- ieties, (2) to assess the genomic diversity of a set of bread wheat accessions comprising 189 Spanish landraces and 29 reference varieties, and (3) to compare the genetic diversity of landraces and modern cultivars in both wheat species.. - When the markers were located in the T. - Ac- cording to the raw data, approximately 58% of the DArTs, and 37% of the SNPs were not located in the T. - around 64% of raw DArTs and 41% of raw SNPs were not located in the bread wheat reference genome, a percentage similar to that of the durum wheat (Table 1). - In durum wheat, 82% of the DArTs and 75% of the SNP markers showed a PIC value >. - Genetic structure of the durum wheat collection. - All but one (BGE021775) of the 14 accessions belonging to subsp. - dicoccon were grouped in Pop5, and all 37 of the subsp. - All of the 140 subsp. - Pop6 showed the least genetic differentiation from the rest of the populations, including those of subsp. - When the diversity between the three subspe- cies was estimated, regardless of the structured popula- tions, the dicoccon and durum landraces showed the highest value of genetic differentiation between the sub- species (F ST = 0.42) whereas subsp. - We also explored the genomic structure of the durum wheat collection, including the landraces and reference varieties, through a principal coordinate analysis (PCoA) based on the 9324 filtered SNP markers. - The first two principal coordinates explained 21% of the total vari- ation. - accessions were differentiated from the others by PCo1, but the difference between turgidum and dicoccon was due to PCo2, demonstrating that different sets of markers are responsible of the genetic divergence among subspe- cies, as detected in the Hs analysis. - The representation of allelic variation in the PCoA showed that most of the accessions carrying the winter- type allele, vrn-A1, were grouped together and corre- sponded to dicoccon accessions (Fig. - Most of the ref- erence cultivars and subsp. - durum accessions carried the Vrn-A1c allele, and almost all of the subsp. - When analyzed within the population structure, all but one durum ac- cession from Pop2, Pop7, and Pop1 presented the Vrn- A1c allele, which was also identified in the 80% of the durum wheat landraces clustered in Pop 6. - This accession, col- lected at the end of the 1990, is characterized by early-. - b Collection sites of the different T. - When GPS coordinate data were not available, the coordinates of the capital of the province of origin were used. - Genetic structure of the bread wheat collection. - In the whole landrace collection, the D est. - As in durum wheat, we investigated the allelic variabil- ity of the Vrn-A1 gene in relation to the bread wheat population structure. - The representation of Glu-B1 alleles specific to Iberian landraces in the PCoA showed that the accessions that carried the Glu-B1f allele (HMW-GS 13 + 16) were clus- tered on the right side of the PCoA and corresponded to most of the Pop4 samples. - Some of the landraces located closer to the reference varieties were collected in the 1990s (e.g., BGE025410), and according to their early flowering and lower height phenotypes (http://webx.inia.. - b Collection sites of the different T.. - When GPS coordinate data were not available, the coordinate of the capital of the province of origin were used. - Approximately, 40% of the SNP markers were fixed in the durum wheat reference varieties, and the number of mono- morphic markers (3791) was comparable to that found in subsp. - We decided to explore the genetic diversity of these valuable materials, by performing an analysis at the genomic level of 380 selected landraces representing the genetic variability of the wheat collection main- tained at the Spanish Plant Genetic Resources Center, which is composed of more than 1600 accessions.. - This is the first report of the high-throughput genotyp- ing by GBS of Spanish wheat germplasm. - 7 Genetic diversity (Hs) distribution across the genome in the reference varieties and landraces. - In our study, 50 K SNP and 100 K DArT markers were analyzed in each of the wheat species, from which we were able to select approximately 10 K SNP and 40 K DArT high quality markers. - The availability of the refer- ence bread wheat genome [4] and durum wheat genome [5] allowed the marker location to be performed in both species. - Several previous studies have shown the reduced diversity of the wheat D gen- ome, which has been explained by the close genetic dis- tance between the Ae. - The informativeness of the markers was assessed from their PIC values, and the distribution and average PIC value were found to be comparable to those previously reported in wheat . - Population structure was assessed with the fastSTRUCTURE algorithm, which was developed by the authors of the classical STRUCTURE software but shows faster runs and provides comparable ancestry esti- mates and prediction accuracies [42]. - Durum wheat landraces. - cultivated and well adapted to the dry-summer condi- tions of the South. - In a previous study, SSRs (Single Sequence Repeats) were used to assess the gen- etic structure of the collection of durum wheat landraces analyzed here and 9 populations were established. - Some of the populations included more than one subspecies and several genotypes could not be classified into any population [27]. - Vernalization genes are the main determinants of the growth habit (i.e., winter or spring) in temperate cereals, and by affecting the vegetative to reproductive transition, these genes are involved in the ability of wheat plants to adapt to a wide range of environments [48]. - None of the durum wheat accessions characterized here showed the Vrn-A1a allele described in spring-habit hexaploid wheat varieties, which is in accordance with what has been found in other studies [50, 51]. - All of the available data seem to indicate that this allele appeared during wheat evolution after the last polyploidization event. - In our study, 78% of the durum accessions presented this allele, but almost all turgidum accessions (83%) carried Vrn-A1b, and 7 out of the 11 dicoccon landraces characterized for Vrn-A1 carried the winter vrn-A1 allele (Fig. - The pres- ence of the spring-habit associated alleles Vrn-A1b and Vrn-A1c in the remaining four dicoccon accessions is re- markable. - Under the predicted climate change scenario, temperature warming may prevent the fulfilment of the requirements for vernalization in current temperate zones, thus having a negative global impact on winter wheat yields. - The identified clusters seemed to be influenced by the accessions’ ori- gin relatively little, although some geographic areas were predominant in some of the populations. - The exchange of seeds by farmers has been noted as one of the likely explanations for the low or absent influence of geographic origin on the genetic structure of durum wheat landraces in Iran, the Central Fertile Crescent and Ethiopia . - The great majority of the Spanish bread wheat landraces conserved at CRF-INIA belong to Triticum aestivum subsp. - The population stratification of the bread wheat panel identified four groups of landraces with high divergence according to the obtained F ST values. - This clustering reflected the geographic origin of the accessions better than in the subsp. - One of the four groups detected (Pop4) was clearly more genetically distant. - Most of the accessions from this population show spring growth habit and carry the f al- lele at the Glu-B1 locus. - Vrn-A1 has been de- scribed as the main genotypic determinant of the vernalization requirements of temperate crops, but there are other genes, such as Vrn-B1 and Vrn-D1, whose allelic variability has not yet been characterized in these Spanish wheat landrace collections.. - Concerning the durum wheat materials examined here, the great genetic divergence between the bulk of the landraces and the reference set is remarkable (Fig. - Moreover, some of the durum landraces were located closer to turgidum and dicoccon accessions than to the reference varieties (which all belong to subsp. - Nevertheless, our results supported little involvement of Spanish landraces in the development of the modern durum wheat varieties grown in Spain at present.. - The clustering of the land- races and reference varieties could also indicate a pedi- gree relationship. - Hence, it is possible that some of the landraces characterized in our study were among the un- identified “Mediterranean” local varieties utilized by the early breeders as starting material to develop pure lines that were further involved in cross-breeding (see http://. - The overall genetic diversity of the reference cultivars was much lower than that of the landraces in both spe- cies (Table 2. - As expected, some of the chromosomes including fixed regions har- bored genes related to agronomically important pheno- types, such as Rht-D1, associated with dwarf phenotype, and Vrn-B1, associated with vernalization response, on bread wheat chromosomes 4D and 5B, respectively [68, 69]. - Coupling this analysis with future GWA studies will help to identify the traits under- lying each of the fixed regions detected in this work.. - The replacement of local landraces by high-yielding wheat varieties that began at the time of the Green Revolution has led to a loss of genetic variation in crop wheat varieties. - A complexity reduction method including two en- zymes (PstI and HpaII) was used to create a genome representation of the set of samples. - of base call accuracy for at least 50% of the bases. - More stringent filtering was also performed on barcode se- quences using a Phred quality score of 10, which repre- sent 99.9% of base call accuracy for at least 75% of the bases. - The DArT markers were scored as binary data (0/1) indicating the presence or ab- sence of a marker in each accession, and the SNP markers were scored as 0/1/2 indicating the presence of the reference allele in homozygosity, the alternative al- lele in homozygosity or a heterozygous genotype, re- spectively. - To locate the markers in the. - For comparison with the population structure based on GBS-DArTseq markers, we investigated the allelic variability of functional markers in the Vrn-A1 gene, one of the most determinant loci involved in the transition from vegetative to reproductive growth [74, 75]. - First, when several markers presented the same al- lelic profile, all of the markers but the one with the least missing data were removed. - When the genotypic values for a marker was only 0 and 2, we considered the heterozy- gous calling [2] to be an error caused by the presence of the SNP marker flanking sequence in homoeologous ge- nomes. - Fixed genomic regions in the reference varieties were identified by performing a scan of the Hs values along the different chromosomes. - Excel file with the description of the accessions analyzed, passport data, population according to fastSTRUCTURE analysis, HMW-GS and VRN-A1 alleles. - Durum wheat. - Figure showing the genetic diversity (Hs) distribution across the A and B genomes in the different durum wheat subspecies.. - JM Carrillo for helpful comments during the preparation of the original and revised versions of the manuscript.. - ML is a recipient of a predoctoral fellowship from the Programa Propio of the Universidad Politécnica de Madrid.. - Development of DArT marker platforms and genetic diversity assessment of the US collection of the new oilseed crop lesquerella and related species. - Analysis of genetic variability in a sample of the durum wheat (Triticum durum Desf.) Spanish collection based on gliadin markers. - The structure of the Aegilops tauschii genepool and the evolution of hexaploid wheat. - Exploiting the repetitive fraction of the wheat genome for high-throughput single-nucleotide polymorphism discovery and genotyping. - Tetraploid wheat landraces in the Mediterranean basin: taxonomy, evolution and genetic diversity. - Positional cloning of the wheat vernalization gene VRN1. - The genes of the green revolution. - Control by homoeologous group 1 chromosomes of the high-molecular weight subunits of glutenin, a major protein of wheat endosperm
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