- Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. - Full list of author information is available at the end of the article. - which is an important cereal crop grown worldwide on 220 million ha, accounts for 20% of the total calories con- sumed by the global population. - One of the mile- stones toward the development of high-yielding and climate-smart ‘next generation varieties’ was the se- quencing of the 17 Gb allohexaploid wheat (AABBDD) genome [5, 6]. - Evaluating the extent of the genetic diversity among adapted, elite germplasm may be useful for esti- mating the genetic variability among segregating pro- geny [7]. - Irrespective of the final system used for hybrid seed production, the components should represent separate gene pools to. - In the present study, 509 European wheat culti- vars and advanced breeding lines (Table S1) were exam- ined regarding their genetic diversity and population structure. - and d) define a core collection representative of the European gene pool currently used for breeding.. - Tyrka et al. - Additionally, 86.3 and 88.9% of the SNP and silicoDArT markers were mapped uniquely (i.e., the maximum score was recorded for a single location), respectively. - A com- parative analysis of the distribution of trimmed se- quences classified by the sequence length and maximum BLAST score indicated that most of the SNP and silico- DArT markers between 20 and 50 bp had a maximum score below 95%, which corresponded to decreased specificity.. - Following the filtering of the SNP markers and of the silicoDArT markers were retained.. - The highest quality markers mapped at a single position, with a score of 100, constituted 25.7 and 38.8% of the SNP and silico- DArT markers, respectively (Table S3).. - The heterozygosity of the SNP markers did not exceed 0.75, with 10,310 markers exhibiting a heterozygosity of less than 0.1 (Fig. - Additional analyses were performed to clarify the in- creased heterozygosity of the markers in subgenome D.. - Further ana- lyses of the total number of hits for the sequences with one best hit indicated that the SNPs from subgenome D (ascribed based on the best hit) were mapped more fre- quently in alternative loci than the SNPs from subge- nomes A or B (chi-square test, p <. - An ex- ample of the SNP marker clusters for chromosome 1A is presented in Fig. - Analyses of the LD between inter- secting SNP and silicoDArT markers revealed some pairs with a low LD resulting from non-unique mapping or genotyping errors.. - A prediction of the effects of 3060 SNPs (23.27%) located in protein-coding regions uncovered variants with “HIGH” effects with “LOW” (synonymous) effects, and with “MODERATE” (nonsynonymous) effects.. - The GO annotation and overrepresentation analysis of the 48 genes harboring SNPs related to PCO1 revealed several overrepresented processes (i.e., response to auxin stimulus, response to hormone stimulus, response to endogenous stimulus, and response to organic substance) (genes: TraesCS2 D02G494600, TraesCS2B02G522500, TraesCS2A02G49 4300, and TraesCS2B02G522200). - The population structure visualized by a PCoA of the kinship (coancestry coefficients) matrix of accessions de- rived from SNP and silicoDArT markers revealed similar features (Fig. - 6 Visualization of the population structure revealed via principal coordinate analysis of kinship matrices for SNP and silicoDArT data. - Two of the genes with polymor- phisms related to the registration year were orthologs of the GA2 gene involved in gibberellin biosynthesis, and a third gene was identified as an ortholog of the SAG12 senescence-associated gene of Arabidopsis thaliana. - S5) and as a list of the selected accessions (Fig. - In one case, the difference between the data for A1 and A2 was due to cultivars Florus and Franz, with mean yields differing in A1 by 0.33% (of the yield of. - 7 Comparison of the distributions of kinship coefficients derived from SNP and silicoDArT data (a) and within groups of accessions (b). - The shift to PAV markers in the SNP method may be due to the sensi- tivity of the applied restriction enzymes (PstI, HpaII, and HhaI) to cytosine methylation and the destruc- tion of some fragments by excess TaqI endonuclease.. - As a consequence of Table 3 Genotypes of the oldest and newest varieties at six loci associated with the registration year. - 8 Plot of the average within-group similarity relative to the number of groups (a). - For wheat, which has a large and complex genome, an analysis of the LD decay enabling the evaluation of marker density is especially important for high-quality association mapping and marker-assisted selection [53–. - The 5 Mb LD decay means that 3400 equally dispersed, non-redundant markers should be sufficient to scan 17 Gb of the wheat genome. - The markers were unequally distributed among three subgenomes, with fewer markers in subgenome D (16.1 and 19.7% of the SNPs and silicoDArTs, respectively).. - An analysis of the whole-genome resequencing data for eight wheat lines identified 3.3 million SNPs, with 41% located in subge- nome A, 49% in subgenome B, and 10% in subgenome D [48]. - As suggested by Würschum et al. - Rosyara et al. - [62], Lopes et al.. - [63], Liu et al. - [64], and Eltaher et al. - [57] as well as in a study by Mir et al. - The heterozygosity of SNP markers in the studied population did not exceed 0.75. - Moreover, the heterozy- gosity of nearly a third of the markers was lower than 0.1. - Similarly, Liu et al. - In contrast, Bhatta et al. - During mapping, marker se- quences were compared with the reference genome sequence of the primitive ‘Chinese Spring’ variety.. - that most of the primitive alleles in modern wheat var- ieties and lines are from subgenome D rather than from subgenomes A and B.. - In an earlier study by Wang et al. - Additionally, Akhunov et al.. - Chao et al. - The low LD in subgenome D in our population may have been a consequence of a relatively high heterozygosity in this subgenome reflecting the actual hemizygous state of some of the markers.. - In the current study, only 23.1% of the SNPs (3129) were located in coding regions. - Only a few (ap- proximately 1%) of the polymorphic SNPs detected in coding regions were classified as highly affecting protein functions. - Most of the polymorphic SNP loci had low or moderate effects. - In the current study, the transi- tions and transversions respectively accounted for 63 and 37% of the SNPs, which were consistent with the corresponding percentages calculated by Wang et al.. - Genetic diversity and population structure. - In a study by Wang et al. - [57] and Kumar et al. - Despite the weak yield po- tential, some of the group no. - 5 accessions, distinct from most of the contemporary wheat Polish breeding mate- rials, may be valuable resources for agronomically desir- able traits.. - The differ- ences in yielding of the oldest and newest varieties were visible in the studied population, although they were not as large as the differences demonstrated in [82], primar- ily because we used data from contemporary experi- ments, whereas in [82] historical data, obtained under different management, were used. - An important objective of this study was to construct a core collection representative of the structure of the whole collection. - As described by Odong et al. - First, the whole collection is represented by the most similar accessions, whereas the second type charac- terizes the extreme accessions of the whole collection and the third type represents the distribution of the ac- cessions in the original set. - The first core collection type is ideally a uniform representation of the original genetic content, unlike the second type, which includes entries that are as diverse as possible, and the third type, which provides an overview of the composition of the whole collection. - It consisted of 47 accessions, representing ap- proximately 17% of the whole collection. - that the core collection should comprise between 5 and 20% of the base collection. - Additionally, a comparison of the distributions of kinship coefficients in the whole col- lection and in the core collections confirmed that our re- sults satisfy the requirements for the third core collection type described by Odong et al. - The two versions of the core collection corresponding to two agricultural practices were very similar, implying that the genotype × environ- ment interaction minimally influenced our approach.. - Because of their quality and regardless of the rela- tively few markers located in coding sequences, the mapped populations may be used for association map- ping, which will serve as the basis for the marker- assisted genomic selection of agronomically important traits. - The core collection of wheat cultivars representative of the genetic diversity of the currently grown European wheat germplasm described herein may help breeders to increase the genetic diversity of wheat and develop het- erotic pools to more efficiently exploit heterosis. - Advanced breeding lines were represented by 232 accessions from the ongoing programs of the Plant Breeding Strzelce (STH) and Poznań Plant Breeding (PHR) companies (Table S1). - The processing of the DArTseq data produced two data- sets. - This enabled the application of the same principles for determining marker parameters, including the variant frequency, minor variant frequency (MVF), and polymorphism information content (PIC), for the SNPs and silicoDArTs.. - all authors contributed to writing and critical reviewing of the manuscript. - A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. - Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding. - Longin CFH, et al. - Longin C, et al. - Bohra A, Jha UC, Adhimoolam P, et al. - Genetic diversity in the U.S.. - Sansaloni C, Petroli C, Jaccoud D, et al. - Courtois B, Audebert A, Dardou A, et al. - Sehgal D, Vikram P, Sansaloni CP, et al. - Jordan KW, Wang S, Lun Y, et al. - Riaz A, Hathorn A, Dinglasan E, et al. - Into the vault of the Vavilov wheats:. - Shi F, Tibbits J, Pasam RK, et al. - Ren J, Sun D, Chen L, et al. - Tadesse W, Ogbonnaya FC, Jighly A, et al. - Massman J, Cooper B, Horsley R, et al. - Sequence-based mapping of the polyploid wheat genome. - Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. - Würschum T, et al. - Genetic characterization of the wheat association mapping initiative (WAMI) panel for dissection of complex traits in spring wheat. - Liu J, He Z, Rasheed A, et al. - Bhatta M, Morgounov A, Belamkar V, et al. - Analysis of the bread wheat genome using whole-genome shotgun sequencing. - Allopolyploidy - a shaping force in the evolution of wheat genomes. - Kumar D, Chhokar V, Sheoran S, et al. - Reanalysis of the historical series of UK variety trials to quantify the contributions of genetic and environmental factors to trends and variability in yield over time. - Rosyara U, Kishii M, Payne T, et al
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