Development of DArT-based PCR markers for selecting drought-tolerant spring barley

Genetic diversity and population structure in Ethiopian mustard (Brassica carinata A. Braun) revealed by high-density DArTSeq SNP genotyping

BACKGROUND

Ethiopian mustard (Brassica carinata (A) Braun) is a promising oilseed crop with the potential for sustainable biofuel and bio-industrial applications. Despite the presence of diverse germplasms in Ethiopia, their genetic diversity remains largely unexplored. This study evaluated the genetic diversity and population structure of 188 B. carinata genotypes using high-density Single Nucleotide Polymorphism (SNP) markers generated though DArTseq™ Genotyping-by-Sequencing (GBS). Of the 15,515 identified DArTSeq SNPs, 3,793 high-quality markers were retained and used to analyze the genetic diversity and population structure.

RESULTS

The results from STRUCTURE, principal coordinate analysis (PCoA), and neighbor-joining tree analyses revealed two slightly distinct subpopulations, with Pop1 predominantly comprising genotypes from the Oromia and Amhara regions (86.17%), whereas Pop2 primarily consisted of released varieties, suggests the influence of targeted selection. Despite the presence of subpopulations, PCoA indicated a relatively limited overall genetic diversity among the genotypes. Analysis of Molecular Variance (AMOVA) revealed higher genetic variation within populations (65.19%) than between populations (34.81%), resulting in low genetic differentiation (PhiPT = 0.02) and high gene flow (Nm = 5.74). Notably, subpopulation formation was not strongly correlated with geographical origin, highlights that factors beyond geography, such as gene flow and selection pressure, may have played a significant role in shaping the observed genetic diversity. Genetic diversity indices revealed a slightly low-to-moderate variation within the B. carinata populations, as evidenced by the slightly low expected heterozygosity (He = 0.21) and moderate polymorphic information content (PIC = 0.36).

CONCLUSION

Overall, this study revealed a moderate level of genetic diversity within the evaluated B. carinata genotypes. The results offer valuable insights into the genetic structure of this species and highlight the need for targeted strategies to enhance genetic diversity in future breeding initiatives and conservation efforts.

DArTseq-based silicoDArT and SNP markers reveal the genetic diversity and population structure of Kenyan cashew (Anacardium occidentale L.) landraces

Cashew (Anacardium occidentale L.) is an important tree grown worldwide for its edible fruits, nuts and other products of industrial applications. The ecologically sensitive cashew-growing region in coastal Kenya is significantly affected by rising temperatures, droughts, floods, and shifting rainfall patterns. These changes adversely impact cashew growth by altering flowering patterns, increasing pests and diseases, and causing postharvest losses, which ultimately result in reduced yields and tree mortality. This is exacerbated by the long juvenile phase, high heterozygosity, lack of trait correlations, large mature plant size, and inadequate genomic resources. For the first time, the Diversity Array Technology (DArT) technology was employed to identify DArT (silicoDArT) and single nucleotide polymorphisms (SNPs) markers for genomic understanding of cashew in Kenya. Cashew leaf samples were collected in Kwale, Kilifi and Lamu counties along coastal Kenya followed by DNA extraction. The reduced libraries were sequenced using Hiseq 2500 Illumina sequencer, and the SNPs called using DarTsoft14. A total of 27,495 silicoDArT and 17,008 SNP markers were reported, of which 1340 silicoDArT and 824 SNP markers were used for analyses after screening, with > 80% call rate, > 95% reproducibility, polymorphism information content (PIC ≥  0.25) and one ratio (>0.25). The silicoDArT and SNP markers had mean PIC values ranging from 0.02-0.50 and 0.0-0.5, with an allelic richness ranging from 1.992 to 1.994 for silicoDArT and 1.862 to 1.889 for SNP markers. The observed heterozygosity and expected values ranged from 0.50-0.55 and 0.34-0.37, and 0.56-0.57 and 0.33 for both silicoDArT and SNP markers respectively. Understanding cashew genomics through the application of SilicoDArT and SNP markers is crucial for advancing cashew genomic breeding programs aimed at improving yield and nut quality, and enhancing resistance or tolerance to biotic and abiotic stresses. Our study presents an overview of the genetic diversity of cashew landraces in Kenya and demonstrates that DArT systems are a reliable tool for advancing genomic research in cashew breeding.

New PCR-specific markers for pollen fertility restoration QRfp-4R in rye (Secale cereale L.) with Pampa sterilizing cytoplasm

Pampa cytoplasmic male sterility phenomenon is used extensively in the rye hybrid breeding programs. It relies on sterilizing action of the cytoplasm resulting in non-viable pollen of female lines. The sterilizing effect is problematic for reversion, and efficient restores are needed. The most promising QTL is located on chromosome 4R, but other chromosomes may also code the trait. Advanced recombinant inbred lines formed bi-parental mapping population genotyped with DArTseq markers. Genetic mapping allowed the seven linkage groups to construct with numerous markers and represent all rye chromosomes. Single marker analysis and composite interval mapping were conducted to identify markers linked to the pollen fertility. Association mapping was used to detect additional markers associated with the trait. A highly significant QTL (QRfp-4R) that explained 42.3% of the phenotypic variation was mapped to the distal part of the long arm of the 4R chromosome. The markers localized in the QRfp-4R region achieve R² association values up to 0.59. The homology of the 43 marker sequences to the loci responsible for fertility restoration in other species and transcription termination factor (mTERF) linked to Rf genes was established. Ten markers were successfully converted into PCR-specific conditions, and their segregation pattern was identical to that of unconverted DArTs.

Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa

Cytoplasmic male sterility (CMS) is a widely applied plant breeding tool for hybrid seed production. The phenomenon is often caused by chimeric genes with altered open reading frames (ORFs) located in the mitochondrial genomes and expressed as novel genotoxic products that induce pollen abortion. The fertility of CMS plants can be restored by nuclear-encoded genes that inhibit the action of ORFs responsible for pollen sterility. A recombinant inbred line (RIL) mapping population S64/04/01, encompassing 175 individuals, was used for genetic map construction and identification of quantitative trait loci (QTLs) responsible for fertility restoration in rye (Secale cereale L.) with CMS Pampa. The genetic map of all seven rye chromosomes included 15,516 SNP and silicoDArT markers and covered 1070.5 cm. Individual QTLs explaining 60% and 5.5% of the fertility trait’s phenotypic variance were mapped to chromosomes 4R (QRft-4R) and 5R (QRft-5R), respectively. Association mapping identified markers with the highest R² value of 0.58 (p value = 2.21E-28). Markers showing the highest associations with the trait were also mapped to the 4R chromosome within the QRft-4R region. Based on marker sequence homology, putative genes involved in pollen fertility restoration were suggested. Five silicoDArTs were converted into PCR-based markers for further breeding purposes.

Reference Genome Anchoring of High-Density Markers for Association Mapping and Genomic Prediction in European Winter Wheat

In this study, we anchored genotyping-by-sequencing data to the International Wheat Genome Sequencing Consortium Reference Sequence v1.0 assembly to generate over 40,000 high quality single nucleotide polymorphism markers on a panel of 376 elite European winter wheat varieties released between 1946 and 2007. We compared association mapping and genomic prediction accuracy for a range of productivity traits with previous results based on lower density dominant DArT markers. The results demonstrate that the availability of RefSeq v1.0 supports higher precision trait mapping and provides the density of markers required to obtain accurate predictions of traits controlled by multiple small effect loci, including grain yield.

Association mapping of drought tolerance-related traits in barley to complement a traditional biparental QTL mapping study

Association mapping of drought-related traits in barley was used to increase the density of existing QTL maps without recreating mapping populations. We used 109 spring barley genotypes exhibiting high or low drought tolerance to elucidate the associations between diversity array technology sequencing (DArTseq) and single nucleotide polymorphism (SNP) markers and various physiological parameters related to plant responses to drought conditions. The study was performed in controlled conditions (growth chambers), drought tolerance was phenotyped in the four-leaf seedlings. We identified 58 associations including 34 new markers (i.e., 16 DArTseq and 18 SNP markers). The results for three markers were consistent with the data obtained in an earlier traditional biparental QTL mapping study. The regions neighboring markers on linkage group 2H contained the highest number of significant marker-trait associations. Five markers related to the photosynthetic activity of photosystem II were detected on chromosome 4H. The lowest number of associations were observed for the sequences neighboring DArT markers on linkage group 6H. A chromosome 3H region related to water use efficiency and net photosynthesis rate in both biparental QTL, and association study, may be particularly valuable, as these parameters correspond to the ability of plants to remain highly productive under water deficit stress. Our findings confirm that association mapping can increase the density of existing QTL maps without recreating mapping populations.

A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL) population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM^-1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%). QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain) and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2) was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.

Development and characterization of polymorphic EST based SSR markers in barley (Hordeum vulgare)

In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study. A cDNA library of the cultivar Gwanbori was constructed for use in analysis of genetic relationships, and 58 EST-SSR markers were developed and characterized. In total, 47 SSR markers were employed to analyze polymorphisms. A relationship dendrogram based on the polymorphism data was constructed to compare genetic diversity. We found that the polymorphism information content among the examined cultivars was 0.519, which indicates that there is low genetic diversity among Korean barley cultivars. The results obtained in this study may be useful in preventing redundant investment in new cultivars and in resolving disputes over seed patents. Our approach can be used by companies and government groups to develop different cultivars with distinguishable markers. In addition, the developed markers can be used for quantitative trait locus analysis to improve both the quantity and the quality of cultivated barley.

Magnetic Activated-ATP@Fe3O4 Nanocomposite as an Efficient Fenton-Like Heterogeneous Catalyst for Degradation of Ethidium Bromide

Magnetic attapulgite-Fe₃O₄ nanocomposites (ATP-Fe₃O₄) were prepared by coprecipitation of Fe₃O₄ on ATP. The composites were characterized by scanning electron microscopey, X-ray diffractometry, Brunauer-Emmett-Teller analysis, X-ray photoelectron spectroscopy, energy dispersive spectrometer and transmission electron microscopy. Surface characterization showed that Fe₃O₄ particles with an average size of approximately 15 nm were successfully embedded in matrix of ATP. The capacity of the Fe₃O₄-activated ATP (A-ATP@Fe₃O₄) composites for catalytic degradation of ethidium bromide (EtBr, 80 mg/L) at different pH values, hydrogen peroxide (H₂O₂) concentrations, temperatures, and catalyst dosages was investigated. EtBr degradation kinetics studies indicated that the pseudo-first-order kinetic constant was 2.445 min⁻¹ at T = 323 K and pH 2.0 with 30 mM H₂O₂, and 1.5 g/L of A-ATP@Fe₃O₄. Moreover, a regeneration study suggested that A-ATP@Fe₃O₄ maintained over 80% of its maximal EtBr degradation ability after five successive cycles. The effects of the iron concentrations and free radical scavengers on EtBr degradation were studied to reveal possible catalytic mechanisms of the A-ATP@Fe₃O₄ nanocomposites. Electron Paramagnetic Resonance revealed both hydroxyl (∙OH) and superoxide anion (∙O₂⁻) radicals were involved in EtBr degradation. Radical scavenging experiment suggested EtBr degradation was mainly ascribed to ∙OH radicals, which was generated by reaction between Fe²⁺ and H₂O₂ on the surface of A-ATP@Fe₃O₄.

Genetic Map of Triticale Integrating Microsatellite, DArT and SNP Markers

Triticale (×Triticosecale Wittm) is an economically important crop for fodder and biomass production. To facilitate the identification of markers for agronomically important traits and for genetic and genomic characteristics of this species, a new high-density genetic linkage map of triticale was constructed using doubled haploid (DH) population derived from a cross between cultivars 'Hewo' and 'Magnat'. The map consists of 1615 bin markers, that represent 50 simple sequence repeat (SSR), 842 diversity array technology (DArT), and 16888 DArTseq markers mapped onto 20 linkage groups assigned to the A, B, and R genomes of triticale. No markers specific to chromosome 7R were found, instead mosaic linkage group composed of 1880 highly distorted markers (116 bins) from 10 wheat chromosomes was identified. The genetic map covers 4907 cM with a mean distance between two bins of 3.0 cM. Comparative analysis in respect to published maps of wheat, rye and triticale revealed possible deletions in chromosomes 4B, 5A, and 6A, as well as inversion in chromosome 7B. The number of bin markers in each chromosome varied from 24 in chromosome 3R to 147 in chromosome 6R. The length of individual chromosomes ranged between 50.7 cM for chromosome 2R and 386.2 cM for chromosome 7B. A total of 512 (31.7%) bin markers showed significant (P < 0.05) segregation distortion across all chromosomes. The number of 8 the segregation distorted regions (SDRs) were identified on 1A, 7A, 1B, 2B, 7B (2 SDRs), 5R and 6R chromosomes. The high-density genetic map of triticale will facilitate fine mapping of quantitative trait loci, the identification of candidate genes and map-based cloning.

Diversity Arrays Technology-based PCR markers for marker assisted selection of aluminum tolerance in triticale (x Triticosecale Wittmack)

The tolerance of triticale (x Triticosecale Wittmack) cultivars to aluminum (Al) stress observed in acid soils is an important agronomic trait affecting seed yield. Traditionally, breeding of Al-tolerant cultivars was selection based; for example, using a physiological test. However, such selection methods are relatively slow and require numerous plants for phenotype evaluation. Alternatively, DNA-based molecular marker systems could be applied to identify markers useful for selection purposes. Among many marker platforms available, Diversity Arrays Technology (DArT) is one of the most promising. DArT markers preselected for conversion to specific PCR assays were chosen based on association mapping studies using diverse materials. Forty-nine DArT markers were selected and tested for redundancy based on their segregation patterns and sequences, and 40 were successfully converted into specific PCR assays. However, only 24 of these proved to be polymorphic. Where possible, the chromosomal locations of the converted markers were verified. The markers assigned to chromosome 7R that were the most highly correlated with Al-tolerant and non-tolerant plants were chosen for marker assisted selection using genetically diverse triticale materials.