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Associative and Physical Mapping of Markers Related to Fusarium in Maize Resistance, Obtained by Next-Generation Sequencing (NGS)
On the basis of studies carried out in the last few years, it is estimated that maize diseases cause yield losses of up to 30% each year. The most dangerous diseases are currently considered to be caused by fungi of the genus Fusarium, which are the main culprits of root rot, ear rots, and stalk rot. Early plant infection causes grain diminution, as well as a significant deterioration in nutritional value and fodder quality due to the presence of harmful mycotoxins. Therefore, the aim of the research was to identify new markers of the SilicoDArT and SNP type, which could be used for the mass selection of varieties resistant to fusarium. The plant material consisted of 186 inbred maize lines. The lines came from experimental plots belonging to two Polish breeding companies: Plant Breeding Smolice Ltd., (Co., Kobylin, Poland). Plant Breeding and Acclimatization Institute—National Research Institute Group (51°41′23.16″ N, 17°4′18.241″ E), and Małopolska Plant Breeding Kobierzyce, Poland Ltd., (Co., Kobierzyce, Poland) (50°58′19.411″ N, 16°55′47.323″ E). As a result of next-generation sequencing, a total of 81,602 molecular markers were obtained, of which, as a result of the associative mapping, 2962 (321 SilicoDArT and 2641 SNP) significantly related to plant resistance to fusarium were selected. Out of 2962 markers significantly related to plant resistance in the fusarium, seven markers (SilicoDArT, SNP) were selected, which were significant at the level of 0.001. They were used for physical mapping. As a result of the analysis, it was found that two out of seven selected markers (15,097—SilicoDArT and 58,771—SNP) are located inside genes, on chromosomes 2 and 3, respectively. Marker 15,097 is anchored to the gene encoding putrescine N-hydroxycinnamoyltransferase while marker 58,771 is anchored to the gene encoding the peroxidase precursor 72. Based on the literature data, both of these genes may be associated with plant resistance to fusarium. Therefore, the markers 15,097 (SilicoDArT) and 58,771 (SNP) can be used in breeding programs to select lines resistant to fusarium.
Identification and Analysis of Candidate Genes Associated with Maize Fusarium Cob Resistance Using Next-Generation Sequencing Technology
The pressure to reduce mineral fertilization and the amount of pesticides used has become a factor limiting production growth, as has the elimination of many crop protection chemicals from the market. A key condition for this to be an effective form of protection is the use of varieties with higher levels of resistance. The most effective and fastest way to assist in the selection and control of pathogens is the conducting of genome-wide association studies. These are useful tools for identifying candidate genes, especially when combined with QTL mapping to map and validate loci for quantitative traits. The aim of this study was to identify new markers coupled to genes that determine maize plant resistance to fusarium head blight through the use of next-generation sequencing, association and physical mapping, and to optimize diagnostic procedures to identify selected molecular markers coupled to plant resistance to this fungal disease. As a result of field experiments and molecular analyses, molecular markers coupled to potential genes for resistance to maize ear fusariosis were selected. The newly selected markers were tested against reference genotypes. As a result of the analyses, it was found that two markers (11801 and 20607) out of the ten that were tested differentiated between susceptible and resistant genotypes. Marker number 11801 proved to be the most effective, with a specious product of 237 bp appearing for genotypes 1, 3, 5, 9 and 10. These genotypes were characterized by a field resistance of 4–6 on the 9° scale (1 being susceptible, 9 being resistant) and for all genotypes except 16 and 20, which were characterized by a field resistance of 9. In the next step, this marker will be tested on a wider population of extreme genotypes in order to use it for the preliminary selection of fusarium-resistant genotypes, and the phosphoenolpyruvate carboxylase kinase 1 gene coupled to it will be subjected to expression analysis.
Using Genome-Wide Association Studies to Reveal DArTseq and SNP Loci Associated with Agronomic Traits and Yield in Maize
Next-generation sequencing (NGS) has revolutionized genetic research, enabling the massive, rapid, and relatively inexpensive analysis of the genomes, transcriptomes, and epigenomes of various organisms, including maize. Therefore, this paper uses NGS, association mapping, and physical mapping to identify candidate genes associated with yield structure traits and yield in maize (Zea mays L.). Furthermore, expression analysis of selected candidate genes was performed to confirm their contribution to yield formation. The plant material used for the study was 186 F1 hybrids and 20 reference genotypes (high-yielding and low-yielding). Field experiments were conducted simultaneously in two locations (in Smolice and Kobierzyce). NGS yielded a total of 45,876 molecular markers (24,437 SilicoDArT markers and 21,439 SNP markers) relevant to yield and crop structure. The largest number of markers in both localities (Smolice and Kobierzyce) was related to: the number of grain rows (6960), dry matter content after harvest (6616), the number of grains in a row (6721), mass of grain from the cob (6616), and cob length (6564). The smallest number of markers in both localities was related to yield (t ha−1) (1114) and yield from the plot (1237). To narrow down the number of markers for physical mapping, ten were selected from all the significant ones associated with the same traits in both localities (Kobierzyce and Smolice). Significant markers included eight silicoDArT markers (459199, 2447305, 4768759, 4579916, 4764335, 2448946, 2492509, 4774802) and two SNP markers (9692004, 5587791). These markers were used for physical mapping. These markers are located on chromosomes 7, 8, and 10. Some of these markers are located at a considerable distance from characterized genes or within uncharacterized genes. Two markers caught our attention: SNP 5587791 and silicoDArT 4774802. The first one is located on chromosome 8 inside exon 5 of the LOC100383455 U-box domain-containing protein 7 gene, the second marker is also located on chromosome 8 near (300 bp) the LOC103635953 putative WUSCHEL-related homeobox 2 protein gene. Our own research and literature reports indicate the usefulness of next-generation sequencing, association mapping, and physical mapping for identifying candidate genes associated with economically important traits in maize. Furthermore, two genes characterized in detail in the publication, LOC100383455 U-box domain-containing protein 7 gene and LOC103635953 putative WUSCHEL-related homeobox 2 protein gene, may be involved in processes related to maize yield.
Identification and Analysis of Candidate Genes Associated with Yield Structure Traits and Maize Yield Using Next-Generation Sequencing Technology
The main challenge of agriculture in the 21st century is the continuous increase in food production. In addition to ensuring food security, the goal of modern agriculture is the continued development and production of plant-derived biomaterials. Conventional plant breeding methods do not allow breeders to achieve satisfactory results in obtaining new varieties in a short time. Currently, advanced molecular biology tools play a significant role worldwide, markedly contributing to biological progress. The aim of this study was to identify new markers linked to candidate genes determining grain yield. Next-generation sequencing, gene association, and physical mapping were used to identify markers. An additional goal was to also optimize diagnostic procedures to identify molecular markers on reference materials. As a result of the conducted research, 19 SNP markers significantly associated with yield structure traits in maize were identified. Five of these markers (28629, 28625, 28640, 28649, and 29294) are located within genes that can be considered candidate genes associated with yield traits. For two markers (28639 and 29294), different amplification products were obtained on the electrophorograms. For marker 28629, a specific product of 189 bp was observed for genotypes 1, 4, and 10. For marker 29294, a specific product of 189 bp was observed for genotypes 1 and 10. Both markers can be used for the preliminary selection of well-yielding genotypes.
Identification of SNP and SilicoDArT Markers and Characterization of Their Linked Candidate Genes Associated with Maize Smut Resistance
The implementation of biological advancements in agricultural production is the response to the needs of the agricultural sector in the 21st century, enabling increased production and improved food quality. Biological progress in the maize breeding and seed industries is unique in terms of their social and ecological innovation aspects. It affects agricultural productivity and the adaptation of cultivated maize varieties to market demands and changing climate conditions without compromising the environment. Modern maize resistance breeding relies on a wide range of molecular genetic research techniques. These technologies enable the identification of genomic regions associated with maize smut resistance, which is crucial for characterizing and manipulating these regions. Therefore, the aim of this study was to identify molecular markers (SilicoDArT and SNP) linked to candidate genes responsible for maize smut resistance, utilizing next-generation sequencing, as well as association and physical mapping. By using next-generation sequencing (NGS) and statistical tools, the analyzed maize genotypes were divided into heterotic groups, which enabled the prediction of the hybrid formula in heterosis crosses. In addition, Illumina sequencing identified 60,436 SilicoDArT markers and 32,178 SNP markers (92,614 in total). For association mapping, 32,900 markers (26,234 SilicoDArT and 6666 SNP) meeting the criteria (MAF > 0.25 and the number of missing observations < 10%) were used. Among the selected markers, 61 were highly statistically significant (LOD > 2.3). Among the selected 61 highly statistically significant markers (LOD > 2.3), 10 were significantly associated with plant resistance to maize smut in two locations (Smolice and Kobierzyce). Of the 10 selected markers, 3 SilicoDArT (24016548, 2504588, 4578578) and 3 SNP (4779579, 2467511, 4584208) markers were located within genes. According to literature reports, of these six genes, three (ATAD3, EDM2, and CYP97A3) are characterized proteins that may play a role in the immune response that develops in response to corn smut infection. In the case of genotypes belonging to the same origin groups, markers linked to these genes can be used to select varieties resistant to corn smut. These markers will also be tested on genotypes belonging to other maize origin groups to demonstrate their universality.