Identification of Markers Associated with Yield Traits and Morphological Features in Maize (Zea mays L.)

Tomkowiak, Agnieszka; Bocianowski, Jan; Wolko, Łukasz; Adamczyk, J.; Mikołajczyk, Sylwia; Kowalczewski, Przemysław Łukasz

doi:10.3390/plants8090330

Cited by 15 publications

(11 citation statements)

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“…Extensive transcriptome profiling comparing inbred lines and their hybrids by means of DNA micro-array technology in maize [ 15 , 16 , 17 ] and allelic transcription variation due to cis -regulatory elements in maize [ 18 ] indicated that transcriptional regulation and transcriptional overdominance could play an important role as molecular mechanisms establishing hybrid vigor. Tomkowiak et al [ 19 ] examined inbred maize lines and consequently identified three SilicoDArT markers, 4591115, 7059939, and 5587991, related to the size of crop structure features. Tomkowiak et al [ 20 ] also tested SNP and SilicoDArT molecular markers on the same pool of plant materials in the context of selecting the parental components for heterosis crossing, and concluded that such markers could be useful in selecting plant material.…”

Section: Introductionmentioning

confidence: 99%

Dependence of the heterosis effect on genetic distance, determined using various molecular markers

et al. 2020

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AbstractA number of studies have shown that the greater the genetic diversity of parental lines, the greater the heterosis effect. Genetic or phenotypic variation can be estimated by genotype testing on the basis of the observations obtained through prediction (a priori) or the observations and studies (a posteriori). The first method uses data such as the genealogy of a given subject and the information about its geographical origin. The second method is based on the phenotypic observation and studies, as well as on the molecular research. The development of molecular genetics and genotype testing methods at the DNA level has made it possible to rapidly assess the genetic variability regardless of the modifying effect of the environment. The aim of this study was to determine the relationship between the degree of relatedness and the DNA polymorphism (determined using AFLP, RAPD, and SSR markers) of inbred maize lines and the effect of hybrid-form heterosis. Our analysis demonstrated that the parental components for heterosis crosses can be selected on the basis of the genetic similarity determined using the molecular SSR markers and the Jaccard, Kluczyński, Nei, and Rogers coefficients. Molecular AFLP markers proved less useful for selecting the parental components, but may be used to group lines with incomplete origin data. In the case of the RAPD markers, no clear relationship between genetic distance and the heterosis effect was found in this study.

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Section: Introductionmentioning

confidence: 99%

Dependence of the heterosis effect on genetic distance, determined using various molecular markers

et al. 2020

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“…It is an effective diagnostic technique for examining genetic diversity. The approach yields higher polymorphic markers, including codominant SNPs and dominant silicoDArT (Tomkowiak et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of selected Moringa oleifera lam. Provenances from the coastal region of Kenya

Sarah Kwamboka Ondieki,

Carol W. Hunja,

Geoffrey M. Muluvi

et al. 2023

Magna Sci. Adv. Res. Rev.

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Moringa oleifera Lam (syn. M. Pterygosperma Gaertn) is one of the most economically important crops widely cultivated globally. Traditionally, it has been used as a remedy for conditions such as diabetes, inflammation, cancer, bacterial, viral, and fungal infections, joint pain and heart disease. Moringa oleifera has also been utilized for human consumption, as forage and for water purification. Considering it is a cross pollinated plant, M. oleifera has huge variability. Due to the fast-growing nature and adaptability to variable climatic conditions, M. oleifera has been popularly cultivated in Coastal and Eastern Kenya. Studying the genetic diversity of the drumstick tree is essential in selecting valuable genotypes and for improvement of its cultivars for improved breeding programs. The use of marker-assisted selection of cultivar for the desired traits will benefit faster breeding programs. Single nucleotide polymorphisms (SNPs), being the most recent molecular markers, were used in this study. Seventeen M. oleifera provenances from Coastal Kenya were analyzed by genotyping by sequencing (GBS). Briefly, M. oleifera leaves were homogenized, crushed and DNA extracted, genome complexity reduction and library preparation was carried out followed by barcoding, electrophoresis, pooling, preparation of sequencing libraries and sequencing. Next generation sequencing (NGS) technologies, Illumina Hiseq 2500, was used for sequencing and SNP mining. Binning was carried out to remove noise. In silico assembly of sequence contigs was undertaken. Data analysis was undertaken using DArT R and KDCompute Platforms. Genetic characterization was achieved by carrying out cluster analysis, principle coordinate analysis (PCoA), 3D plot and phylogenetic tree. One hundred and sixty four (164) genotypes were identified. It was evident from the analysis undertaken that the genotypes consistently clustered into four clades/groups. However, the clusters obtained by each analysis tool comprised different genotypes due to the assumptions employed by each tool. The similarity coefficient from Hierarchical clustering ranged from 63% to 100% indicating that the genotypes had low variability. An interactive and highly robust 3D plot was produced using DArT R (Adegenet package). Interestingly, Pwani University genotypes clustered separately. It is noteworthy that these genotypes consistently clustered uniquely and independently irrespective of the tool used. This is possibly due to the seeds being of unique origin. Nevertheless, the high similarity between the genotypes could be attributed to the M. oleifera plants in the various provenances having the same ancestry. Given the high frequency of SNPs and their involvement as a source of allele variations, this research could contribute to the discovery of associations between gene allelic forms and phenotypes, enabling the alleles to be linked to desirable traits (fast growth and high seed production).

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“…The methodology used for next-generation sequencing was described in detail in the publication presenting the research by Tomkowiak et al [ 53 ]. The DArTseq analysis was performed at Diversity Arrays Technology Pty Ltd. (Canberra, Australia).…”

Section: Methodsmentioning

confidence: 99%

Associative and Physical Mapping of Markers Related to Fusarium in Maize Resistance, Obtained by Next-Generation Sequencing (NGS)

Sobiech

Tomkowiak

Nowak³

et al. 2022

IJMS

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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. , 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., 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.

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Identification of Markers Associated with Yield Traits and Morphological Features in Maize (Zea mays L.)

Cited by 15 publications

References 44 publications

Dependence of the heterosis effect on genetic distance, determined using various molecular markers

Dependence of the heterosis effect on genetic distance, determined using various molecular markers

Genetic diversity of selected Moringa oleifera lam. Provenances from the coastal region of Kenya

Associative and Physical Mapping of Markers Related to Fusarium in Maize Resistance, Obtained by Next-Generation Sequencing (NGS)

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