SNP Genotyping with Amplifluor-Like Method

Khassanova, Gulmira; Khalbayeva, Sholpan; Serikbay, Dauren; Mazkirat, Shynar; Bulatova, Kulpash; Utebayev, Maral; Shavrukov, Yuri

doi:10.1007/978-1-0716-3024-2_14

Cited by 2 publications

(4 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genetic control of photoperiodic response of plants to day-length is one of the major causes and limitations for the distribution of soybean crops to higher latitude areas [5]. This also applies to Kazakhstan, a Central Asian country, where very high-yield soybean cultivars are produced and grown in the southern part at 43 • N, but more adapted soybean genotypes with a neutral reaction to photoperiod are required to grow in the northern part with a higher latitude at 50-53 • N [35][36][37].…”

Section: Discussionmentioning

confidence: 99%

“…Plant genotyping using molecular markers is one of the most rapidly developing areas in plant biology [35] and crop breeding [36], including soybean [37]. Simple sequence repeat (SSR) or microsatellite markers [38,39] are not only 'simple' in their structure but also in the application, where laboratories with regular equipment and tools can carry out routine molecular analyses in various crops including soybean [40].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan

et al. 2023

View full text Add to dashboard Cite

The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92–102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan

et al. 2023

View full text Add to dashboard Cite

show abstract

“…This method, described in Jatayev et al (2017) and Mohanrao et al (2023), is a method of allele-specific PCR that is used for SNP genotyping [7,35]. This method has been applied for agricultural research before [36,37]. The method functions basically as follows.…”

Section: Amplifluor-based Snp Genotypingmentioning

confidence: 99%

“…This method appears to be a cheap, accurate method of genotyping a small number of SNPs at a large scale. While it is reportedly very cheap and easy to design and use, it is still limited by the number of SNPs it can target in a given assay [36,37]. In Shavrukov et al (2016), the amplifluor method was applied to study gene expression differences relative to drought resistance in wheat [37].…”

Section: Amplifluor-based Snp Genotypingmentioning

confidence: 99%

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Lawrie,

Massey

2023

Applied Biosciences

View full text Add to dashboard Cite

Single Nucleotide Polymorphisms (SNPs) are variations that occur at single nucleotides in the genome and are present at an appreciable level in a population. SNPs can be linked to phenotypes of interest, for example diseases, recent adaptations, or species hybridization. They can also be used to study phylogeny and evolutionary history. Technologies that rapidly identify and catalog the presence of SNPs in a DNA sample are known as SNP genotyping panels, and they continue to undergo rapid development. Such methods have great utility across the agricultural sciences in diverse areas such as plant and animal breeding, pathogen and pesticide resistance identification, outbreak tracing, and hybridization detection. Here, we provide an overview of 14 different SNP genotyping technologies and weigh some of the pros and cons associated with each platform. This review is not comprehensive or technical, nor does it aim to be. Rather, the objective is to provide an introduction to the landscape of genotyping technologies for researchers who do not have experience with these methods. Three classes of SNP genotyping methods are Polymerase Chain Reaction (PCR)-based (nine different methods), microarray-based (one method), and Next-Generation Sequencing (NGS)-based (four different methods). We discuss how each genotyping class is suited for different niches; PCR-based has a low SNP count and high sample number, microarray-based has a very high SNP count and a moderate sample number, and Next-Generation Sequencing-based has a moderate SNP count and moderate number of samples. Included are basics about how the methods function and example use cases of each method. Additionally, we introduce and discuss the potential for the MinION sequencer in SNP genotyping. For each technology, we provide insights into cost, equipment needs, labor costs, experimental complexity, data output complexity, and accessibility. These considerations address the feasibility of deploying the technologies in an agricultural science environment.

show abstract

SNP Genotyping with Amplifluor-Like Method

Cited by 2 publications

References 27 publications

Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan

Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan

Agrigenomic Diversity Unleashed: Current Single Nucleotide Polymorphism Genotyping Methods for the Agricultural Sciences

Contact Info

Product

Resources

About