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Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane. Genes (Basel) 2022; 13:genes13081477. [PMID: 36011388 PMCID: PMC9408448 DOI: 10.3390/genes13081477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding
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Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Jatayev S, Hu YG, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET. FRONTIERS IN PLANT SCIENCE 2021; 12:747886. [PMID: 35082803 PMCID: PMC8784781 DOI: 10.3389/fpls.2021.747886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- *Correspondence: Ruslan Kalendar
| | - Akmaral Baidyussen
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
- Yuri Shavrukov
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