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Identification of starch candidate genes using SLAF-seq and BSA strategies and development of related SNP-CAPS markers in tetraploid potato
- Source :
- PLoS ONE, PLoS ONE, Vol 16, Iss 12, p e0261403 (2021)
- Publication Year :
- 2021
- Publisher :
- Public Library of Science, 2021.
-
Abstract
- Potato starch is an essential nutrient for humans and is widely used worldwide. Locating relevant genomic regions, mining stable genes and developing candidate gene markers can promote the breeding of new high-starch potato varieties. A total of 106 F1 individuals and their parents (YSP-4 × MIN-021) were used as test materials, from which 20 plants with high starch content and 20 with low starch content were selected to construct DNA pools for site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). A genomic region related to the starch traits was first identified in the 0–5.62 Mb of chromosome 2 in tetraploid potato. In this section, a total of 41 non-synonymous genes, which were considered as candidate genes related to the starch trait, were annotated through a basic local alignment search tool (BLAST) search of multiple databases. Six candidate genes for starch (PGSC0003DMG400017793, PGSC0003DMG400035245, PGSC0003DMG400036713, PGSC0003DMG400040452, PGSC0003DMG400006636 and PGSC0003DMG400044547) were further explored. In addition, cleaved amplified polymorphic sequence (CAPS) markers were developed based on single nucleotide polymorphism (SNP) sites associated with the starch candidate genes. SNP-CAPS markers chr2-CAPS6 and chr2-CAPS21 were successfully developed and validated with the F2 population and 24 tetraploid potato varieties (lines). Functional analysis and cloning of the candidate genes associated with potato starch will be performed in further research, and the SNP-CAPS markers chr2-CAPS6 and chr2-CAPS21 can be further used in marker-assisted selection breeding of tetraploid potato varieties with high starch content.
- Subjects :
- Physiology
Science
Single Nucleotide Polymorphisms
Quantitative Trait Loci
Carbohydrates
Solanum
Research and Analysis Methods
Polymorphism, Single Nucleotide
Starches
Chromosomes, Plant
Polyploidy
Gene Expression Regulation, Plant
Vegetables
Genetics
Molecular Biology Techniques
Molecular Biology
Plant Proteins
Solanum tuberosum
Evolutionary Biology
Multidisciplinary
Population Biology
Organic Compounds
fungi
Organic Chemistry
Gene Mapping
Chemical Compounds
Organisms
food and beverages
Biology and Life Sciences
Eukaryota
Starch
Gene Pool
Genomics
Plants
Tetraploidy
Chemistry
Phenotype
Physical Sciences
Medicine
Digestion
Physiological Processes
Potato
Departures from Diploidy
Population Genetics
Biomarkers
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 16
- Issue :
- 12
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....6b4c532cc7b3324e33a5dffe5c548284