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Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data
- Source :
- Breeding Science
- Publication Year :
- 2016
- Publisher :
- Japanese Society of Breeding, 2016.
-
Abstract
- Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Citrullus lanatus
SNP
Single-nucleotide polymorphism
Plant Science
Quantitative trait locus
01 natural sciences
Genome
Citrullus
03 medical and health sciences
re-sequencing data
Genetic linkage
Cleaved amplified polymorphic sequence
Genetics
CAPS
biology
watermelon
biology.organism_classification
linkage map
Perl
Restriction enzyme
030104 developmental biology
Agronomy and Crop Science
Research Paper
010606 plant biology & botany
Subjects
Details
- ISSN :
- 13473735 and 13447610
- Volume :
- 66
- Database :
- OpenAIRE
- Journal :
- Breeding Science
- Accession number :
- edsair.doi.dedup.....64da7044ef2fdc6ee1de7ebe5a68200d