Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (7): 1282-1293.doi: 10.3864/j.issn.0578-1752.2017.07.011

• HORTICULTURE • Previous Articles     Next Articles

The QTL Analysis of Fruit and Seed Associated Traits in Watermelon Based on CAPS Markers

CHI YingYing, GAO Peng, ZHU ZiCheng, LUAN FeiShi, LI GuiYing, YU Peng   

  1. Horticulture College, Northeast Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Harbin 150030
  • Received:2016-08-22 Online:2017-04-01 Published:2017-04-01

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Abstract: 【Objective】 Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). The aim of this study is to convert SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon for linkage map construction and quantitative trait locus (QTL). 【Method】 A genetic map was constructed using a BC1P1 segregating population consists of 225 individuals, which F1 was obtained to backcross with P1 from female parent (garden female parent) and male parent (PI186490). The center and edge brix, center and edge flesh firmness, 100-seed-weight and seed coat color were investigated, respectively, then the obtained data were analyzed by SPSS19. Two inbred lines which are female and male parents, were re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. It was found that 90% and 88% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. With the published genome as a reference, the obtained data were assembled with BWA, and explored for the SNP by SAMTOOLS. The sequence of the SNP loci was extracted by in house perl script and then input into SNP2CAPS to transform into CAPS markers. The 450 CAPS restriction sites were selected evenly on the markers whole-genome. CAPS primers were designed 100-500 bp around the mutation by Primer Premier 6.Screening polymorphic CAPS markers for each plant within 225 BC1P1 populations were genotyped. Finally QTL analysis of fruit and seed associated traits in watermelon was done by using QTL IciMapping and Windows QTL CartographerV2.5 softwares. 【Result】 A total of 751 532 SNPs were detected, 450 pairs of CAPS were designed with 7 restriction enzymes among which 200 pairs of primers were polymorphic. An initial CAPS-based genetic linkage map was constructed with the BC1P1 population which spanned 1 376.95 cM with 11 linkage groups, 15 QTLs were detected and the rate of contribution explained 5.25%-74.59%. Among the additive loci there were 3 loci for center brix (CTSS2.1, CTSS2.2, CTSS8.1), 1 for edge brix (ETSS2.1), 3 for center flesh firmness (CFF6.1, CFF6.2, CFF8.1), 2 for edge flesh firmness (EFF6.1, EFF6.2), 4 for seed coat color (SCC8.1, SCC8.2, SCC8.3, SCC8.4), and 2 for 100-seed-weight (SHW6.1, SHW9.1). 【Conclusion】 A total of 751 532 SNPs were detected. Phenotypic contribution rate of 15% or more has five QTL (CTSS8.1, SCC8.1, SCC8.2, SCC8.3, SCC8.4) which are center brix and seed coat color. The research will provide a scientific basis for further fine positioning and cloning the genes controlling superior traits of fruit in watermelon.

Key words: watermelon, genetic linkage map, SNP, CAPS, QTL

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