PMID- 25534138
OWN - NLM
STAT- MEDLINE
DCOM- 20150814
LR  - 20240109
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 15
IP  - 1
DP  - 2014 Dec 22
TI  - An SNP-based saturated genetic map and QTL analysis of fruit-related traits in 
      cucumber using specific-length amplified fragment (SLAF) sequencing.
PG  - 1158
LID - 10.1186/1471-2164-15-1158 [doi]
LID - 1158
AB  - BACKGROUND: Cucumber, Cucumis sativus L., is an economically important vegetable 
      crop which is processed or consumed fresh worldwide. However, the narrow genetic 
      base in cucumber makes it difficult for constructing high-density genetic maps. 
      The development of massively parallel genotyping methods and next-generation 
      sequencing (NGS) technologies provides an excellent opportunity for developing 
      single nucleotide polymorphisms (SNPs) for linkage map construction and QTL 
      analysis of horticultural traits. Specific-length amplified fragment sequencing 
      (SLAF-seq) is a recent marker development technology that allows large-scale SNP 
      discovery and genotyping at a reasonable cost. In this study, we constructed a 
      high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs. 
      RESULTS: An F2 population of 148 individuals was developed from an intra-varietal 
      cross between CC3 and NC76. Genomic DNAs extracted from two parents and 148 F2 
      individuals were subjected to high-throughput sequencing and SLAF library 
      construction. A total of 10.76 Gb raw data and 75,024,043 pair-end reads were 
      generated to develop 52,684 high-quality SLAFs, out of which 5,044 were 
      polymorphic. 4,817 SLAFs were encoded and grouped into different segregation 
      patterns. A high-resolution genetic map containing 1,800 SNPs was constructed for 
      cucumber spanning 890.79 cM. The average distance between adjacent markers was 
      0.50 cM. 183 scaffolds were anchored to the SNP-based genetic map covering 46% 
      (168.9 Mb) of the cucumber genome (367 Mb). Nine QTLs for fruit length and weight 
      were detected, a QTL designated fl3.2 explained 44.60% of the phenotypic 
      variance. Alignment of the SNP markers to draft genome scaffolds revealed two 
      mis-assembled scaffolds that were validated by fluorescence in situ hybridization 
      (FISH). CONCLUSIONS: We report herein the development of evenly dispersed SNPs 
      across cucumber genome, and for the first time an SNP-based saturated linkage 
      map. This 1,800-locus map would likely facilitate genetic mapping of complex QTL 
      loci controlling fruit yield, and the orientation of draft genome scaffolds.
FAU - Wei, Qingzhen
AU  - Wei Q
FAU - Wang, Yunzhu
AU  - Wang Y
FAU - Qin, Xiaodong
AU  - Qin X
FAU - Zhang, Yunxia
AU  - Zhang Y
FAU - Zhang, Zhentao
AU  - Zhang Z
FAU - Wang, Jing
AU  - Wang J
FAU - Li, Ji
AU  - Li J
FAU - Lou, Qunfeng
AU  - Lou Q
AD  - State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of 
      Horticulture, Nanjing Agricultural University, Weigang Street No,1, Nanjing 
      210095, China. qflou@njau.edu.cn.
FAU - Chen, Jinfeng
AU  - Chen J
LA  - eng
SI  - SRA/SRP050237
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20141222
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
SB  - IM
MH  - Chromosome Mapping/economics/*methods
MH  - Cost-Benefit Analysis
MH  - Cucumis sativus/anatomy & histology/*genetics
MH  - Fruit/*anatomy & histology/genetics
MH  - Genotyping Techniques
MH  - High-Throughput Nucleotide Sequencing/economics/*methods
MH  - Organ Size
MH  - *Polymorphism, Single Nucleotide
MH  - *Quantitative Trait Loci
MH  - Sequence Analysis, DNA/economics/*methods
PMC - PMC4367881
EDAT- 2014/12/24 06:00
MHDA- 2015/08/15 06:00
PMCR- 2014/12/22
CRDT- 2014/12/24 06:00
PHST- 2014/05/27 00:00 [received]
PHST- 2014/12/11 00:00 [accepted]
PHST- 2014/12/24 06:00 [entrez]
PHST- 2014/12/24 06:00 [pubmed]
PHST- 2015/08/15 06:00 [medline]
PHST- 2014/12/22 00:00 [pmc-release]
AID - 1471-2164-15-1158 [pii]
AID - 6913 [pii]
AID - 10.1186/1471-2164-15-1158 [doi]
PST - epublish
SO  - BMC Genomics. 2014 Dec 22;15(1):1158. doi: 10.1186/1471-2164-15-1158.