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A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber.

Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, Yao DQ, Guo CL, Lian HL, He HL, Pan JS, Cai R - Front Plant Sci (2016)

Bottom Line: The average genetic distance is 0.35 cM.Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter.There are 15 QTLs for the two fruit traits were detected.

View Article: PubMed Central - PubMed

Affiliation: School of Agriculture and Biology, Shanghai Jiaotong University Shanghai, China.

ABSTRACT
High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.

No MeSH data available.


Related in: MedlinePlus

The process of the genetic map construction (Liu et al., 2014). (A) Calculate the mLOD value of the high quality molecular tags, using this value to analysis seven linkage groups (LGs). (B) Using the software of HighMap to construct the genetic map for each LG. (C) According to the result of mapping to correct the tags genotyping. (D) Get the high-density genetic map and evaluate the quality of the map.
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Figure 1: The process of the genetic map construction (Liu et al., 2014). (A) Calculate the mLOD value of the high quality molecular tags, using this value to analysis seven linkage groups (LGs). (B) Using the software of HighMap to construct the genetic map for each LG. (C) According to the result of mapping to correct the tags genotyping. (D) Get the high-density genetic map and evaluate the quality of the map.

Mentions: Based on the locations of SLAF markers on chromosomes, they were assigned into seven linkage groups (LGs). The NGS data may exist some genotyping errors and deletion, which can reduce the quality of the genetic map. These errors were corrected by the High Map Strategy (Liu et al., 2014). All the genotype data from the F2 mapping population was used to perform linkage analysis using JoinMap 4.0 software (Van Ooijen, 2006). The SLAFs can be divided into seven LGs with the position of the reference genome. By computing the MLOD value between two adjacent markers (Vision et al., 2000), to filter out the SLAFs with the MLOD values are less than 5. Using Marker HighMap (Liu et al., 2014) software to analysis the linear array of markers in each LG, and estimate the genetic distances of between two adjacent markers. The method of Internal Mapping and the software of R/qtl were used in QTLs analysis, the confidence intervals of QTLs were calculated according 95% Bayes credible interval method (Sen and Churchill, 2001) with R/qtl. The process of the genetic map construction was shown in Figure 1 (Liu et al., 2014).


A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber.

Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, Yao DQ, Guo CL, Lian HL, He HL, Pan JS, Cai R - Front Plant Sci (2016)

The process of the genetic map construction (Liu et al., 2014). (A) Calculate the mLOD value of the high quality molecular tags, using this value to analysis seven linkage groups (LGs). (B) Using the software of HighMap to construct the genetic map for each LG. (C) According to the result of mapping to correct the tags genotyping. (D) Get the high-density genetic map and evaluate the quality of the map.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835494&req=5

Figure 1: The process of the genetic map construction (Liu et al., 2014). (A) Calculate the mLOD value of the high quality molecular tags, using this value to analysis seven linkage groups (LGs). (B) Using the software of HighMap to construct the genetic map for each LG. (C) According to the result of mapping to correct the tags genotyping. (D) Get the high-density genetic map and evaluate the quality of the map.
Mentions: Based on the locations of SLAF markers on chromosomes, they were assigned into seven linkage groups (LGs). The NGS data may exist some genotyping errors and deletion, which can reduce the quality of the genetic map. These errors were corrected by the High Map Strategy (Liu et al., 2014). All the genotype data from the F2 mapping population was used to perform linkage analysis using JoinMap 4.0 software (Van Ooijen, 2006). The SLAFs can be divided into seven LGs with the position of the reference genome. By computing the MLOD value between two adjacent markers (Vision et al., 2000), to filter out the SLAFs with the MLOD values are less than 5. Using Marker HighMap (Liu et al., 2014) software to analysis the linear array of markers in each LG, and estimate the genetic distances of between two adjacent markers. The method of Internal Mapping and the software of R/qtl were used in QTLs analysis, the confidence intervals of QTLs were calculated according 95% Bayes credible interval method (Sen and Churchill, 2001) with R/qtl. The process of the genetic map construction was shown in Figure 1 (Liu et al., 2014).

Bottom Line: The average genetic distance is 0.35 cM.Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter.There are 15 QTLs for the two fruit traits were detected.

View Article: PubMed Central - PubMed

Affiliation: School of Agriculture and Biology, Shanghai Jiaotong University Shanghai, China.

ABSTRACT
High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.

No MeSH data available.


Related in: MedlinePlus