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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

Gnotype distribution of SLAF markers. The Y axis is the number of SLAFs, the X axis is the type of SLAFs.
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Figure 2: Gnotype distribution of SLAF markers. The Y axis is the number of SLAFs, the X axis is the type of SLAFs.

Mentions: Among the 115,789 high-quality SLAFs detected, 15,946 were polymorphic with a rate of 13.77% (Table 2). Of the 15,946 polymorphic SLAFs, 15,196 were classified into eight segregation patterns (Figure 2). F2 population was obtained by selfing the F1 of a cross between two parents with homozygous genotype of aa or bb. So, only the F2 plants with aa × bb segregation pattern were used to construct the high-density genetic linkage map, and there are totally 14,712 markers fell into this type. Among these 14,712 markers, 3,077 markers were used for the high-density genetic map construction, which are homozygous in the two parents, with sequence depth more than 10-fold, and over 70% integrity of SLAF tags.


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)

Gnotype distribution of SLAF markers. The Y axis is the number of SLAFs, the X axis is the type of SLAFs.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Gnotype distribution of SLAF markers. The Y axis is the number of SLAFs, the X axis is the type of SLAFs.
Mentions: Among the 115,789 high-quality SLAFs detected, 15,946 were polymorphic with a rate of 13.77% (Table 2). Of the 15,946 polymorphic SLAFs, 15,196 were classified into eight segregation patterns (Figure 2). F2 population was obtained by selfing the F1 of a cross between two parents with homozygous genotype of aa or bb. So, only the F2 plants with aa × bb segregation pattern were used to construct the high-density genetic linkage map, and there are totally 14,712 markers fell into this type. Among these 14,712 markers, 3,077 markers were used for the high-density genetic map construction, which are homozygous in the two parents, with sequence depth more than 10-fold, and over 70% integrity of SLAF tags.

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