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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.


Quantitative trait loci (QTL) analysis with two fruit traits using the high-density genetic map. (A) QTL analysis of fruit length in 2013 autumn; (B) QTL analysis of fruit length in 2014 spring; (C) QTL analysis of fruit length in 2015 spring; (D) QTL analysis of fruit diameter in 2013 autumn; (E) QTL analysis of fruit diameter in 2014 spring; (F) QTL analysis of fruit diameter in 2015 spring. Horizontal line on the chart represents LOD threshold.
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Figure 4: Quantitative trait loci (QTL) analysis with two fruit traits using the high-density genetic map. (A) QTL analysis of fruit length in 2013 autumn; (B) QTL analysis of fruit length in 2014 spring; (C) QTL analysis of fruit length in 2015 spring; (D) QTL analysis of fruit diameter in 2013 autumn; (E) QTL analysis of fruit diameter in 2014 spring; (F) QTL analysis of fruit diameter in 2015 spring. Horizontal line on the chart represents LOD threshold.

Mentions: Phenotypic data of two parents, F1, F2, and F2:3 families are presented in Figure 3. QTLs for two fruit traits were detected in F3 families (Table 4; Figures 4 and 5), and mapped to unique positions. QTLs were detected for all fruit traits. A total of 15 QTLs were detected with seven and eight QTLs indentified per trait. The proportion of phenotypic variance explained by a single QTL (r2) ranged from 5.7 to 13.6% and LOD scores from 2.05 to 5.49. Seven QTLs were detected for fruit length, which were localized on chromosomes 3, 4, 6 and 7, accounting for 7.6–13.6% of the phenotypic variation. There were eight QTLs were detected for fruit diameter, which were localized on chromosome 1, 3, 5, 6 and 7, and the phenotypic variation was from 5.7 to 13.3%. (Table 4; Figures 4 and 5.


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)

Quantitative trait loci (QTL) analysis with two fruit traits using the high-density genetic map. (A) QTL analysis of fruit length in 2013 autumn; (B) QTL analysis of fruit length in 2014 spring; (C) QTL analysis of fruit length in 2015 spring; (D) QTL analysis of fruit diameter in 2013 autumn; (E) QTL analysis of fruit diameter in 2014 spring; (F) QTL analysis of fruit diameter in 2015 spring. Horizontal line on the chart represents LOD threshold.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Quantitative trait loci (QTL) analysis with two fruit traits using the high-density genetic map. (A) QTL analysis of fruit length in 2013 autumn; (B) QTL analysis of fruit length in 2014 spring; (C) QTL analysis of fruit length in 2015 spring; (D) QTL analysis of fruit diameter in 2013 autumn; (E) QTL analysis of fruit diameter in 2014 spring; (F) QTL analysis of fruit diameter in 2015 spring. Horizontal line on the chart represents LOD threshold.
Mentions: Phenotypic data of two parents, F1, F2, and F2:3 families are presented in Figure 3. QTLs for two fruit traits were detected in F3 families (Table 4; Figures 4 and 5), and mapped to unique positions. QTLs were detected for all fruit traits. A total of 15 QTLs were detected with seven and eight QTLs indentified per trait. The proportion of phenotypic variance explained by a single QTL (r2) ranged from 5.7 to 13.6% and LOD scores from 2.05 to 5.49. Seven QTLs were detected for fruit length, which were localized on chromosomes 3, 4, 6 and 7, accounting for 7.6–13.6% of the phenotypic variation. There were eight QTLs were detected for fruit diameter, which were localized on chromosome 1, 3, 5, 6 and 7, and the phenotypic variation was from 5.7 to 13.3%. (Table 4; Figures 4 and 5.

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.