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Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing.

Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W, Zhang X - BMC Plant Biol. (2013)

Bottom Line: The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers.A total of 205 markers on the map showed significant (P < 0.05) segregation distortion.The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time.

View Article: PubMed Central - HTML - PubMed

Affiliation: Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No,2 Xudong 2nd Rd, 430062 Wuhan, China. zhangxr@oilcrops.cn.

ABSTRACT

Background: The genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scale de novo SNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame.

Results: In total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2 individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only' markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P < 0.05) segregation distortion.

Conclusions: We report here the first high-density genetic map for sesame. The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence.

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Number of markers for eight segregation patterns.
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Figure 2: Number of markers for eight segregation patterns.

Mentions: Among the 71,793 high-quality SLAFs that were detected, 3,673 were polymorphic with a polymorphism rate of only 5.12% (Table 1). Of the 3,673 polymorphic SLAFs, 2,703 were classified into eight segregation patterns (Figure 2). An F2 population is obtained by selfing the F1 of a cross between two fully homozygous parents with genotype aa or bb. Therefore, only the aa × bb segregation pattern in the F2 population was used to construct a genetic map, and 1,476 markers fell into this class. Among these 1,476 markers, 1,272 markers had more than 20-fold of parental sequence depth, and more than 14-fold of individual sequence depth, and over 80% integrity of SLAF tags, and these were used for the genetic map construction.


Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing.

Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W, Zhang X - BMC Plant Biol. (2013)

Number of markers for eight segregation patterns.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852768&req=5

Figure 2: Number of markers for eight segregation patterns.
Mentions: Among the 71,793 high-quality SLAFs that were detected, 3,673 were polymorphic with a polymorphism rate of only 5.12% (Table 1). Of the 3,673 polymorphic SLAFs, 2,703 were classified into eight segregation patterns (Figure 2). An F2 population is obtained by selfing the F1 of a cross between two fully homozygous parents with genotype aa or bb. Therefore, only the aa × bb segregation pattern in the F2 population was used to construct a genetic map, and 1,476 markers fell into this class. Among these 1,476 markers, 1,272 markers had more than 20-fold of parental sequence depth, and more than 14-fold of individual sequence depth, and over 80% integrity of SLAF tags, and these were used for the genetic map construction.

Bottom Line: The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers.A total of 205 markers on the map showed significant (P < 0.05) segregation distortion.The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time.

View Article: PubMed Central - HTML - PubMed

Affiliation: Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No,2 Xudong 2nd Rd, 430062 Wuhan, China. zhangxr@oilcrops.cn.

ABSTRACT

Background: The genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scale de novo SNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame.

Results: In total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2 individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only' markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P < 0.05) segregation distortion.

Conclusions: We report here the first high-density genetic map for sesame. The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence.

Show MeSH
Related in: MedlinePlus