벼의 CAPS 마커 개발 및 줄기굵기 특성의 양적형질 유전자좌(QTL) 분석
Development of New CAPS Markers and Their Application in Qjavascript:void(0);TL Analysis of Stem Diameter in Rice
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초록
The next generation sequencing (NGS) has been developed rapidly in recent years, paving ways of discovering vastsequence variations among germplasms. Whole-genome sequencing was performed on the genomic DNA of Milyang23 andGihobyeo using NGS and developed new CAPS (cleaved amplified polymorphic sequence) markers based on the single nucleotidepolymorphisms (SNPs) in coding sequence between these varieties. The NGS sequencing yielded sequences of 60x coverage ofthe Nipponbare reference genome on average. A molecular genetic map was constructed with the recombinant inbred populationderived from Milyang23/Gihobyeo cross (MGRIL) integrating the newly developed 146 CAPS makers and previously reported219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internodediameters, culm length and panicle length in rice with MGRIL population. A total of 4 new QTLs were detected for stemdiameter traits including the first internode diameter (I1D), second internode diameter (I2D), third internode diameter (I3D), andfourth internode diameter (I4D). Among stem diameter QTLs, qI1D5 had relatively 6.09 LOD (likelihood of odds) score andexplained 8.99% of total variation. Only very small portion of SNPs through re-sequencing were used in this study. Much moremarkers can be developed by using SNP information acquired in this study, which will enable construction of high-density geneticmap and more accurate QTL analysis of important agronomical traits with MGRIL population.
Abstract
The next generation sequencing (NGS) has been developed rapidly in recent years, paving ways of discovering vastsequence variations among germplasms. Whole-genome sequencing was performed on the genomic DNA of Milyang23 andGihobyeo using NGS and developed new CAPS (cleaved amplified polymorphic sequence) markers based on the single nucleotidepolymorphisms (SNPs) in coding sequence between these varieties. The NGS sequencing yielded sequences of 60x coverage ofthe Nipponbare reference genome on average. A molecular genetic map was constructed with the recombinant inbred populationderived from Milyang23/Gihobyeo cross (MGRIL) integrating the newly developed 146 CAPS makers and previously reported219 PCR-based DNA markers. This map was applied to the detection of quantitative trait loci (QTLs) for stem internodediameters, culm length and panicle length in rice with MGRIL population. A total of 4 new QTLs were detected for stemdiameter traits including the first internode diameter (I1D), second internode diameter (I2D), third internode diameter (I3D), andfourth internode diameter (I4D). Among stem diameter QTLs, qI1D5 had relatively 6.09 LOD (likelihood of odds) score andexplained 8.99% of total variation. Only very small portion of SNPs through re-sequencing were used in this study. Much moremarkers can be developed by using SNP information acquired in this study, which will enable construction of high-density geneticmap and more accurate QTL analysis of important agronomical traits with MGRIL population.
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