fluidigm snp genotyping platform  (fluidigm)

Journal: Rice

Article Title: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

doi: 10.1186/s12284-016-0084-7

Figure Lengend Snippet: Gn1a markers. a Identification of nucleotide polymorphisms in Gn1a gene for marker development. Gn1a gene consists of four exons ( orange boxes ) in which translation initiation codon ( Start ) and stop codon ( Stop ) are depicted. Each nucleotide variation with corresponding markers (PCR-gel-based markers and Fluidigm genotyping platform (-FD) markers) is mapped on the gene structure. The sequence alignment showed nucleotide polymorphisms in the promoter and 5’UTR regions of Gn1a among 15 varieties, including the reference genome (Nipponbare), two Gn1a donors, and 12 recipients. DNA polymorphisms were highlighted with pink and green color. The number of unrepresented nucleotides (bp) in a sequence was shown in parentheses. Based on the context of the promoter sequences, three Gn1a alleles (Types 1-3: T1-T3) were found. Variety name with asterisk (*) was used as the donor line of target allele. b Agarose gel images analyzed by three Gn1a markers (Gn1a-17SNP, Gn1a-indel3, and Gn1a-indel1 markers) from two donor lines and 12 recipients. Predicted PCR product sizes for yield-positive allele (P), non-target allele (N), and common band (OP) were shown at the right side of the gel image. Primer combination for each marker was shown on the gel images and its sequences were listed in Table . M, DNA size marker. c Application of Gn1a markers in the intermediate breeding line. Fourteen BC 1 F 3 plants derived from PR37951 x Habataki cross were genotyped with Gn1a-17SNP and Gn1a-indel3 marker, respectively. Genotyping result was scored for each plant as PP (homozygous for positive allele), NN (homozygous for non-target allele), and PN (heterozygote)

Article Snippet: Markers for Fluidigm SNP genotyping platform. (DOC 36 kb)

Techniques: Marker, Sequencing, Agarose Gel Electrophoresis, Derivative Assay

Journal: Rice

Article Title: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

doi: 10.1186/s12284-016-0084-7

Figure Lengend Snippet: GS5 markers. a The selected DNA polymorphisms in the GS5 promoter region for marker development. The location of the 4-bp indel is 320-bp distance from the translation initiation codon. The C/T SNP was used for designing GS5-03SNP (PCR-gel-based marker) and GS5-03SNP-FD (Fluidigm genotyping marker) markers. b Capillary electrophoresis image from the parental lines analyzed by the GS5-indel1 marker. Aikawa1 and ST6 were used as donors of GS5 -WG allele. The WG, MG, and NG alleles of the GS5 gene were designated as W, M, and N, respectively. c Agarose gel image analyzed by the GS5-03SNP marker from the parental lines. d Application of the GS5-03SNP marker in intermediate breeding line. Fourteen BC 2 F 2 plants derived from PR37951 x ST6 cross were tested

Article Snippet: Markers for Fluidigm SNP genotyping platform. (DOC 36 kb)

Techniques: Marker, Electrophoresis, Agarose Gel Electrophoresis, Derivative Assay

Journal: Rice

Article Title: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

doi: 10.1186/s12284-016-0084-7

Figure Lengend Snippet: Genotyping of five yield-related genes from 39 rice accessions using nine Fluidigm SNP genotyping markers. The marker name with the detected-nucleotide polymorphism was shown on the top of each graph. The allele-specific primers were labeled with HEX fluorescence dye ( green ) for the yield-positive allele and with FAM fluorescence dye ( red ) for the non-target allele. After PCR on Fluidigm array, the alleles of samples were determined by fluorescent signal intensity. In each marker result, the yield-positive allele of the genes was shown with a green letter. Black spot, non-template control; gray spot, invalid call; blue spot, heterozygote

Article Snippet: Markers for Fluidigm SNP genotyping platform. (DOC 36 kb)

Techniques: Marker, Labeling, Fluorescence

Journal: Rice

Article Title: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

doi: 10.1186/s12284-016-0084-7

Figure Lengend Snippet: Gn1a markers. a Identification of nucleotide polymorphisms in Gn1a gene for marker development. Gn1a gene consists of four exons ( orange boxes ) in which translation initiation codon ( Start ) and stop codon ( Stop ) are depicted. Each nucleotide variation with corresponding markers (PCR-gel-based markers and Fluidigm genotyping platform (-FD) markers) is mapped on the gene structure. The sequence alignment showed nucleotide polymorphisms in the promoter and 5’UTR regions of Gn1a among 15 varieties, including the reference genome (Nipponbare), two Gn1a donors, and 12 recipients. DNA polymorphisms were highlighted with pink and green color. The number of unrepresented nucleotides (bp) in a sequence was shown in parentheses. Based on the context of the promoter sequences, three Gn1a alleles (Types 1-3: T1-T3) were found. Variety name with asterisk (*) was used as the donor line of target allele. b Agarose gel images analyzed by three Gn1a markers (Gn1a-17SNP, Gn1a-indel3, and Gn1a-indel1 markers) from two donor lines and 12 recipients. Predicted PCR product sizes for yield-positive allele (P), non-target allele (N), and common band (OP) were shown at the right side of the gel image. Primer combination for each marker was shown on the gel images and its sequences were listed in Table . M, DNA size marker. c Application of Gn1a markers in the intermediate breeding line. Fourteen BC 1 F 3 plants derived from PR37951 x Habataki cross were genotyped with Gn1a-17SNP and Gn1a-indel3 marker, respectively. Genotyping result was scored for each plant as PP (homozygous for positive allele), NN (homozygous for non-target allele), and PN (heterozygote)

Article Snippet: Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a , OsSPL14 , Ghd7 , GS5 , and GS3 genes were developed for high-throughput genotyping.

Techniques: Marker, Sequencing, Agarose Gel Electrophoresis, Derivative Assay

Journal: Rice

Article Title: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

doi: 10.1186/s12284-016-0084-7

Figure Lengend Snippet: GS5 markers. a The selected DNA polymorphisms in the GS5 promoter region for marker development. The location of the 4-bp indel is 320-bp distance from the translation initiation codon. The C/T SNP was used for designing GS5-03SNP (PCR-gel-based marker) and GS5-03SNP-FD (Fluidigm genotyping marker) markers. b Capillary electrophoresis image from the parental lines analyzed by the GS5-indel1 marker. Aikawa1 and ST6 were used as donors of GS5 -WG allele. The WG, MG, and NG alleles of the GS5 gene were designated as W, M, and N, respectively. c Agarose gel image analyzed by the GS5-03SNP marker from the parental lines. d Application of the GS5-03SNP marker in intermediate breeding line. Fourteen BC 2 F 2 plants derived from PR37951 x ST6 cross were tested

Article Snippet: Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a , OsSPL14 , Ghd7 , GS5 , and GS3 genes were developed for high-throughput genotyping.

Techniques: Marker, Electrophoresis, Agarose Gel Electrophoresis, Derivative Assay

Journal: Rice

Article Title: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

doi: 10.1186/s12284-016-0084-7

Figure Lengend Snippet: Genotyping of five yield-related genes from 39 rice accessions using nine Fluidigm SNP genotyping markers. The marker name with the detected-nucleotide polymorphism was shown on the top of each graph. The allele-specific primers were labeled with HEX fluorescence dye ( green ) for the yield-positive allele and with FAM fluorescence dye ( red ) for the non-target allele. After PCR on Fluidigm array, the alleles of samples were determined by fluorescent signal intensity. In each marker result, the yield-positive allele of the genes was shown with a green letter. Black spot, non-template control; gray spot, invalid call; blue spot, heterozygote

Article Snippet: Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a , OsSPL14 , Ghd7 , GS5 , and GS3 genes were developed for high-throughput genotyping.

Techniques: Marker, Labeling, Fluorescence