Fig. 1

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 2. M, DNA size marker. c Application of Gn1a markers in the intermediate breeding line. Fourteen BC₁F₃ 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)