In recent years, the efficiency and accuracy of QTL analysis for identification of useful traits have been increased by high-throughput genotyping. In a previous study, the genome variation of significant DNA polymorphism was observed in early maturing type rice mutant (EMT) by comparing with that of wild type (WT). For detection of major QTL for flowering time, we constructed a linkage map of 36 InDel- and 6 SNP- markers. In the linkage analysis of F2 plants derived from the cross “WT x EMT”, we have detected one potential QTL region on chromosome 6 by M6-3 marker. Also, the Hd1, which contained the target fragment of M6-3 marker, exhibited the relatively high nonsynonymous substitutions in genes located on chromosomal region from M6-2 to M6-4. To evaluate the reliable allele segregation related to expected Mendelian ratio between M6-3 and its flanking markers, M6-3 marker developed in Hd1 gene exhibited the 1:2:1 ratio as clear monogenic segregation in heterozygous F3 plant. Additionally, we further analyzed the different transcript regulations of OsGI and Hd3a gene related to Hd1 involved in photoperiodic flowering pathway. Although the mRNA levels of Hd1 had no difference between WT and EMT, the Hd3a as downstream effector of Hd1 significantly upregulated in EMT, suggesting that Hd1 gene may become nonfunctional.

Asterales are dicotyledonous flowering plants and are one of the Asterid clade, incuding many species as well as Codonopsis and Platycodon. Here, we have determined the complete chloroplast genome sequences of C. lanceolata and P. grandiflorus by using the targeted denovo assembly method of short reads derived from whole genome resequencing. The total lengths of each chloroplast genome sequence are 156,180 bp for C. lanceolata and 155,453 bp for P. grandiflorus. In their chloroplast genomes, 106 genes (75 protein-coding genes, 4 rRNA genes, 23 tRNA genes, and 4 hypothetical chloroplast open reading frames [ycfs]) exhibited the relatively similar positions. Also, 7 protein-coding genes commonly showed to contain introns in both C. lanceolata and P. grandiflorus chloroplast genome, while psaA gene contain intragenic regions only in P. grandiflorus chloroplast genome. In further analysis, we identified the codon usage bias to A or T and found the different simple sequence repeat (SSR) loci of each chloroplast genome (18 SSR loci of C. lanceolata and 16 SSR loci of P. grandiflorus). In the phylogenetic trees based on 72 protein-coding genes, C. lanceolata is more closely related to P. grandiflorus than the other plant species order Asterales. Also, we found the highest sequence diversities of 12 protein-coding genes in small single copy (SSC) region than in the inverted repeat (IRs) and large single copy (LSC) region, and 3 genes such as rpoC2 (LSC region), ndhB (IRs region), and ndhF (SSC region) showed the highest number of segregating sites in each region. Additionally, we developed the molecular markers for phylogenetic applications of C. lanceolata and P. grandiflorus chloroplast genome.