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Kim, Seungill,Kim, Myung-Shin,Kim, Yong-Min,Yeom, Seon-In,Cheong, Kyeongchae,Kim, Ki-Tae,Jeon, Jongbum,Kim, Sunggil,Kim, Do-Sun,Sohn, Seong-Han,Lee, Yong-Hwan,Choi, Doil Oxford University Press 2015 DNA research Vol.22 No.1
<P>The onion (<I>Allium cepa</I> L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from <I>de novo</I> sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and <I>ab initio</I> gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on <I>de novo</I> transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in <I>Allium</I> spp.</P>
Seongjun Kim,Sunggil Kim 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
For efficient introgression of the downy mildew resistance gene from a resistant cultivar into domestic breeding lines, molecular markers used for marker-assisted backcrossing (MAB) were developed in onion (Allium cepa L.). The resistance gene (Pd) was originally introgressed from a wild species, A. roylei, by interspecific hybridization, and the resistant gene was known to be positioned at the end of chromosome 3. Therefore, cDNA sequences of loci located at the ends of chromosome 3 of two linkage maps were obtained from a transcriptome database. Primer pairs were designed on exon sequences of eight loci. Among them, the PCR products of the i25255 locus showed length polymorphism between A. roylei and onions, and both large and small-sized PCR products were observed in the resistant cultivar. Sequence analysis showed that a 67-bp indel existed in the intron sequences. Based on this indel polymorphism, a simple PCR marker, designated DMR1, was developed. Analysis of diverse onion accessions showed that no accessions contained the A. roylei-specific marker genotype except for the resistant cultivar. These results indicated that the DMR1 marker was successfully tagging the A. roylei fragment harboring the downy mildew resistance gene, and the resistant cultivar was heterozygous for the resistance gene. After further analysis of multiple loci positioned at chromosome 3, a range of the A. roylei fragment introgressed in the resistant cultivar was determined in two linkage maps. On the basis of the range of the A. roylei fragment, three molecular markers used for recombinant selection in MAB were also developed.