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Kim, Daeun,Jin, Bingkui,Je, Byoung Il,Choi, Youngmi,Kim, Byung Sup,Jung, Hee-Jeong,Nou, Ill-Sup,Park, Younghoon,Archambault, A. Canadian Science Publishing 2018 Genome Vol.61 No.10
<P> Reductions in growth and quality due to powdery mildew (PM) disease cause significant economic losses in tomato production. Oidium neolycopersici was identified as the fungal species responsible for tomato PM disease in South Korea in the present study, based on morphological and internal transcribed spacer DNA sequence analyses of PM samples collected from two remote regions (Muju and Miryang). The genes involved in resistance to this pathogen in the tomato accession ‘KNU-12’ (Solanum lycopersicum var. cerasiforme) were evaluated, and the inheritance of PM resistance in ‘KNU-12’ was found to be conferred via simple Mendelian inheritance of a mutant allele of the PM susceptibility locus Ol-2 (SlMlo1). Full-length cDNA analysis of this newly identified mutant allele (Slmlo1.1) showed that a 1-bp deletion in its coding region led to a frameshift mutation possibly resulting in SlMlo1 loss-of-function. An alternatively spliced transcript of Slmlo1.1 was observed in the cDNA sequences of ‘KNU-12’, but its direct influence on PM resistance is unclear. A derived cleaved amplified polymorphic sequence (dCAPS) and a high-resolution melting (HRM) marker were developed based on the 1-bp deletion in Slmlo1.1, and could be used for efficient marker-assisted selection (MAS) using ‘KNU-12’ as the source for durable and broad-spectrum resistance to PM. </P>
Bingkui Jin,Joonyup Kim,Jaemin Jung,Daeun Kim,Younghoon Park 한국원예학회 2018 원예과학기술지 Vol.36 No.1
The SUN gene is responsible for an elongated fruit shape in tomato and belongs to the IQ domain (IQD) gene family, which is involved in growth and development in plants. In the present study, IQD gene homologs were evaluated for their roles in determining fruit shape in cucurbit crops. A total of 151 IQD homologs and their chromosomal locations in Arabidopsis, tomato, and three cucurbit species, watermelon, melon, and cucumber, were compared based on their genomic information. A phylogenetic dendrogram of these IQD homologs revealed putative orthologous and paralogous relationships among these genes, and showed that previously reported candidate fruit shape IQD genes in watermelon (ClSUN8), melon (CmSUN14), and cucumber (CsSUN2) were clustered under the same node with a similarity coefficient of 0.97. A comparison of the physical locations of the IQD homologs with fruit shape QTLs in genetic maps indicated that ClSUN8, CmSUN14, and CsSUN2 were co-localized with the major QTLs for the fruit shape index (FSI). This co-localization further indicated that minor QTLs for FSI were also associated with the IQD gene family. We used early developmental stages of immature fruits to conduct a morphological assay and characterize ClSUN8 in watermelon. Histological analysis indicated that elongated or round fruit shape is determined at the early stage of ovary formation, at least earlier than -4 days after fertilization (-4 DAF), and fruit elongation is due to increased cell division in the longitudinal direction. Quantitative RT-PCR showed that the highest expression of ClSUN8 occurred at -4 days after fertilization and gradually decreased; however, there was no direct relationship between the gene expression level and fruit shape. RACE-PCR revealed a non-synonymous SNP between the ClSUN8 alleles of elongated- and round-fruited watermelon accessions, suggesting that the SNP might be a causative mutation affecting fruit shape.
Jung, Jaemin,Kim, Joonyup,Jin, Bingkui,Choi, Youngmi,Hong, Chang Oh,Lee, Hyun Ho,Choi, Youngwhan,Kang, Jumsoon,Park, Younghoon Korean Society of Horticultural Science 2017 원예과학기술지 Vol.35 No.3
Bloomless cucumber fruits are commercially produced by grafting onto the pumpkin stocks (Cucurbita moschata) to restricted silicon ($SiO_2$) absorption. Inhibition of silicon absorption in bloomless stocks is conferred by a mutant allele of the CmLsi1 homologous to Lsi1 in rice. In this study, we characterized the Lsi1 homologs in pumpkin (C. moschata) and its cold-tolerant wild relative C. ficifolia ('Heukjong') in order to develop a DNA marker for selecting a bloomless trait and to establish the molecular basis for breeding bloomless stock cultivars of C. ficifolia. A Cleaved amplified polymorphic sequence (CAPS) marker (CM1-CAPS) was designed based on a non-sysnonymous single nucleotide polymorphism (SNP, C>T) of the CmLsi1 mutant-type allele, and its applicability for Marker-assisted selection (MAS) was confirmed by evaluating three bloom and five bloomless pumpkin stock cultivars. Quantitative RT-PCR of the CmLsi1 for these stock cultivers implied that expression level of the CmLsi1 gene does not appear to be associated with the bloom/bloomless trait and may differ depending on plant species and tissues. A full length cDNA of the Lsi1 homolog [named CfLsi1($B^+$)] of 'Heukjong' (C. ficifolia), was cloned and sequence comparison between CmLsi1($B^+$) and CfLsi1($B^+$) revealed that there exists total 24 SNPs, of which three were non-synonymous. Phylogenetic analysis of CfLsi1($B^+$) and Lsi1 homologs further revealed that CfLsi1($B^+$) is closesly related to Nodulin 26-like intrinsic proteins (NIPs) and most similar to CpNIP1 of C. pepo than C. moschata.
Girim Park,Joonyup Kim,Bingkui Jin,Hee-Bum Yang,Sung-Woo Park,Sun-Cheol Kang,Sang-Min Chung,Younghoon Park 한국원예학회 2018 원예과학기술지 Vol.36 No.2
Watermelon is an economically important member of the Cucurbitaceae family. Cultivated watermelons (C. lanatus ssp. lanatus) have diverse fruit-related traits such as size, shape, color of flesh and skin, and the striped rind pattern. In this study, the whole genomes of 19 inbred watermelon lines were resequenced and genome-wide sequence variations were analyzed for the development of markers for MABC (marker-assisted backcross). Based on the single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) detected, we evaluated the distribution of genome-wide diversity, genetic relationship, cultivar type-specific allele abundance, and sequence divergence at quantitative trait loci (QTLs). For MABC, a total of 1,374 SNPs were selected at intervals of 0.5 Mb based on the Polymorphism Information Content (PIC) value. Principal components analysis (PCA) of the 19 cultivars was based on 1,374 SNPs to classify them into three major groups, which indicated a clear grouping pattern between Crimson-type and Jubilee-type watermelons. In addition, a set of SNPs (259) that discriminated Crimson-type cultivars from the non-Crimson-type were also selected. For the verification of SNPs, 26 cleavage amplified polymorphic sequence (CAPS) markers were designed based on the SNPs and used to genotype 11 cultivars, which resulted in high agreement rates above 0.8 for most of the markers. Our study uncovers the genetic diversity underlying cultivated watermelon species and provides genetic information useful for the development of molecular markers for marker-assisted breeding (MAB) strategies.
Jaemin Jung,Joonyup Kim,Bingkui Jin,Youngmi Choi,Chang Oh Hong,Hyun Ho Lee,Youngwhan Choi,Jumsoon Kang,Younghoon Park 한국원예학회 2017 원예과학기술지 Vol.35 No.3
Bloomless cucumber fruits are commercially produced by grafting onto the pumpkin stocks (Cucurbita moschata ) to restricted silicon (SiO₂) absorption. Inhibition of silicon absorption in bloomless stocks is conferred by a mutant allele of the CmLsi1 homologous to Lsi1 in rice. In this study, we characterized the Lsi1 homologs in pumpkin (C. moschata ) and its coldtolerant wild relative C. ficifolia (‘Heukjong’) in order to develop a DNA marker for selecting a bloomless trait and to establish the molecular basis for breeding bloomless stock cultivars of C. ficifolia . A Cleaved amplified polymorphic sequence (CAPS) marker (CM1-CAPS) was designed based on a non-sysnonymous single nucleotide polymorphism (SNP, C>T) of the CmLsi1 mutant-type allele, and its applicability for Marker-assisted selection (MAS) was confirmed by evaluating three bloom and five bloomless pumpkin stock cultivars. Quantitative RT-PCR of the CmLsi1 for these stock cultivers implied that expression level of the CmLsi1 gene does not appear to be associated with the bloom/bloomless trait and may differ depending on plant species and tissues. A full length cDNA of the Lsi1 homolog [named CfLsi1 (B⁺)] of ‘Heukjong’ (C. ficifolia ), was cloned and sequence comparison between CmLsi1 (B⁺) and CfLsi1 (B⁺) revealed that there exists total 24 SNPs, of which three were non-synonymous. Phylogenetic analysis of CfLsi1 (B⁺) and Lsi1 homologs further revealed that CfLsi1 (B⁺) is closesly related to Nodulin 26-like intrinsic proteins (NIPs) and most similar to CpNIP1 of C. pepo than C. moschata.