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( Khandker Shazia Afrin ),( Md Abdur Rahim ),( Hee-jeong Jung ),( Jong-in Park ),( Hoy-taek Kim ),( Ill-sup Nou ) 한국미생물생명공학회(구 한국산업미생물학회) 2019 Journal of microbiology and biotechnology Vol.29 No.5
Black rot caused by Xanthomonas campestris pv. campestris (Xcc) is the most damaging disease in Brassica crops around the world. In this study, we developed a molecular marker specific to Xcc race 5. To do this, the available whole genome sequences of Xcc races/strains and Xc subspecies were aligned and identified a highly variable genomic region (XccR5-89.2). Subsequently, a primer set covering the ‘XccR5-89.2’ region was designed and tested against the genomic DNA of Xcc races/strains, Xc subspecies and other plant-infecting bacterial strains (Pseudomonas syringae pv. maculicola and Erwinia carotovora subsp. carotovora). The results showed that the ‘XccR5-89.2’ primer pair amplified a 2,172-bp fragment specific to Xcc race 5. Moreover, they also amplified a 1,515-bp fragment for Xcc race 1 and an over 3,000-bp fragment for Xcc race 3. However, they did not amplify any fragments from the remaining Xcc races/strains, subspecies or other bacterial strains. The ‘XccR5-89.2’ primer pair was further PCR amplified from race-unknown Xcc strains and ICMP8 was identified as race 5 among nine race-unknown Xcc strains. Further cloning and sequencing of the bands amplified from race 5 and ICMP8 with ‘XccR5-89.2’ primers revealed both carrying identical sequences. The results showed that the ‘XccR5-89.2’ marker can effectively and proficiently detect, and identify Xcc race 5 from Xcc races/strains, subspecies and other plant-infecting bacteria. To our knowledge, this is the first report for an Xcc race 5-specific molecular marker.
Khandker Shazia Afrin,Md Abdur Rahim,Mehede Hassan Rubel,Jong-In Park,Hee-Jeong Jung,Hoy-Taek Kim,Ill-Sup Nou 한국식물병리학회 2020 Plant Pathology Journal Vol.36 No.5
Xanthomonas campestris pv. campestris (Xcc), the pathogen of black rot which is the most destructive disease of Brassica vegetables throughout the world. Here, we reported two novel sequence-characterized amplified region (SCAR) markers (i.e., XccR6-60 and XccR6-67) for the detection of Xcc race 6 via re-alignment of the complete genome sequences of Xcc races/ strains/pathovars. The specificity of SCAR primer sets was verified by mean of PCR amplification using the genomic DNA template of Xcc races/strains/pathovars and two other plant infecting bacterial strains. The PCR result revealed that the XccR6-60 and XccR6-67 primer sets amplified 692-bp and 917-bp DNA fragments, respectively, specifically from race 6, while no visible amplification was detected in other samples. In addition, the SCAR primers were highly sensitive and can detect from a very low concentration of genomic DNA of Xcc race 6. However, the complete genome sequence of Xcc race 6 is not yet publicly available. Therefore, the cloning and sequencing of XccR6-60 and XccR6-67 fragments from race 6 provide more evidence of the specificity of these markers. These results indicated that the newly developed SCAR markers can successfully, effectively and rapidly detect Xcc race 6 from other Xcc races/strains/pathovars as well as other plant pathogenic bacteria. This is the first report for race-specific molecular markers for Xcc race 6.
Screening of Cabbage (Brassica oleracea L.) Germplasm for Resistance to Black Rot
Khandker Shazia Afrin,Md Abdur Rahim,박종인,Sathishkumar Natarajan,Mehede Hassan Rubel,김회택,노일섭 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.1
Black rot of Brassica crops is the most devastating disease which causes substantial yield reduction of cabbagethroughout the world. The use of resistant cabbage cultivars could be inexpensive and effective measure to combat this destructivedisease. We screened cabbage inbred lines for black rot disease resistance through bioassay and identified some novel lines that showedrace-specific resistance to Xanthomonas campestris pv. campestris (Xcc) races. The pathogenicity test revealed that out of 27 cabbagelines, one (SCNU-C-4074), six (SCNU-C-3631, SCNU-C-3637, SCNU-C-3639, SCNU-C-4072, SCNU-C-4073 and SCNU-C-3273),two (SCNU-C-3273 and SCNU-C-4118), two (SCNU-C-3270 and SCNU-C-4118), two (SCNU-C-3470 and SCNU-C-41148) and four(SCNU-C-107, SCNU-C-3270, SCNU-C-3470 and SCNU-C-4059) were shown to be resistant to Xcc races 1, 2, 3, 5, 6 and 7,respectively while none of these showed resistance against race 4. Furthermore, these resistant and susceptible lines were evaluated bypreviously reported molecular markers for black rot resistance. The molecular screening results were also revealed the existence ofrace-specific resistance in these cabbage lines. This result will help Brassica breeder to develop race-specific black rot resistant cabbagecultivars.
Expression of anthocyanin biosynthesis-related genes reflects the peel color in purple tomato
강송이,Md Abdur Rahim,Khandker Shazia Afrin,정희정,김효택,박종인,노일섭 한국원예학회 2018 Horticulture, Environment, and Biotechnology Vol.59 No.3
Tomato (Solanum lycopersicum L.) is one of the most important and popular vegetables worldwide. A wide range of tomato cultivars with different colored fruits is presently available. The purple peel of tomato fruit is due to the accumulation anthocyanin pigments, which are beneficial to both plants and humans. Cultivated tomatoes normally do not make anthocyanin in their fruit peel, but there are some wild relatives of cultivated tomato like Solanum chilense, S. habrochaites, S. cheesmanii, and S. lycopersicoides that do produce anthocyanins in their fruits. In this study, the purple fruit color was obtained by crossing ‘OSU blue’ (blue fruit) and ‘Purple mini’ (brown fruit) and subsequent self-pollination. Anthocyanins are produced via the flavonoid pathway and are regulated by the transcriptional complex of MYB, bHLH, and WD40 repeats transcription factors. We determined the expression profiles of genes related to anthocyanin biosynthesis in tomato genotypes with distinct fruit colors by qRT-PCR. Both the early and late biosynthetic genes of the anthocyanin pathway were up-regulated in the peels of purple tomato fruits, except Sl5GT. Moreover, the expression of the regulatory genes SlANT1 and SlAN1 was dramatically increased in the peels of purple tomato fruits. These results indicate that SlANT1 and SlAN1 might play an important role on anthocyanin biosynthesis in the peels of purple-fruited tomatoes via up-regulation of structural genes in the anthocyanin pathway.
Rahim, Md Abdur,Afrin, Khandker Shazia,Jung, Hee-Jeong,Kim, Hoy-Taek,Park, Jong-In,Hur, Yoonkang,Nou, Ill-Sup National Research Council of Canada, Conseil natio 2019 Genome Vol. No.
<P> Broccoli <I>(Brassica oleracea var. italica L.)</I> is a highly nutritious vegetable that typically forms pure green or purple florets. However, green broccoli florets sometimes accumulate slight purplish pigmentation in response environmental factors, decreasing their market value. In the present study, we aimed to develop molecular markers to distinguish broccoli genotypes as pure green or purplish floret color at the early seedling stage. Anthocyanins are known to be involved in the purple pigmentation in plants. The purplish broccoli lines were shown to accumulate purple pigmentation in the hypocotyls of very young seedlings; therefore, the expression profiles of the structural and regulatory genes of anthocyanin biosynthesis were analyzed in the hypocotyls using <I>qRT-PCR. BoPAL, BoDFR, BoMYB114, BoTT8, BoMYC1.1, BoMYC1.2,</I> and <I>BoTTG1</I> were identified as putative candidate genes responsible for the purple hypocotyl color. <I>BoTT8</I> was much more highly expressed in the purple than green hypocotyls; therefore, it was cloned and sequenced from various broccoli lines, revealing SNP and InDel variations between these genotypes. We tested four SNPs (G > A; A > T; G > C; T > G) in the first three exons and a 14-bp InDel (ATATTTATATATAT) in the <I>BoTT8</I> promoter in 51 broccoli genotypes, and we found these genetic variations could distinguish the green lines, purple lines, and F<SUB>1</SUB> hybrids. These novel molecular markers could be useful in broccoli breeding programs to develop a true green or purple broccoli cultivar. </P>
Md Abdur Rahim,Khandker Shazia Afrin,Hee-Jeong Jung,Hoy-Taek Kim,Jong-In Park,Ill-Sup Nou 한국원예학회 2021 Horticulture, Environment, and Biotechnology Vol.62 No.1
We explored the relationship between skin color and the expression of genes related to carotenoid biosynthesis during fruitripening in two citrus cultivars, ‘Shiranuhi’ (a hybrid mandarin cultivar) and ‘Suneat’ (mutant cultivar derived from a naturalbud mutation of ‘Shiranuhi’). We identifi ed 16 and 7 genes putatively involved in carotenoid biosynthesis and regulationvia phylogenetic analysis in sweet orange. Further, we determined the expression pattern of these genes by quantitative realtime reverse transcriptase PCR (qRT-PCR). The result showed that the expression levels of CsPSY (Cs6g15910), CsZDS(Cs3g11180), CsZ-ISO (Cs5g24730), CsBCH1 (Cs9g19270), CsFUL2 (Cs5g12280), CsTAGL1 (Cs7g16960), CsRIN1(Cs6g19680), CsRIN2 (Cs7g10980), and CsHY5 (Cs7g05140) were up-regulated in the skin of mutant cultivar ‘Suneat’ thanany other tissues of both citrus cultivars. Of these CsPSY , CsZDS , CsZ-ISO and CsBCH1 genes were related to carotenoidbiosynthesis and CsFUL2 , CsTAGL1 , CsRIN1 , CsRIN2 , and CsHY5 were known to involve in the regulation of carotenoidbiosynthesis. Our results reveal that the attractive dark orange skin color of ‘Suneat’ might be due to the up-regulation ofcarotenoid biosynthetic as well as regulatory genes and thereby higher levels carotenoids at ripening.
Md Abdur Rahim,AKM Zilani Rabbi,Khandker Shazia Afrin,정희정,Hoy-Taek Kim,박종인,노일섭 한국육종학회 2019 Plant Breeding and Biotechnology Vol.7 No.3
Cherry tomatoes are highly nutritious, flavory with a pleasant taste and are becoming increasingly popular to the consumers. The cherry tomato cv. ‘Minichal’ produced some dwarf plants along with normal plants. Lignin, a phenolic biopolymer is the key component of cell walls in plants. Here, we analyzed lignin biosynthesis-related genes in leaves, inflorescences and fruits of dwarf and normal cherry tomato plants by reverse-transcription quantitative PCR (RT-qPCR). Among analyzed genes, SlCCOAOMT1, SlCCOAOMT2, SlCCOAOMT3, SlF5H, and SlCOMT showed significantly higher expressions, in leaf and inflorescence of dwarf plants compared with the normal plants, while SlPAL1 showed a significantly higher expression only in the leaves. On the contrary, SlHCT and SlC3H showed significantly lower expression levels in the leaves and inflorescences of dwarf plants compared with normal ones. The results suggest that SlHCT and SlC3H might have an impact on the dwarf cherry tomato plants.