Fingerprinting in Cucumber and Melon (Cucumis spp.) Genotypes Using Morphological and ISSR Markers

Senthil Natesan,Rajiv Krishna Parvathaneni,Ashok Arunachalam Devaraj,Raveendran Muthuraja,Rajasree Venkatachalam,Arun Prathap Subramani,Pugalendhi Laxmanan 한국작물학회 2011 Journal of crop science and biotechnology Vol.14 No.1

In the present investigation, 13 Cucumis genotypes from different geographical areas of India were screened for genetic diversity using 19 morphological traits and 15 ISSR primers. The analysis of morphological traits grouped the accessions into six clusters. Cluster V contained the maximum number of genotypes namely Kanivellari, Long Green, Andaman Local, Perundurai Local, and Sempatti Local. Clusters I and VI contained the minimum number of genotypes. Among all the characters, the highest mean value was observed in fruit length (23.38) and the lowest mean value was observed in stripes on the blossom end (1.31). The 15 ISSR primers generated 109 polymorphic alleles. The average number of ISSR alleles generated was 8.3 per primer and the level of polymorphism was 87.20%. The ISSR primer UBC 825 was highly informative with a PIC value of 0.8934. The 13 genotypes were grouped into six clusters based on ISSR markers. Cluster III contained the maximum number of genotypes, namely Kanivellari,Sankagiri Local, Perundurai Local, Long Melon, and Sempatti Local, while Clusters I, II, IV, and V (Karur Local, Andaman Local,Edapaddi Local, and N 78, respectively) contained the minimum number of genotypes. The ISSR profile generated genotypes specific allele namely, UBC812_(700bp) and UBC812_(1000bp) for Cluster VI which contained Cucumis genotypes collected from the northern part of India. Similarly, UBC 808 produced specific allele UBC808_(650bp) formed in Cluster III which contained genotypes collected from Tamil Nadu and Kerala.

Starch Content and Cassava Mosaic Disease Genetic Diversity with Relation to Yield in South Indian Cassava (Manihot esculenta Crantz) Germplasm

Raghu Duraisamy,Senthil Natesan,Sakthi Ambothi Rathinasamy,Raveendran Muthurajan,Jana Jeevan Ramineni,Nageswari Karuppusamy,Pugalenthi Lakshmanan,Mohan Chokkappan,Karthikeyan Gandhi 한국작물학회 2011 Journal of crop science and biotechnology Vol.14 No.3

Cassava, family Euphorbiaceae, is the fifth most important staple food crop. The study of variability and diversity present in diverse cassava accessions maintained at the field genebank of TCRS, TNAU is essential to design the breeding program of cassava in TNAU. Hence, a study was carried out to assess the genetic diversity based on morphological traits and Simple Sequence Repeat (SSR) markers, identifying the SSR markers linked to a cassava mosaic disease-resistant QTL region. Genetic diversity among cassava germplasm accessions was estimated using 28 morphological traits and three SSR markers. The polymorphic information content (PIC) result gives high information for all the SSR markers. Morphological traits revealed 10 clusters and the SSR markers revealed 13 clusters at a similarity coefficient of 2.514 and 0.75, respectively. The SSR marker diversity revealed that the most promising clusters (II and XII) possessing accessions with yield attributing traits and cluster IX were grouped together due to low yield and CMD susceptibility. Morphological descriptors revealed variance for yield contributing traits. The first three principle components accounted for 10.8, 9.1, and 8.4%, respectively. Correlation studies showed significant correlation among yield and yield-attributing traits, which in turn influences yield. The morphological traits diversity reveals that cluster VI was the most promising cluster in which genotypes ME209 and ME460 possess higher yield and starch content with cassava mosaic disease (CMD) resistance. Most of the accessions grouped under cluster X belong to selection from International Centre for Tropical Agriculture (CIAT) collections and the cultivars under clusters I and II were true cassava seed (TCS) selections of India. The CMD-linked SSR marker which is reported in the previous studies have generated eight alleles and each were regressed with CMD resistance and resulted in non-significant linkage to CMD resistance.

Fingerprinting in Cucumber and Melon (Cucumis spp.) Genotypes Using Morphological and ISSR Markers

Parvathaneni, Rajiv Krishna,Natesan, Senthil,Devaraj, Ashok Arunachalam,Muthuraja, Raveendran,Venkatachalam, Rajasree,Subramani, Arun Prathap,Laxmanan, Pugalendhi 한국작물학회 2011 Journal of crop science and biotechnology Vol.14 No.1

Starch Content and Cassava Mosaic Disease Genetic Diversity with Relation to Yield in South Indian Cassava (Manihot esculenta Crantz) Germplasm

Duraisamy, Raghu,Rathinasamy, Sakthi Ambothi,Natesan, Senthil,Muthurajan, Raveendran,Ramineni, Jana Jeevan,Karuppusamy, Nageswari,Lakshmanan, Pugalenthi,Chokkappan, Mohan,Gandhi, Karthikeyan 한국작물학회 2011 Journal of crop science and biotechnology Vol.14 No.3

Cassava, family Euphorbiaceae, is the fifth most important staple food crop. The study of variability and diversity present in diverse cassava accessions maintained at the field genebank of TCRS, TNAU is essential to design the breeding program of cassava in TNAU. Hence, a study was carried out to assess the genetic diversity based on morphological traits and Simple Sequence Repeat (SSR) markers, identifying the SSR markers linked to a cassava mosaic disease-resistant QTL region. Genetic diversity among cassava germplasm accessions was estimated using 28 morphological traits and three SSR markers. The polymorphic information content (PIC) result gives high information for all the SSR markers. Morphological traits revealed 10 clusters and the SSR markers revealed 13 clusters at a similarity coefficient of 2.514 and 0.75, respectively. The SSR marker diversity revealed that the most promising clusters (II and XII) possessing accessions with yield attributing traits and cluster IX were grouped together due to low yield and CMD susceptibility. Morphological descriptors revealed variance for yield contributing traits. The first three principle components accounted for 10.8, 9.1, and 8.4%, respectively. Correlation studies showed significant correlation among yield and yield-attributing traits, which in turn influences yield. The morphological traits diversity reveals that cluster VI was the most promising cluster in which genotypes ME209 and ME460 possess higher yield and starch content with cassava mosaic disease (CMD) resistance. Most of the accessions grouped under cluster X belong to selection from International Centre for Tropical Agriculture (CIAT) collections and the cultivars under clusters I and II were true cassava seed (TCS) selections of India. The CMD-linked SSR marker which is reported in the previous studies have generated eight alleles and each were regressed with CMD resistance and resulted in non-significant linkage to CMD resistance

Prevalence, Patterns, and Genetic Association Analysis of Modic Vertebral Endplate Changes

Rishi Mugesh Kanna,Rajasekaran Shanmuganathan,Veera Ranjani Rajagopalan,Senthil Natesan,Raveendran Muthuraja,Kenneth Man Chee Cheung,Danny Chan,Patrick Yu Ping Kao,Anita Yee,Ajoy Prasad Shetty 대한척추외과학회 2017 Asian Spine Journal Vol.11 No.4

Study Design: A prospective genetic association study. Purpose: The etiology of Modic changes (MCs) is unclear. Recently, the role of genetic factors in the etiology of MCs has been evaluated. However, studies with a larger patient subset are lacking, and candidate genes involved in other disc degeneration phenotypes have not been evaluated. We studied the prevalence of MCs and genetic association of 41 candidate genes in a large Indian cohort. Overview of Literature: MCs are vertebral endplate signal changes predominantly observed in the lumbar spine. A significant association between MCs and lumbar disc degeneration and nonspecific low back pain has been described, with the etiopathogenesis implicating various mechanical, infective, and biochemical factors. Methods: We studied 809 patients using 1.5-T magnetic resonance imaging to determine the prevalence, patterns, distribution, and type of lumbar MCs. Genetic association analysis of 71 single nucleotide polymorphisms (SNPs) of 41 candidate genes was performed based on the presence or absence of MCs. SNPs were genotyped using the Sequenome platform, and an association test was performed using PLINK software. Results: The mean age of the study population (n=809) was 36.7±10.8 years. Based on the presence of MCs, the cohort was divided into 702 controls and 107 cases (prevalence, 13%). MCs were more commonly present in the lower (149/251, 59.4%) than in the upper (102/251, 40.6%) endplates. L4–5 endplates were the most commonly affected levels (30.7%). Type 2 MCs were the most commonly observed pattern (n=206, 82%). The rs2228570 SNP of VDR (p =0.02) and rs17099008 SNP of MMP20 (p =0.03) were significantly associated with MCs. Conclusions: Genetic polymorphisms of SNPs of VDR and MMP20 were significantly associated with MCs. Understanding the etiopathogenetic mechanisms of MCs is important for planning preventive and therapeutic strategies.

Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

Jayakodi, Murukarthick,Lee, Sang-Choon,Park, Hyun-Seung,Jang, Woojong,Lee, Yun Sun,Choi, Beom-Soon,Nah, Gyoung Ju,Kim, Do-Soon,Natesan, Senthil,Sun, Chao,Yang, Tae-Jin The Korean Society of Ginseng 2014 Journal of Ginseng Research Vol.38 No.4

Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

Comparative root protein profiles of Korean ginseng (Panax ginseng) and Indian ginseng (Withania somnifera).

Nagappan, Arulkumar,Karunanithi, Nithya,Sentrayaperumal, Sundareswaran,Park, Kwang-Ii,Park, Hyeon-Soo,Lee, Do Hoon,Kang, Sang-Rim,Kim, Jin-A,Senthil, Kalaiselvi,Natesan, Senthil,Muthurajan, Raveendran Institute for Advanced Research in Asian Science a 2012 The American journal of Chinese medicine Vol.40 No.1

<P>Ginsenosides and withanolides are the secondary metabolites from Panax ginseng and Withania somnifera, respectively. These compounds have similar biological properties. Two-dimensional electrophoresis (2-DE) analysis was utilized to reveal the protein profile in the roots of both plants, with the aim of clarifying similarly- and differentially-expressed proteins. Total proteins of Korea ginseng (P. ginseng) and Indian ginseng (W. somnifera) roots were separated by 2-DE using a pH 4-7 immobilized pH gradient strip in the first dimension and 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis in the second dimension. The protein spots were visualized by silver staining. Twenty-one P. ginseng proteins and 35 W. somnifera proteins were chosen for identification by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry; of these, functions were ascribed to 14 and 22 of the P. ginseng and W. somnifera proteins, respectively. Functions mainly included general cell metabolism, defense and secondary metabolism. ATPase and alcohol dehydrogenase proteins were expressed in both plants. The results of this study, to our knowledge, are the first to provide a reference 2-DE map for the W. somnifera root proteome, and will aid in the understanding of the expression and functions of proteins in the roots of Korean ginseng and Indian ginseng.</P>