Article
Multidisciplinary Sciences
Venugopal Vidya, Duraisamy Prasath, Mohandas Snigdha, Ramasamy Gobu, Charles Sona, Chandan Suravi Maiti
Summary: This study identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger for the first time, providing valuable resources for genetic diversity analysis and molecular verification of ginger genotypes. Gene ontology results indicated that the SSR loci identified in ginger are involved in various biological processes such as metabolism, growth, and development. The validation of 12 novel EST-SSR markers using PCR amplification and capillary electrophoresis revealed a total of 111 alleles, with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp.
Article
Plant Sciences
Shengfu Zhong, Wei Chen, Huai Yang, Jinliang Shen, Tianheng Ren, Zhi Li, Feiquan Tan, Peigao Luo
Summary: This study characterized the profile of SSRs in the high-quality assembled genome of Akebia trifoliata and developed a set of effective molecular markers. The results showed that the genome of A. trifoliata contained abundant SSRs, mainly consisting of single-nucleotide repeats and dinucleotide repeats. These SSRs were physically mapped on the chromosomes, and a positive correlation was found between the number of SSRs and chromosomal length. Furthermore, the SSR loci exhibited broad transferability, particularly the dinucleotide repeats, among all angiosperms. Additionally, the dinucleotide repeats were found to be potentially responsible for microsatellite origin and gene function protection.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Sudhakar Pandey, Punam Singh Yadav, Waquar Akhter Ansari, Maneesh Pandey, Luming Yang, Bijendra Singh, Rakesh Kumar Dubey, Prabhakar Mohan Singh, Jagdish Singh
Summary: The study on genome-wide SSR markers derived from cucumber provided valuable information on genetic diversity in 16 different cucurbits species, as well as comparative mapping with melon and watermelon. The large number of developed SSR markers in cucumber can be used for genetic linkage map construction, molecular mapping, and marker-assisted selection, while the cross-species transferable SSR markers could also be useful in other related species within the Cucurbitaceae family.
SCIENTIA HORTICULTURAE
(2021)
Article
Fisheries
Haitao Ma, Dongmei Yu, Jun Li, Yanping Qin, Yuehuan Zhang, Ziniu Yu
Summary: In this study, a consensus genetic map of Hong Kong oyster was constructed using microsatellite markers. The map will be important for future marker assisted selection and gene mapping. Tri-nucleotide microsatellite markers showed greater potential for these applications compared to di-nucleotide markers.
Article
Plant Sciences
Zifeng Ouyang, Yimeng Wang, Tiantian Ma, Gisele Kanzana, Fan Wu, Jiyu Zhang
Summary: This study utilized LTR retrotransposon-based markers to analyze the genetic diversity and population structure of Melilotus. A high amount of LTR retrotransposon sequences were identified, and 350 pairs of primers were designed for assessing polymorphisms. The transferable primers showed high informativeness, with 292 alleles detected at 47 LTR retrotransposon loci. The results provide important data for future breeding programs and implementing genetic improvements in the Melilotus genus.
Article
Agronomy
Manjushri Dinkar Dongare, Swapna Alex, K. B. Soni, K. P. Sindura, Deepa S. Nair, Roy Stephen, Elizabeth Jose
Summary: In this study, retrotransposon activity in the Piper nigrum L. genome was identified using IRAP retrotransposon-based molecular marker system. Three retrotransposons, Sukkula, Nikita, and 3'LTR, were found to be polymorphic in black pepper. Additionally, combinations of different primers were used to discover more polymorphic markers and evaluate the genetic diversity of black pepper.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Plant Sciences
Michele Antonio Savoia, Loredana Del Faro, Andrea Turco, Valentina Fanelli, Pasquale Venerito, Cinzia Montemurro, Wilma Sabetta
Summary: This research aimed to genetically and morphologically characterize traditional apricot and peach germplasms collected in old family orchards. Through genetic analysis, diversity masked by morphological traits was revealed. Genotyping in 15 and 18 SSRs showed an average polymorphic informativeness of 0.44 and 0.59 for apricot and peach, respectively, with a total of 70 and 144 alleles. These results have significant economic consequences for bioresource conservation and management.
Article
Plant Sciences
Sogo Nishio, Miyuki Kunihisa, Fumiya Taniguchi, Hiromi Kajiya-Kanegae, Shigeki Moriya, Yukie Takeuchi, Yutaka Sawamura
Summary: Developing new fruit and tea varieties is costly and labor-intensive, highlighting the importance of establishing a variety discrimination system to protect breeders' rights and producers' profits. Simple sequence repeat (SSR) databases are valuable for both next-generation sequencing and PCR-CE methods, aiding in variety discrimination.
Article
Agronomy
Samriti Sharma, Rajinder Kaur, Krishan Kumar, Heerendra Sagar
Summary: This study characterized seven peach cultivars based on morphological descriptors and EST-SSR markers of R. ellipticus. The results showed a wide range of phenotypic variability among the peach cultivars and high genetic variability based on the polymorphism of EST-SSR markers. Morphological descriptors and EST-SSR markers from R. ellipticus are an efficient source for detecting genetic variability among peach cultivars.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biochemical Research Methods
Jonatas Chagas de Oliveira, Andre Lucas Domingos da Silva, Lucielio Manoel da Silva, Eduardo Fernandes Formighieri, Leila Priscila Peters, Giselle Mariano Lessa de Assis, Carla Cristina da Silva, Anete Pereira de Souza, Tatiana de Campos
Summary: This study successfully created gene-derived microsatellite markers for forage peanut and found high polymorphism and information content. The study also discovered sequences related to multiple gene ontology functional groups. Furthermore, the microsatellite markers showed variable transferability to peanut and other wild Arachis species.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Article
Horticulture
Zhenshan Liu, Jing Zhang, Yan Wang, Hao Wang, Lei Wang, Lu Zhang, Muran Xiong, Wen He, Shaofeng Yang, Qing Chen, Tao Chen, Ya Luo, Yong Zhang, Haoru Tang, Xiaorong Wang
Summary: In this study, a comparative genomics strategy was used to construct a database containing thousands of polymorphic SSR loci for genetic identification and trait-association analysis of Chinese cherry. The results showed that these markers exhibited high levels of informativeness and transferability, and were significantly associated with traits such as soluble solids and fruit size in Chinese cherry.
Article
Biotechnology & Applied Microbiology
Hosam Safaa, Rawan Khaled, Suzy Isaac, Rofida Mostafa, Mohamed Ragab, Dalia A. A. Elsayed, Mostafa Helal
Summary: This study compares whole-genome and chromosome-wise microsatellite mining approaches in ducks and tests the transferability of markers between different duck species. The results show that there is no difference in the results obtained from chromosome-wise mining compared to the whole-genome approach.
JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Varun Hiremath, Kanwar Pal Singh, Neelu Jain, Kishan Swaroop, Pradeep Kumar Jain, Sapna Panwar, Nivedita Sinha
Summary: This study investigated the genetic diversity and relationships among 84 gladiolus genotypes using SSR markers. The results showed that these SSR markers can be used for cultivar identification, conservation, and crop improvement of gladiolus genotypes.
Review
Biochemical Research Methods
Natalia Segura-Alabart, Francesc Serratosa, Sergio Gomez, Alberto Fernandez
Summary: Agglomerative hierarchical clustering is a common tool for data analysis and visualization, but the nonuniqueness of clustering solutions when distances are tied is a critical problem. This study shows that about 46% of publications in the Scopus database are affected by this issue, with some articles having multiple possible hierarchical clusterings.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Chemistry, Physical
Viktor Klippenstein, Nico F. A. van der Vegt
Summary: In this study, a new approach is proposed to correct the dynamics of coarse-grained models by including memory effects, leading to more accurate simulation results and revealing previously neglected important factors in simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
V. Patial, R. Krishna, G. Arya, V. K. Singh, M. Agarwal, S. Goel, A. Jagannath, A. Kumar
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2016)
Article
Plant Sciences
Kamal Das, Showkat Hussain Ganie, Yash Mangla, Tanvir-Ul-Hassan Dar, Manju Chaudhary, Rakesh Kumar Thakur, Rajesh Tandon, S. N. Raina, Shailendra Goel
Article
Plant Sciences
Shivendra Kumar, Heena Ambreen, Murali T. Variath, Atmakuri R. Rao, Manu Agarwal, Amar Kumar, Shailendra Goel, Arun Jagannath
FRONTIERS IN PLANT SCIENCE
(2016)
Article
Plant Sciences
Neha Shukla, Rachita Yadav, Pritam Kaur, Simon Rasmussen, Shailendra Goel, Manu Agarwal, Arun Jagannath, Ramneek Gupta, Amar Kumar
MOLECULAR PLANT PATHOLOGY
(2018)
Article
Plant Sciences
Tanvir H. Dar, Soom N. Raina, Shailendra Goel
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2017)
Article
Medicine, General & Internal
Anita Sahu, Prabhash Kumar Jha, Amit Prabhakar, Heisnam Dinesh Singh, Neha Gupta, Tathagata Chatterjee, Tarun Tyagi, Swati Sharma, Babita Kumari, Somnath Singh, Velu Nair, Shailendra Goel, Mohammad Zahid Ashraf
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Ecology
Yash Mangla, Kamal Das, Sapinder Bali, Heena Ambreen, Soom Nath Raina, Rajesh Tandon, Shailendra Goel
Article
Plant Sciences
Heena Ambreen, Shivendra Kumar, Amar Kumar, Manu Agarwal, Arun Jagannath, Shailendra Goel
FRONTIERS IN PLANT SCIENCE
(2018)
Article
Multidisciplinary Sciences
Pritam Kaur, Neha Shukla, Gopal Joshi, Cheeni VijayaKumar, Arun Jagannath, Manu Agarwal, Shailendra Goel, Amar Kumar
Article
Genetics & Heredity
Nikhil K. Chrungoo, Rajkumari Jashmi Devi, Shailendra Goel, Kamal Das
JOURNAL OF GENETICS
(2019)
Article
Plant Sciences
Vivek Kumar Raxwal, Sourav Ghosh, Somya Singh, Surekha Katiyar-Agarwal, Shailendra Goel, Arun Jagannath, Amar Kumar, Vinod Scaria, Manu Agarwal
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Ecology
Sri N. S. Veera, Rajendra M. Panda, Mukunda D. Behera, Shailendra Goel, Partha S. Roy, Saroj K. Barik
Article
Genetics & Heredity
Daniel Regie Wahlang, Judith Mary Lamo, Shailendra Goel, Satyawada Rama Rao
Article
Microbiology
Chhavi Dawar, Ramesh K. Aggarwal
GENOME ANNOUNCEMENTS
(2015)
Article
Microbiology
Chhavi Dawar, Ramesh K. Aggarwal
GENOME ANNOUNCEMENTS
(2015)