Article
Multidisciplinary Sciences
Neha Mittal, Juhi Bhardwaj, Shruti Verma, Rajesh Kumar Singh, Renu Yadav, D. Kaur, Akshay Talukdar, Neelam Yadav, Rajendra Kumar
Summary: The present study aimed to assess the nutritional diversity of chickpea and identify novel genetic resources for breeding purposes. Nine chickpea genotypes were analyzed for their nutritional and phytochemical properties. EST sequences from the NCBI database were analyzed for SSRs and primers were designed. The genotypes PUSA-1103, K-850, PUSA-1108, PUSA-1053, and several newly designed EST-SSR markers were identified as potential resources for macro and micro nutrients. The genotypes showed significant differences in nutritional properties. Cluster analysis based on both nutritional and molecular diversity showed some partial matching. The identified genetic resources can be used for expanding the germplasm base and developing breeding strategies for chickpea targeting macro and micro nutrients.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Huahao Jiang, Muhammad Waseem, Yong Wang, Sana Basharat, Xia Zhang, Yun Li, Pingwu Liu
Summary: Sugarcane is an important agricultural crop used for sugar production and biofuel. The genetic complexity of sugarcane makes it a challenging crop to improve. This study developed SSR markers from sugarcane ESTs, which can be used for genetic characterization and breeding efforts. Functional annotation analysis showed that the markers cover molecular, cellular, and biological pathways.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Yongxue Huo, Yikun Zhao, Liwen Xu, Hongmei Yi, Yunlong Zhang, Xianqing Jia, Han Zhao, Jiuran Zhao, Fengge Wang
Summary: This study introduced an integrated strategy for accurate SSR genotyping based on targeted sequencing, including a broad matching algorithm for efficient and precise typing of SSRs with single nucleotide variations. Experimental validation demonstrated extremely accurate typing results for both homozygous and heterozygous samples using this tool.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Jung Min Kim, Jae Il Lyu, Dong-Gun Kim, Nguyen Ngoc Hung, Jaihyunk Ryu, Jin-Baek Kim, Joon-Woo Ahn, Bo-Keun Ha, Soon-Jae Kwon
Summary: This study developed 58 novel EST-SSR markers from P. frutescens var. crispa and its mutant cultivar Antisperill, which can be used for population genetics and recombinant inbred line mapping analyses. These markers revealed significant genetic diversity and relationships among 94 P. frutescens genotypes, forming two major groups: Group I (var. crispa) and Group II (var. frutescens). The results provide insights into the genetic diversity and relationships of P. frutescens.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Forestry
Guliz Dogan, Ryunosuke Saito, Saneyoshi Ueno, Yoichi Hasegawa, Asako Matsumoto, Yoshinari Moriguchi
Summary: In this study, 16 EST-SSR markers were developed for Thujopsis dolabrata var. hondae using RNA sequencing data. These markers can be used for future linkage analysis and population genetic studies of this endemic conifer.
JOURNAL OF FOREST RESEARCH
(2023)
Article
Plant Sciences
Yang Liu, Xiaomei Fang, Tian Tang, Yudong Wang, Yinhuan Wu, Jinyu Luo, Haotian Wu, Yingqian Wang, Jian Zhang, Renwu Ruan, Meiliang Zhou, Kaixuan Zhang, Zelin Yi
Summary: This study sequenced the transcriptome of common buckwheat and Ukrainian daliqiao using high-throughput sequencing technology, obtaining a large amount of gene information and differentially expressed genes. SSR and EST-SSR loci were also detected. The clustering results verified the genetic relationship between common buckwheat and Ukrainian daliqiao. These findings are important for enriching the genetic information and marker-assisted selection breeding of buckwheat.
Article
Plant Sciences
Zhen Li, Lan Yun, Zhiqi Gao, Tian Wang, Xiaomin Ren, Yan Zhao
Summary: This study analyzed the genetic diversity and population structure of Psathyrostachys juncea using molecular markers, and evaluated the genetic differentiation related to tillering traits. The results showed that the overall genetic relationship of P. juncea individuals was relatively close, and there was a significant correlation between genetic relationship and geographical distribution.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biodiversity Conservation
Bin Dong, Zheng Deng, Wen Liu, Fazal Rehman, Tae-Jin Yang, Yongfang Huang, Haiguang Gong
Summary: SSRs derived from EST sequences in this study can be used for resource identification and dendrogram construction for resource collection and conservation.
CONSERVATION GENETICS RESOURCES
(2022)
Article
Agronomy
Abdelhalim I. Ghazy, Talal K. Al-Ateeq, Eid I. Ibrahim, Hussein M. Migdadi, Kotb A. Attia, Muhammad Javed, Muhammad Altaf Khan, Ibrahim Al-Ashkar, Abdullah Al-Doss
Summary: Morphological and SSR approaches were used to study the genetic diversity of Lolium rigidum genotypes from Saudi Arabia. The results showed that genotype location plays a major role in clustering. Additionally, SSR markers revealed considerable genetic variations among the genotypes and could differentiate between tolerant and sensitive populations.
Article
Agriculture, Dairy & Animal Science
S. Sajid Ali, S. Kuralkar, Ramendra Das, Varinder Raina, R. S. Kataria, Vikas Vohra
Summary: This study aimed to genetically characterize the Purnathadi buffalo population and explore genetic diversity using STR markers. The results showed high genetic diversity and suitability of markers for evaluating genetic diversity in Purnathadi buffaloes. These findings will support breeding plan design for genetic improvement and conservation strategies for the Purnathadi buffalo population.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Plant Sciences
S. Divakar, Ratnesh Kumar Jha, D. N. Kamat, Ashutosh Singh
Summary: In this study, EST-SSR primers related to sugar content were selected and validated using association analysis. One functional marker, SEM 407, was significantly associated with Brix% and sucrose content, potentially accelerating the sugarcane breeding program for sugar yield traits.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Luiza Chaves de Miranda Leonhardt Losada, Ruan Campos Monteiro, Jamile Ambrosio de Carvalho, Ferry Hagen, Matthew C. Fisher, Bram Spruijtenburg, Jacques F. Meis, Theun de Groot, Sarah Santos Goncalves, Ricardo Negroni, Rui Kano, Alexandro Bonifaz, Zoilo Pires de Camargo, Anderson Messias Rodrigues
Summary: This study developed a panel of highly polymorphic SSR markers suitable for genotyping Sporothrix species. PCR amplification revealed 240 alleles in 180 Sporothrix isolates, supporting the effectiveness of SSR markers in uncovering cryptic genetic diversity. The analysis of SSR diversity provided insights into the origins and transmission dynamics of cat-transmitted sporotrichosis.
Article
Biochemical Research Methods
Matthys J. Potgieter, Andrew J. M. M. Nel, Suereta Fortuin, Shaun Garnett, Jerome Wendoh, David Tabb, Nicola Mulder, Jonathan Blackburn
Summary: MetaNovo is an open-source software pipeline that integrates existing tools with a custom algorithm to produce targeted protein sequence databases for mass spectrometry metaproteomic analysis as an intermediate filtering step prior to standard sequence database search approaches. The software uses open-source tools to match peptide mass spectrometry spectra to sequence database entries and can be installed in a cluster or run standalone on a Linux machine. It is relevant for analyzing protein data from multiple organisms, where the exact species composition is unknown, and provides an avenue for analysis when accurate taxonomic characterization is not available.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Forestry
Mateja Kisek, Kristjan Jarni, Robert Brus
Summary: The study focuses on the morphological and genetic characteristics of European crab apple and the occurrence of hybrids in its populations. Hybridization with domesticated apples is observed in European crab apple populations, but hybrids and feral cultivars are limited in occurrence.
Article
Genetics & Heredity
Jie Lu, Yichen Zhang, Xia Diao, Kun Yu, Xiongwei Dai, Peng Qu, M. James C. Crabbe, Ticao Zhang, Qin Qiao
Summary: Fragaria nilgerrensis is a diploid wild strawberry widely distributed in Southwest China, showing high genetic diversity and significant genetic differentiation among populations. The study revealed that the species has high genetic diversity, while displaying little gene flow between populations.
