Article
Education, Scientific Disciplines
Hai-feng Tian, Qiao-mu Hu, Zhong Li
Summary: The study characterized SSRs in the assembled genome of M. albus and developed polymorphic SSRs for future breeding programs. High genetic diversity but excess of homozygotes were found in one breeding population, providing baseline information for future breeding programs. The SSR markers will be useful for genetic mapping and diversity analysis studies in swamp eel.
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
Biotechnology & Applied Microbiology
Kai Liu, Nan Xie
Summary: Microsatellites, also known as SSRs, are widely used markers in genetic applications. This study presents a pipeline for discovering polymorphic SSRs in species without reference genomes, using black Amur bream as a model. The pipeline successfully identified polymorphic SSRs and designed primers for SSR genotyping, providing an alternative approach for mining SSRs in non-model organisms.
Article
Multidisciplinary Sciences
Qianqian Tian, Bin Huang, Jianjian Huang, Bo Wang, Le Dong, Xin Yin, Chun Gong, Qiang Wen
Summary: This study identified 97,510 SSR loci in Camellia chekiangoleosa based on the full-length transcriptome sequence. Mononucleotide and dinucleotide SSRs were found to be the main repeat types. Functional annotations of unigene sequences containing SSR sites were obtained by comparing the data with databases. The experiments verified that dinucleotide and pentanucleotide SSRs located in UTR regions produced more polymorphic markers. The developed SSR markers showed higher levels of polymorphism in several C. chekiangoleosa populations.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Hui Wang, Shenghan Gao, Yu Liu, Pengcheng Wang, Zhengwang Zhang, De Chen
Summary: The study introduces a pipeline for the rapid development of polymorphic SSR markers from multi-sample genomic data. By genotyping multiple individuals using bioinformatic software based on resequencing data, highly polymorphic SSRs can be detected prior to experimental validation, significantly improving efficiency and reducing experimental effort. Overall, the pipeline demonstrates a successful application of NGS technology for mining and developing molecular markers for ecological and evolutionary studies.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Shuai-Peng Si, Chun-Jing Wang, Ji-Zhong Wan, Yu-Lin Qian, Chun-Hui Zhang
Summary: In this study, genomic DNA of P. brachytyla was sequenced and 10 useful microsatellite loci were identified. These polymorphic microsatellite markers showed high polymorphism for P. brachytyla, providing a basis for future conservation and genetic research on this rare plant species.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Multidisciplinary Sciences
Sandhya Tyagi, Anuj Kumar, Tinku Gautam, Renu Pandey, Sachin Rustgi, Reyazul Rouf Mir
Summary: Heat stress is a significant abiotic factor that hinders wheat production worldwide, and miRNA-derived SSR markers have been successfully developed and used in genetic diversity studies in wheat. The study identified 13 miRNA-SSR markers located on 11 common wheat chromosomes, with some markers showing promise in discriminating heat-tolerant and heat-susceptible genotypes. This research suggests the potential of these markers in improving heat tolerance and other adaptive traits in wheat and other crops through marker-assisted breeding programs.
Article
Plant Sciences
Wei Xu, Jiancheng Wang, Changyan Tian, Wei Shi, Lei Wang
Summary: This study developed a set of polymorphic microsatellite markers to analyze the genetic diversity of three populations of S. aralocaspica in Xinjiang, China. The genetic diversity of S. aralocaspica was found to be moderate to high, providing a valuable resource for future genetic studies and breeding programs of S. aralocaspica and other species in Suaeda.
Article
Agronomy
Sundas Shahzad, Muhammad Saeed, Shagufta Perveen, Muhammad Azeem, Iqra Sajjad, Shazia Saeed, Muhammad Naeem, Alia Javed, Iqra Sultan, Ukasha Faria, Sana Maryam, Muhammad Zaid Yousaf
Summary: In this study, genetic diversity and population structure of sixty Saccharum spp. hybrids were assessed using SSR markers. The results showed that SSR markers were effective tools for evaluating genetic diversity and varietal fingerprinting in sugarcane hybrids, which could aid in selecting the best parents for planned crosses.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Song Lu
Summary: In this study, a transcriptome analysis of Anoectochilus emeiensis was conducted, resulting in the identification of numerous unigenes and EST-SSR markers. The findings of this study will be valuable for future population genetic studies of A. emeiensis.
Article
Agronomy
Annu Lata, Hemant Kumar Yadav, Narayanan K. Nair
Summary: This study estimated the genetic diversity and population structure of wood-apple samples from 16 states in India using 24 polymorphic SSRs. The results showed moderate to high genetic diversity among wood-apple samples and identified 14 diverse samples and 9 highly informative SSRs that are useful for breeding and conservation of this species.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Agriculture, Multidisciplinary
Selda Daler, Rustem Cangi
Summary: The study characterized 50 grape varieties grown in Yozgat using molecular methods and SSR analysis, revealing a high level of diversity in alleles and genetic characteristics. Cluster analysis showed that these grape varieties can be grouped into 2 main clusters, with varying genetic similarity rates among them.
TURKISH JOURNAL OF AGRICULTURE AND FORESTRY
(2022)
Article
Multidisciplinary Sciences
Marta Jaskulak, Franck Vandenbulcke, Agnieszka Rorat, Maxime Pauwels, Kararzyna Zorena, Pawel Grzmil, Barbara Plytycz
Summary: E. fetida and E. andrei are important earthworm species that play crucial roles in soil. By sequencing their genomes, we identified a large number of microsatellite markers that can be used for studying their genetic diversity and population genetics.
Article
Biochemistry & Molecular Biology
Anita Tilwari, Rajesh Sharma
Summary: The genetic diversity of Gloriosa superba studied in this research can be utilized for identification, conservation, and future breeding program, benefiting pharmaceutical industries. The study highlighted the importance of genetic diversity in endangered medicinal plants like Gloriosa superba.
MOLECULAR BIOLOGY REPORTS
(2021)
Review
Plant Sciences
Junrey C. Amas, William J. W. Thomas, Yueqi Zhang, David Edwards, Jacqueline Batley
Summary: Improving disease resistance remains a key focus in breeding programs for Brassica species due to intensive cultivation and climate change. Genomic advancements have facilitated the understanding of Brassica genomes and the identification of disease resistance genes, allowing for marker assisted selection and targeted gene manipulation. This review highlights the development of genomic resources, including improved genome references and pathogen genomics, which contribute to the discovery and enhancement of disease resistance traits. Incorporating these advancements with new breeding techniques and improved phenotyping will make disease resistance improvement in Brassica species more efficient and responsive.
Article
Forestry
Saeid Ghasemi Esfahlan, Roghayeh Hemmati, Shohreh Mohebbi, Jacqueline Batley, Mahdi Arzanlou
Summary: Trunk disease is a major problem on grapevine in Zanjan province, and the causes of the decline are still unknown. This study investigated factors related to grapevine decline in vineyards of Zanjan province. Fungal isolates were collected and identified, with Phaeoacremonium minimum, Microsphaeropsis olivacea, and Kalmusia variispora identified as the dominant species and main trunk pathogens in the region.
Article
Plant Sciences
Harsh Raman, Nawar Shamaya, Ramethaa Pirathiban, Brett McVittie, Rosy Raman, Brian Cullis, Andrew Easton
Summary: Canola plants have reduced crop yield and oil content under water-deficit conditions, especially during reproductive stages. This study analysed the genetic factors affecting seed yield and related traits in canola under well-watered and water-deficit conditions. The analysis revealed multiple genomic regions associated with flowering time, plant height, and seed yield under different water regimes. The study identified specific QTLs that were stable across environments and showed potential for improving water-use efficiency in canola breeding programs.
Review
Agronomy
Yuxuan Yuan, Bao Linh Ton, William J. W. Thomas, Jacqueline Batley, David Edwards
Summary: The changing climate poses significant threats to agriculture and the ability to ensure sufficient global food production. With the expanding population, there is an urgent demand to increase crop productivity to meet the rising food demand. Producing climate-smart crop varieties together with developing new agronomic management strategies are strategies that may help address this issue. Recent advances in genomics-assistant breeding, the use of high-throughput DNA sequencing, high-resolution phenotyping, and advanced genome engineering can support the development of advanced, climate resilient crops.
Article
Plant Sciences
Mark C. C. Derbyshire, Jacob Marsh, Soodeh Tirnaz, Henry T. T. Nguyen, Jacqueline Batley, Philipp E. E. Bayer, David Edwards
Summary: This study analyzes the soybean pangenome to identify fatty acid biosynthesis genes and their sequence diversity. It finds possible instances of gene missing in wild soybean and identifies missense variants in fatty acid biosynthesis genes. The frequency of these variants has been significantly reduced during domestication.
Article
Plant Sciences
Muhammad Burhan Bootter, Jing Li, Wenxu Zhou, David Edwards, Jacqueline Batley
Summary: Phytosterols, natural compounds found in higher plants, play various roles in plant growth regulation and stress tolerance. They also influence the development and reproductive rate of herbivorous insects and agronomic traits in plants. This study analysed the phytosterol composition in Brassica napus cultivars and related wild species, revealing significant variability in the wild accessions' phytosterol profiles. Some wild accessions exhibited high levels of specific phytosterols, which could contribute to plant stress tolerance and insect resistance in crop breeding.
Review
Food Science & Technology
Ting Xiang Neik, Kadambot H. M. Siddique, Sean Mayes, David Edwards, Jacqueline Batley, Tafadzwanashe Mabhaudhi, Beng Kah Song, Festo Massawe
Summary: The recent Russia-Ukraine conflict has caused significant concerns about global food security, particularly for low-income countries reliant on grain imports. The conflict has led to restricted access to staple food crops and soaring food prices, impacting the livelihoods of many. This review emphasizes the importance of diversifying agrifood systems to enhance resilience in future food supply chains.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2023)
Review
Genetics & Heredity
Benjamin J. Nestor, Philipp E. Bayer, Cassandria G. Tay Fernandez, David Edwards, Patrick M. Finnegan
Summary: Identifying homologs is crucial for analyzing genetic patterns and evolutionary relationships among species. Manual pipelines are commonly used for identifying small gene families accurately. However, issues with homology searches can affect the validity of the analysis. This article proposes several approaches to mitigate these issues.
Review
Biochemistry & Molecular Biology
Bo Song, Weidong Ning, Di Wei, Mengyun Jiang, Kun Zhu, Xingwei Wang, David Edwards, Damaris A. Odeny, Shifeng Cheng
Summary: Advances in DNA sequencing technology have revolutionized genomics, particularly in plant genetics and crop breeding. Population-based genome resequencing studies have provided insights into genetic diversity and functional significance in plants, with a focus on economically important crops. However, limited access to population genomic datasets hinders further analysis, calling for a more open and collaborative approach to data sharing. The decreasing costs of DNA sequencing and advances in analysis technologies promise further expansion and improved understanding of plant trait genetics and breeding design.
Article
Agronomy
Toby Bird, Benjamin J. Nestor, Philipp E. Bayer, Guannan Wang, Albina Ilyasova, Clement E. Gille, Bryce E. H. Soraru, Kosala Ranathunge, Anita A. Severn-Ellis, Ricarda Jost, Wolf-Ruediger Scheible, Maheshi Dassanayake, Jacqueline Batley, David Edwards, Hans Lambers, Patrick M. Finnegan
Summary: This study investigated the delayed greening mechanism in Hakea prostrata, a phosphorus-use-efficient plant. Gene expression analysis revealed a longer temporal separation between leaf cell growth and chloroplast development in H. prostrata compared to species without delayed greening. This delayed greening strategy is a nutrient-saving adaptation in severely phosphorus-impoverished landscapes.
Article
Biotechnology & Applied Microbiology
Junrey C. C. Amas, Philipp E. E. Bayer, Wei Hong Tan, Soodeh Tirnaz, William J. W. Thomas, David Edwards, Jacqueline Batley
Summary: This study utilized the B. rapa pangenome to identify a comprehensive repertoire of RGAs in B. rapa. It found that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. Comparative analysis with B. napus revealed significant RGA conservation between the two species. The study also identified candidate RGAs located within known B. rapa disease resistance QTL and clarified the genetic relationship of blackleg resistance genes.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Agronomy
Angela P. Van de Wouw, Jack L. Scanlan, Hawlader A. Al-Mamun, Marie-Helene Balesdent, Lydia Bousset, Lenka Burketova, Luis del Rio Mendoza, W. G. Dilantha Fernando, Coreen Franke, Barbara J. Howlett, Yong-Ju Huang, E. Eirian Jones, Birger Koopmann, Suhaizan Lob, Ali Z. Mirabadi, Bridgit C. Nugent, Gary Peng, Franco R. Rossi, Huibrecht Schreuder, Annie R. Tabone, Gert J. Van Coller, Jacqueline Batley, Alexander Idnurm
Summary: This study collected isolates of Leptosphaeria maculans and L. biglobosa from different countries to represent the global diversity of these fungal pathogens. The genomes of L. maculans isolates were sequenced, and the distribution and identity of avirulence gene alleles were determined. The study found geographical separation of populations within L. maculans isolates, providing a resource for studying disease-causing mechanisms and discovering new resistance traits.
Article
Agronomy
Aldrin Y. Cantila, William J. W. Thomas, Philipp E. Bayer, David Edwards, Jacqueline Batley
Summary: This study predicts and identifies the number and function of TM-CC genes in Brassicaceae plants, and suggests that they may play a significant role in disease resistance. It provides a valuable resource for the study of TM-CCs and their potential functional involvement in resistance.
Article
Multidisciplinary Sciences
Muhammad Azam Khan, Wallace A. Cowling, Surinder Singh Banga, Martin J. Barbetti, Aldrin Y. Cantila, Junrey C. Amas, William J. W. Thomas, Ming Pei You, Vikrant Tyagi, Baudh Bharti, David Edwards, Jacqueline Batley
Summary: Identifying the molecular and genetic basis of resistance to Sclerotinia stem rot is crucial for the management of this disease in rapeseed/canola. The study investigated the inheritance pattern of Sclerotinia stem rot resistance in a breeding population of B. napus and identified a significant QTL for resistance. The findings provide valuable insights into the genetics of resistance and offer potential markers for breeding cultivars with enhanced resistance.
Review
Biotechnology & Applied Microbiology
Haifei Hu, Armin Scheben, Jian Wang, Fangping Li, Chengdao Li, David Edwards, Junliang Zhao
Summary: Inversions significantly impact plant adaptation and gene functions. This review highlights advancements in technology and methodology that allow a better understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
