Article
Plant Sciences
Dinakaran Elango, Wanyan Wang, Mahender Thudi, Sheelamary Sebastiar, Bharathi Raja Ramadoss, Rajeev K. Varshney
Summary: This study aimed to identify genetic factors associated with seed oligosaccharides in chickpea and identified potential candidate genes for sugar metabolism and transport. Quantitative analysis of sugar contents in chickpea showed wide variations between different accessions. Nine candidate genes were identified, which could be utilized in breeding and genetic engineering to improve sugar profiles in legumes and other crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Rosy Raman, Annie Warren, Marzena Krysinska-Kaczmarek, Maheswaran Rohan, Niharika Sharma, Nicole Dron, Jenny Davidson, Kevin Moore, Kristy Hobson
Summary: This study conducted genome-wide association analysis using genotyping-by-sequencing data and phenotypic data, identifying genomic regions associated with Ascochyta blight (AB) resistance. The study also validated candidate genes and single nucleotide polymorphism markers associated with resistance. These findings provide valuable information for chickpea breeding programs to make genetic gains through marker-assisted and genomic selection strategies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Manish Roorkiwal, Aditi Bhandari, Rutwik Barmukh, Prasad Bajaj, Vinod Kumar Valluri, Annapurna Chitikineni, Sarita Pandey, Bharadwaj Chellapilla, Kadambot H. M. Siddique, Rajeev K. Varshney
Summary: Micronutrient malnutrition is a global concern, and this study focused on enhancing the nutrient content of chickpea. By evaluating a diverse set of chickpea germplasm, the study identified significant variations in nutritional traits and conducted genome-wide association studies to identify marker-trait associations. The study also explored the effect of heterozygosity on trait detection. Seven promising accessions were identified as potential donors for developing nutrient-rich, high-yielding chickpea varieties.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Ashutosh Kushwah, Dharminder Bhatia, Rutwik Barmukh, Inderjit Singh, Gurpreet Singh, Shayla Bindra, Suruchi Vij, Bharadwaj Chellapilla, Aditya Pratap, Manish Roorkiwal, Shiv Kumar, Rajeev K. Varshney, Sarvjeet Singh
Summary: This study investigated drought tolerance traits and associated quantitative trait loci (QTLs) in chickpea. By evaluating recombinant inbred lines derived from an interspecific cross, the researchers identified major QTLs and genomic regions related to drought tolerance. These findings can be utilized in genomics-assisted breeding to enhance drought tolerance in chickpea varieties.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Daqiu Sun, Sibo Chen, Zhenhai Cui, Jingwei Lin, Meiling Liu, Yueting Jin, Ao Zhang, Yuan Gao, Huiying Cao, Yanye Ruan
Summary: Brace roots are crucial for supporting the above-ground part of maize plants and play a role in growth and development. Understanding the genetic basis of brace root traits can contribute to improving mechanized harvest and increasing production. A GWAS analysis identified 27 candidate genes associated with brace root traits.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Surbhi Shriti, Sampa Das
Summary: The MYB transcription factors, especially the newly discovered CaMYB78, play a crucial role in plants' response to abiotic stress factors such as salinity and drought. The heterologous expression of CaMYB78 in tobacco plants enhances antioxidation activities and confers better stress tolerance capacity. The upregulation of antioxidant genes and stress-related genes in transgenic plants suggests that CaMYB78 is important for abiotic stress response in plants.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Agronomy
Shamseldeen Eltaher, Ahmed Sallam, Hamdy A. Emara, Ahmed A. Nower, Khaled F. M. Salem, Andreas Boerner, P. Stephen Baenziger, Amira M. Mourad
Summary: Wheat is a crucial crop with high genetic variation in yield traits. GWAS identified significant SNP markers associated with yield traits, but no common markers were found between different environments.
Article
Plant Sciences
Jie Li, Xiaohua Yao, Youhua Yao, Likun An, Zongyun Feng, Kunlun Wu
Summary: In this study, a genome-wide association study was performed on hulless barley to identify SNP markers associated with drought-resistance traits. Eight candidate genes potentially contributed to drought resistance were obtained near significant SNPs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Lisi Wu, Yifu Wang, Shenglong Wu, Zhengchang Wu, Wenbin Bao
Summary: In this study, the relationship between FUT8 expression and E. coli resistance was systematically verified. The results showed that FUT8 was significantly upregulated in the duodenum and jejunum of E. coli F18-sensitive individuals. Knockdown of FUT8 decreased the adhesion of E. coli F18 to cells. Transcriptome analysis revealed the significant effect of FUT8 on glycosphingolipid biosynthesis and Toll-like signaling pathways. The core promoter of FUT8 and a mutation inhibiting its transcriptional binding activity were identified. These findings provide insights into the role of FUT8 in regulating E. coli resistance in pigs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
A. S. M. Faridul Islam, Wardah Mustahsan, Rodante Tabien, Joseph M. Awika, Endang M. Septiningsih, Michael J. Thomson
Summary: This study identified the genetic basis of six mineral elements in rice grain through genome-wide association study, and discovered novel SNP markers associated with mineral elements. Analysis of genes near these significant markers can provide insights into their potential functions and guide future experimental validation.
Article
Genetics & Heredity
Dario Rueda, Henry O. Awika, Renesh Bedre, Devi R. Kandel, Kranthi K. Mandadi, Kevin Crosby, Carlos A. Avila
Summary: This study found that there is a high variability in AsA content in spinach germplasm, which can be utilized for breeding improvement. Through genome-wide association study, 490 significant markers associated with AsA content were identified, indicating the complex inheritance of this trait. The identified markers can differentiate between high and low AsA content accessions, providing important information for breeding programs.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Doerthe Siekmann, Gisela Jansen, Anne Zaar, Andrzej Kilian, Franz Joachim Fromme, Bernd Hackauf
Summary: This study conducted a genome-wide association study in rye, identifying key genes associated with multiple traits and establishing an NIRS calibration model and a novel high-density genetic linkage map, providing crucial references for genetic traits and hybrid breeding research in rye.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Chiti Agarwal, Weidong Chen, Rajeev Kumar Varshney, George Vandemark
Summary: This study identified genetic markers and candidate genes associated with resistance to Pythium ultimum in chickpea. It also conducted genome-wide association studies using a chickpea diversity panel to discover significant SNPs and candidate genes associated with disease resistance. The study provides tools for molecular breeding of resistance to P. ultimum in chickpea.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Rahele Panahabadi, Asadollah Ahmadikhah, Lauren S. McKee, Paer K. Ingvarsson, Naser Farrokhi
Summary: The genetic variability of MLG and starch contents in rice whole grains was analyzed, revealing a negative correlation between MLG content and grain starch content. A new genome-wide association study identified seven significant QTLs associated with MLG content and two QTLs associated with starch content. Novel genes related to MLG content included a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Philanim Wungmarong Shimray, C. Bharadwaj, B. S. Patil, S. Mukesh Sankar, Neeraj Kumar, Sneha Priya Pappula Reddy, Tripti Singhal, Venkatraman Hegde, Swarup K. Parida, Manish Roorkiwal, Rajeev K. Varshney, Preeti Verma
Summary: An association mapping panel of 380 chickpea genotypes was evaluated for yield-contributing parameters, focusing on seed weight and seed number. AMMI analysis identified ideal genotypes for these traits, providing strategic planning for yield improvement through component trait breeding.
Review
Biotechnology & Applied Microbiology
Udita Basu, Swarup K. Parida
Summary: Plants have adapted to different environments by regulating developmental factors, resulting in variations in traits that contributed to their survival. Key developmental pathways, such as CLAVATA-WUSCHEL, GID1-DELLA, LAZY1-TAC1, and TFL1-FT, play significant roles in plant architecture. Allelic variants of these regulators shaped crops during domestication. With genome-editing techniques, it is possible to manipulate these developmental pathways to customize crops for specific environments and increase yield stability.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Uday Chand Jha, Harsh Nayyar, Swarup K. Parida, R. Beena, Jiayin Pang, Kadambot H. M. Siddique
Summary: Phosphorus (P) is a crucial nutrient for plant growth, but its sources are non-renewable, raising concerns for sustainable agriculture and food security. Improving plant P-use efficiency (PUE) is necessary for intensive cropping systems, and this review explores various breeding approaches and tools to enhance PUE in grain legumes. The genetic architecture of PUE traits is complex, influenced by both genetics and the environment. Advances in genomics and functional genomics have provided insights into the underlying genetic mechanisms and pathways related to PUE, while novel breeding schemes and tools offer opportunities for designing P-use-efficient cultivars in low-P environments.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Anurag Daware, Ankit Malik, Rishi Srivastava, Durdam Das, Ranjith K. K. Ellur, Ashok K. K. Singh, Akhilesh K. K. Tyagi, Swarup K. K. Parida
Summary: The advent of the pangenome era has uncovered previously unknown genetic variation in diverse crop plants, but conventional single-reference genotyping methods often fail to capture a large portion of this variation, leading to reference bias. To overcome this, a Rice Pangenome Genotyping Array (RPGA) was developed, enabling rapid genotyping based on the entire 3K rice pangenome. This array provides a cost-effective solution and has been successfully applied in various areas, such as genome-wide association studies, population structure analysis, and marker-assisted selection.
Article
Plant Sciences
Virevol Thakro, Naveen Malik, Udita Basu, Rishi Srivastava, Laxmi Narnoliya, Anurag Daware, Nidhi Varshney, Jitendra K. Mohanty, Deepak Bajaj, Vikas Dwivedi, Shailesh Tripathi, Uday Chand Jha, Girish Prasad Dixit, Ashok K. Singh, Akhilesh K. Tyagi, Hari D. Upadhyaya, Swarup K. Parida
Summary: Identifying a bHLH transcription factor, CabHLH10, and its related genes in chickpea provides a potential molecular approach for breeding drought-tolerant and high-yielding cultivars.
Editorial Material
Plant Sciences
Rohini Garg, Prasanta K. K. Subudhi, Rajeev K. K. Varshney, Mukesh Jain
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Genetics & Heredity
Gayacharan, Swarup K. Parida, Nupur Mondal, Rashmi Yadav, Harinder C. Vishwakarma, Jai C. Rana
Summary: Legumes play a crucial role in ensuring food and nutritional security as well as environmental sustainability. However, their yield and production have been hindered by various factors, leading to a decline in legume consumption and protein-related malnutrition in India. To address this, efforts have been made to utilize the vast collection of legume genetic resources conserved globally to identify ideal donors and enhance genetic gains. Large-scale phenotyping combined with omics-based science is being used to identify target traits. Additionally, wild relatives are being explored for pre-breeding to overcome genetic limitations in major legume crops.
FRONTIERS IN GENETICS
(2023)
Article
Biology
Arunima Mahto, Antima Yadav, P. V. Aswathi, Swarup K. Parida, Akhilesh K. Tyagi, Pinky Agarwal
Summary: By analyzing the transcriptomes and miRNomes of small-grained and large-grained indica rice, this study identified the crucial role of the S3 stage in enhancing grain size and discovered several transcription factor and miRNA families that influence grain size. A Domino effect model was proposed to explain the regulation of grain size. Additionally, a rice grain development database was established for easy access to the data generated in this study.
Review
Plant Sciences
Ankita Prusty, Shivam Sharma, Naveen Malik, Sanjay Kapoor, Akhilesh Kumar Tyagi
Summary: The Mediator complex in plants, encoded by multiple paralogous genes, regulates various aspects of plant growth and development through a complex network. It plays critical roles in shaping plant architecture, responding to hormonal signals, maintaining metabolite homeostasis, and producing non-coding RNAs.
CRITICAL REVIEWS IN PLANT SCIENCES
(2023)
Article
Chemistry, Applied
Paras Sharma, Giridhar Goudar, Anil Kumar Chandragiri, R. Ananthan, K. Subhash, Anitha Chauhan, T. Longvah, Mohar Singh, Rakesh Bhardwaj, Swarup Kumar Parida, Amit Kumar Singh, Debasis Chattopadhyay, Debasis Chattopadhyay
Summary: A study evaluated the nutrient composition, anti-nutrients, and mineral composition of 38 ricebean accessions cultivated in India. The accessions showed variation in protein, dietary fiber, oligosaccharides, free sugars, resistant starch, iron, zinc, and selenium content. The study employed hierarchical clustering analysis and principal component analysis to analyze the diversity of nutrients and anti-nutrients across the ricebean accessions.
Article
Plant Sciences
Rama Shankar, Anuj Kumar Dwivedi, Vikram Singh, Mukesh Jain
Summary: Drought stress is a significant threat to rice productivity. This study analyzed the genetic variations between drought-tolerant and drought-sensitive rice cultivars and identified millions of single nucleotide polymorphisms and insertions/deletions. The genetic variations were unevenly distributed throughout the rice genome, with a higher frequency near the transcription start and stop sites. The study also identified cis-regulatory motifs and differentially expressed genes associated with stress-related transcription factors, providing valuable insights into candidate genes for drought stress tolerance in rice.
PHYSIOLOGIA PLANTARUM
(2023)
Review
Biochemistry & Molecular Biology
Udita Basu, Swarup K. Parida
Summary: This review explores the developmental similarities and peculiarities in chickpea and its close relatives pea and Medicago. Key features in chickpea which have potential in yield enhancement have been discussed. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored, despite advancements in next-generation sequencing and genomics tools.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Anuj Kumar Dwivedi, Vikram Singh, Khalid Anwar, Ashwani Pareek, Mukesh Jain
Summary: Drought is a serious threat to rice production caused by climate change. Comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars identified the molecular mechanisms involved in drought tolerance/response. This study characterized the global transcriptome, proteome, and metabolome profiles and integrated them to reveal the role of transporters, translational machinery, aromatic amino acids, soluble sugars, and auxiliary carbohydrate metabolism in drought tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Shalini Tiwari, Mukesh Jain, Sneh Lata Singla-Pareek, Prem L. Bhalla, Mohan B. Singh, Ashwani Pareek
Summary: The study found that the salt-tolerant rice genotype Pokkali plays a crucial role in stress response through the regulation of long non-coding RNA (lncRNA). These lncRNAs modulate various cellular processes, including transcriptional regulation, ion homeostasis, and secondary metabolite production. Furthermore, lncRNAs are predicted to bind to stress-responsive transcription factors. Additionally, some lncRNAs are also regulated under other abiotic stresses and phytohormone treatments, indicating possible cross-talk and further functional characterization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
