Review
Plant Sciences
Pooja Rani Aggarwal, Lydia Pramitha, Pooja Choudhary, Roshan Kumar Singh, Pooja Shukla, Manoj Prasad, Mehanathan Muthamilarasan
Summary: This article summarizes the research trends in studying climate resilience and other essential traits in Setaria millet. It discusses the knowledge gap and explores how this information can be translated for crop improvement in related millets, biofuel crops, and cereals. Additionally, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Multidisciplinary Sciences
Pooja Choudhary, Pooja Shukla, Mehanathan Muthamilarasan
Summary: Agriculture faces the challenge of feeding a projected population of ten billion by 2050, but global warming and climate change threaten agricultural productivity. Genomics and genome modification technologies are crucial for improving climate-resilient traits, but research focuses mainly on staple crops, neglecting naturally climate-resilient small millets. Mainstreaming small millets for cultivation and using omics technologies to identify the molecular determinants of their climate-resilient traits are imperative for food and nutritional security.
Article
Agronomy
Koichi Futakuchi, Kalimuthu Senthilkumar, Aminou Arouna, Elke Vandamme, Mandiaye Diagne, Dule Zhao, Baboucarr Manneh, Kazuki Saito
Summary: Genetic improvement in rice has been a key focus in sub-Saharan Africa, with efforts to develop varieties adapted to the region's diverse production systems resulting in the release of numerous new rice varieties. While NERICA varieties are well-known, recent assessments show potential for further yield improvement with the introduction of upland indica materials from Asia. Adoption studies indicate that older varieties still dominate in many SSA countries, particularly in irrigated and rainfed lowland systems where Asian varieties are still prevalent.
FIELD CROPS RESEARCH
(2021)
Review
Food Science & Technology
Nurul Huda, Xiangdong Li, Tanzim Jahan, Yuqi He, Chaonan Guan, Kaixuan Zhang, Ainong Gao, Milen I. Georgiev, Meiliang Zhou
Summary: Coix is a minor cereal crop with diverse bioactive compounds and significant therapeutic effects, but there is insufficient attention on breeding and genomic studies of Coix.
FOOD REVIEWS INTERNATIONAL
(2023)
Review
Agronomy
Boddupalli M. Prasanna, Jill E. Cairns, P. H. Zaidi, Yoseph Beyene, Dan Makumbi, Manje Gowda, Cosmos Magorokosho, Mainassara Zaman-Allah, Mike Olsen, Aparna Das, Mosisa Worku, James Gethi, B. S. Vivek, Sudha K. Nair, Zerka Rashid, M. T. Vinayan, AbduRahman Beshir Issa, Felix San Vicente, Thanda Dhliwayo, Xuecai Zhang
Summary: Intensive breeding efforts and public-private partnerships have led to an increase in genetic gains, resulting in the deployment of elite climate-resilient maize cultivars in stress-prone environments. These efforts have successfully developed and deployed a variety of stress-tolerant maize cultivars in sub-Saharan Africa, Asia, and Latin America, playing a critical role in improving the livelihoods of smallholder farmers in the tropics facing climate-induced stresses.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Biochemistry & Molecular Biology
William Andres Lopez-Arboleda, Stephan Reinert, Magnus Nordborg, Arthur Korte
Summary: The study demonstrates that sampling locations have an impact on GWAS results in the model plant Arabidopsis thaliana, showing that certain traits are influenced by unique genetic effects in local populations. While using gene expression as a molecular phenotype, some genes are affected by shared variants globally, while others are affected by variants specific to subpopulations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Agronomy
Camilla Beate Hill, Chengdao Li
Summary: This review summarizes the current advances in understanding the detrimental effects of heat stress on cereal crop production at the physiological and genetic levels. It discusses the use of available genomic resources, genetic variation, candidate genes, and molecular markers for heat stress tolerance. Furthermore, it provides insights into crop genetic improvement for heat stress tolerance.
Article
Genetics & Heredity
Partha S. Biswas, M. M. Emam Ahmed, Wazifa Afrin, Anisar Rahman, A. K. M. Shalahuddin, Rafiqul Islam, Fahamida Akter, Md Abu Syed, Md Ruhul Amin Sarker, K. M. Ifterkharuddaula, Mohammad Rafiqul Islam
Summary: Increasing selection differential and decreasing cycle time can accelerate the rate of genetic improvement. Creating and capturing higher genetic with higher accuracy within the shortest possible time is crucial for enhancing genetic gain. Comprehensive yield testing at multi-locations at early generations together with shorter line fixation time can expedite the rapid recycling of parents in the breeding program through recurrent selection. Genomic selection is efficient in capturing high breeding value individuals, considering additive genetic effects of all genes, and reducing breeding cycle time, thereby enhancing genetic gain.
FRONTIERS IN GENETICS
(2023)
Review
Plant Sciences
Matthew P. Reynolds, Janet M. Lewis, Karim Ammar, Bhoja R. Basnet, Leonardo Crespo-Herrera, Jose Crossa, Kanwarpal S. Dhugga, Susanne Dreisigacker, Philomin Juliana, Hannes Karwat, Masahiro Kishii, Margaret R. Krause, Peter Langridge, Azam Lashkari, Suchismita Mondal, Thomas Payne, Diego Pequeno, Francisco Pinto, Carolina Sansaloni, Urs Schulthess, Ravi P. Singh, Kai Sonder, Sivakumar Sukumaran, Wei Xiong, Hans J. Braun
Summary: The review highlights the opportunities for enhancing heat and drought resilience in wheat through innovative breeding technologies, including the use of new tools in genetics and remote sensing, as well as identifying climate resilience traits from global wheat genetic resources. By improving crop design targets, developing field-based screening tools, applying genomic technologies, and advancing next-generation breeding methods, a research pipeline is created to boost heat and drought resilience.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Plant Sciences
Rubab Zahra Naqvi, Hamid Anees Siddiqui, Muhammad Arslan Mahmood, Syed Najeebullah, Aiman Ehsan, Maryam Azhar, Muhammad Farooq, Imran Amin, Shaheen Asad, Zahid Mukhtar, Shahid Mansoor, Muhammad Asif
Summary: Improving crop traits is essential for developing superior crop varieties that can withstand climate change and associated stress challenges. Genomics and marker-assisted breeding have provided new opportunities and methods for enhancing crop yield and quality.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
P. Senguttuvel, G. Padmavathi, C. Jasmine, D. Sanjeeva Rao, C. N. Neeraja, V. Jaldhani, P. Beulah, R. Gobinath, J. Aravind Kumar, S. V. Sai Prasad, Lv Subba Rao, A. S. Hariprasad, K. Sruthi, D. Shivani, RM. Sundaram, Mahalingam Govindaraj
Summary: Rice is a staple cereal consumed in large quantities in Asian countries, providing calories for billions of people. However, the preference for polished rice has led to a loss of nutrition. Micronutrient deficiencies, such as zinc and iron, are major health challenges. Biofortification of rice has made progress in enhancing grain zinc, iron, and protein content.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Christen M. Bossu, Marina Rodriguez, Christine Rayne, Debra A. Chromczak, Philip G. Higgins, Lynne A. Trulio, Kristen C. Ruegg
Summary: The accelerating loss of global biodiversity is worsened by habitat fragmentation and inbreeding in small populations. To address this issue, conservation practitioners often use assisted breeding programs to increase genetic diversity in declining populations. This study demonstrates the value of genomic approaches in enhancing genetic diversity through assisted breeding efforts, focusing on a highly inbred population of Western burrowing owls. The findings highlight the importance of genomic tools in preserving the adaptive potential of small, inbred populations at risk of further decline.
Review
Forestry
Swathi Balakrishnan, Yasodha Ramasamy, Suma Arun Dev
Summary: This article discusses the threat to teak genetic resources in India and suggests the use of genetically diverse planting materials and appropriate geographic niches for establishing new plantations. It emphasizes the importance of considering adaptive potential in the face of climate change for effective conservation and management strategies.
TREE GENETICS & GENOMES
(2023)
Review
Biology
Jun Xiao, Bao Liu, Yingyin Yao, Zifeng Guo, Haiyan Jia, Lingrang Kong, Aimin Zhang, Wujun Ma, Zhongfu Ni, Shengbao Xu, Fei Lu, Yuannian Jiao, Wuyun Yang, Xuelei Lin, Silong Sun, Zefu Lu, Lifeng Gao, Guangyao Zhao, Shuanghe Cao, Qian Chen, Kunpu Zhang, Mengcheng Wang, Meng Wang, Zhaorong Hu, Weilong Guo, Guoqiang Li, Xin Ma, Junming Li, Fangpu Han, Xiangdong Fu, Zhengqiang Ma, Daowen Wang, Xueyong Zhang, Hong-Qing Ling, Guangmin Xia, Yiping Tong, Zhiyong Liu, Zhonghu He, Jizeng Jia, Kang Chong
Summary: This review summarizes recent advances in genomic research and genetic improvement of bread wheat, with a focus on the contributions made by Chinese scientists. The availability of multiple reference wheat genome assemblies and cutting-edge technologies such as precise genome editing tools has opened up new possibilities for functional genomic research in wheat. Insights gained from these advances will enhance our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits, and facilitate the development of modern breeding techniques for more sustainable agriculture worldwide.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Review
Agriculture, Dairy & Animal Science
Frances Margaret Titterington, Rachel Knox, Steven James Morrison, Masoud Shirali
Summary: The study finds that genetic selection for cattle with better temperament can reduce the risk of cattle causing harm to humans and property. By conducting a literature search, the research examines heritability, genomic associations, and correlations between behavioral and production traits. The results suggest that large population studies provide more accurate heritability estimates, and gene associations with behavioral traits are found on most chromosomes. The study also concludes that there is a low correlation between behavior and production traits. A large-scale study of a specific population is needed to further understand the genetic relationships.
Article
Agronomy
Athanasios Sclavounos, Petros Roussos, Sotiria Milla, Panagiotis Kostas, Yiannis Samaras, Carlo Pozzi, Johiruddin Molla, Annapurna Chitikineni, Rajeev K. Varshney, Andreas Voloudakis
Summary: In this study, an ex situ collection of 60 fig accessions from Greece and other Mediterranean countries was established and analyzed using SSR loci. The results showed low allelic variation and high heterozygosity in Greek fig genotypes, indicating extensive outbreeding. Furthermore, there was little correlation between genetic makeup and geographical origin of the fig accessions. An identification key scheme for fig cultivars was developed for cultivar discrimination and intellectual property protection.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Himabindu Kudapa, Rutwik Barmukh, Vanika Garg, Annapurna Chitikineni, Srinivasan Samineni, Gaurav Agarwal, Rajeev K. K. Varshney
Summary: In this study, the transcriptome dynamics of six contrasting heat stress responsive chickpea genotypes were investigated using an RNA-seq approach. A total of 14,544 differentially expressed genes were identified, mainly involved in metabolic processes, cell wall remodeling, calcium signaling, and photosynthesis. Pathway analysis revealed the enrichment of metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction under heat stress conditions. Candidate genes underlying heat tolerance component traits were also identified. This study provides important insights into the molecular mechanisms of heat stress response in chickpea and facilitates the development of climate-resilient chickpea varieties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Bushra Rasool, Baby Summuna, Ivica Djalovic, Tariq Ahmad Shah, Parveez Ahmed Sheikh, Sachin Gupta, Sandhya Tyagi, Sierra Bilal, Rajeev Kumar Varshney, Ishfaq Abidi, Jitendra Kumar, R. Varma Penmetsa, Imtiyaz Khandey, Upendra Kumar, Parvaze Ahmad Sofi, Mohd Anwar Khan, Mohd Ashraf Bhat, Fahim Jeelani Wani, Mahendar Thudi, Reyazul Rouf Mir
Summary: This study identified 26 significant marker-trait associations (MTAs) for Fusarium wilt (FW) resistance in chickpea. Most genotypes showed resistance at the seedling stage but susceptibility at the reproductive stage. Five major and two stable MTAs were identified, which can be useful in chickpea breeding programs.
Editorial Material
Plant Sciences
Rohini Garg, Prasanta K. K. Subudhi, Rajeev K. K. Varshney, Mukesh Jain
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Chong Zhang, Wenping Xie, Huiwen Fu, Yuting Chen, Hua Chen, Tiecheng Cai, Qiang Yang, Yuhui Zhuang, Xin Zhong, Kun Chen, Meijia Gao, Fengzhen Liu, Yongshan Wan, Manish K. Pandey, Rajeev K. K. Varshney, Weijian Zhuang
Summary: QTL-seq was used to identify a candidate genomic region associated with resistance to Ralstonia solanacearum, which contained 180 nonsynonymous SNPs and 14 InDels affecting 75 and 11 putative candidate genes, respectively. Two diagnostic SNP markers were validated and showed high phenotypic variation in resistant and susceptible lines.
FRONTIERS IN PLANT SCIENCE
(2023)
Editorial Material
Plant Sciences
Rajeev K. Varshney
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Jiang Ye, Huabing Liang, Xueyang Zhao, Na Li, Dongji Song, Jiepeng Zhan, Xinfa Wang, Jinxing Tu, Rajeev Kumar Varshney, Jiaqin Shi, Hanzhong Wang
Summary: Heterosis refers to the better performance of cross progeny compared with inbred parents, and its utilization contributes greatly to agricultural production. Several hypotheses have been proposed to explain heterosis mainly including dominance, over-dominance (or pseudo-overdominance) and epistasis. However, systematic dissection and verification of these hypotheses are rarely documented.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Editorial Material
Plant Sciences
Ali Raza, Abhishek Bohra, Rajeev K. Varshney
Summary: A study on crop genomes has demonstrated the significance of structural variations (SVs) in genetic improvement. Researchers, through a graph-based pan-genome approach, identified 424,085 genomic SVs in pearl millet and gained new insights into its heat tolerance. We discuss the potential of these SVs to accelerate breeding of pearl millet under harsh environments.
TRENDS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Himabindu Kudapa, Arindam Ghatak, Rutwik Barmukh, Palak Chaturvedi, Aamir Khan, Sandip Kale, Lena Fragner, Annapurna Chitikineni, Wolfram Weckwerth, Rajeev K. K. Varshney
Summary: In this study, transcriptomics, proteomics, and metabolomics datasets were generated from root tissues of four drought-responsive chickpea genotypes to unravel the complex mechanisms regulating drought response. Integration of transcriptomics and proteomics data identified key hub proteins involved in antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis. Metabolomics data integration revealed significant correlations between six metabolites and galactose metabolism. The integration of root-omics data also identified key candidate genes in the drought-responsive QTL-hotspot region, providing valuable insights into the molecular mechanisms underlying drought stress response in chickpea.
Article
Genetics & Heredity
Muhammad Khuram Razzaq, Reena Rani, Guangnan Xing, Yufei Xu, Ghulam Raza, Muqadas Aleem, Shahid Iqbal, Muhammad Arif, Zahid Mukhtar, Henry T. Nguyen, Rajeev K. Varshney, Kadambot H. M. Siddique, Junyi Gai
Summary: This study characterized J-protein genes in soybean and identified those highly expressed and responsive during flower and seed development. The phylogeny, structure, motif analysis, chromosome location, and expression of these genes were also investigated. The findings suggest that J-protein genes could be involved in the growth period of soybean and provide a basis for further functional research.
Article
Agronomy
Shanjida Rahman, Shahidul Islam, Eviatar Nevo, Md Atik Us Saieed, Qier Liu, Rajeev Kumar Varshney, Wujun Ma
Summary: This study characterized the agronomic and shoot morphological traits of 263 wild emmer accessions and found a large variation in these traits. Correlation analysis and principal component analysis revealed the associations between traits and overall variability. Cluster analysis and comparative analysis further demonstrated the variations between different wild emmer accessions, and some wild emmer accessions showed superior performance based on multiple traits.
Biographical-Item
Biotechnology & Applied Microbiology
Rajeev K. K. Varshney, Nils Stein, Jochen Reif
Summary: Professor Graner has made significant contributions to the field of international crop plant genomics research over the past four decades. His work includes the development of the first integrated RFLP map of barley and advancements in functional genomics. He has also played a key role in plant genetic resources conservation and utilization.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Min Sun, Haidong Yan, Aling Zhang, Yarong Jin, Chuang Lin, Lin Luo, Bingchao Wu, Yuhang Fan, Shilin Tian, Xiaofang Cao, Zan Wang, Jinchan Luo, Yuchen Yang, Jiyuan Jia, Puding Zhou, Qianzi Tang, Chris Stephen Jones, Rajeev K. K. Varshney, Rakesh K. K. Srivastava, Min He, Zheni Xie, Xiaoshan Wang, Guangyan Feng, Gang Nie, Dejun Huang, Xinquan Zhang, Fangjie Zhu, Linkai Huang
Summary: A free, web-accessible, user-friendly millets multi-omics database platform (Milletdb) has been developed, which contains six millets and their one related species genomes, as well as stress-related multi-omics data. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools and can effectively serve researchers in the mining of key genes, genome editing, and molecular breeding of millets.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Cell Biology
Puxuan Du, Quanqing Deng, Wenyi Wang, Vanika Garg, Qing Lu, Lu Huang, Runfeng Wang, Haifen Li, Dongxin Huai, Xiaoping Chen, Rajeev K. Varshney, Yanbin Hong, Hao Liu
Summary: The study reveals that the FAD2 gene regulates the growth pathway in peanut leaves by inhibiting the expression of the cytokinin synthesis gene LOG in vascular cells, thereby repressing leaf growth.
Article
Plant Sciences
Thippeswamy Danakumara, Tapan Kumar, Neeraj Kumar, Basavanagouda Siddanagouda Patil, Chellapilla Bharadwaj, Umashankar Patel, Nilesh Joshi, Shayla Bindra, Shailesh Tripathi, Rajeev Kumar Varshney, Sushil Kumar Chaturvedi
Summary: Identifying a suitable production environment and understanding the genotype by environmental interactions are crucial for achieving yield stability in chickpeas. Different models were used to analyze the interactions and stability of genotypes. Stabile genotypes can serve as parental lines for heat-stress tolerance breeding programs.