Article
Multidisciplinary Sciences
Arun K. Pandey, Libo Jiang, Menachem Moshelion, Sanbon Chaka Gosa, Ting Sun, Qin Lin, Rongling Wu, Pei Xu
Summary: Recent years have seen the emergence of high-throughput phenotyping techniques for studying plant physiological traits in response to environmental changes, yet a general framework linking these traits to DNA variants is still lacking. Researchers have developed a framework that integrates functional physiological phenotyping with functional mapping to understand how genotype translates into phenotype. This framework was demonstrated in a study using a tomato introgression line population to identify quantitative trait loci and explore how these loci control phenotypic plasticity under drought stress.
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.
Article
Agronomy
Edward Mwando, Tefera Tolera Angessa, Yong Han, Gaofeng Zhou, Chengdao Li
Summary: The study demonstrated significant impacts of salinity stress on survival traits of barley seedlings, particularly showing pronounced effects on shoot length and seedling vigour index length. QTL analysis revealed multiple genetic loci associated with salinity tolerance, some of which may potentially harbor candidate genes with functional significance.
Article
Biochemical Research Methods
Mercedeh Movassagh, Steven J. Schiff, Joseph N. Paulson
Summary: Recent advancements in genomics have allowed researchers to explore the interplay between genetic mutations and microbiome data, providing insights into disease progression and individual responses to treatment interventions.
Article
Agronomy
Modester Kachapila, Yuki Horiuchi, Hidetaka Nagasawa, Noe Michihata, Toru Yoshida, Yuta Kato, Paul C. Bethke, Kiyoaki Kato, Masahiko Mori
Summary: By studying the progeny of a cross between two bean cultivars, four genetic loci that affect epicotyl length were found, and the chromosomal location of one of these loci was narrowed down using molecular markers, which can be used for selecting bean cultivars with longer epicotyls that are suitable for mechanical weeding and harvesting.
Article
Plant Sciences
Lu Lu, Hui Liu, Yu Wu, Guijun Yan
Summary: This study identified and validated QTL related to heat tolerance in common wheat, which provides valuable genetic information for wheat breeding. The study found that 6 major QTL associated with different traits under heat stress and validated a hotspot QTL located on chromosome 4D.
Article
Biochemical Research Methods
Stien Mertens, Lennart Verbraeken, Heike Sprenger, Sam De Meyer, Kirin Demuynck, Bernard Cannoot, Julie Merchie, Jolien De Block, Jonathan T. Vogel, Wesley Bruce, Hilde Nelissen, Steven Maere, Dirk Inze, Nathalie Wuyts
Summary: This study evaluates the transferability of commonly used thermography analysis protocols from the field to greenhouse phenotyping platforms and finds that they can be used to monitor drought stress and develop transpiration rate prediction models in an indoor setup. The study also demonstrates that combining thermal infrared with hyperspectral imaging can further improve prediction accuracy.
Article
Biochemistry & Molecular Biology
Jae-Ryoung Park, Yoon-Hee Jang, Eun-Gyeong Kim, Sang-Sun Hur, Kyung-Min Kim, Deyong Ren
Summary: In this study, QTLs and candidate genes related to rice plant height regulation were identified, which can provide information and foundation for marker-assisted selection and breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Yueming Yi, Muhammad A. Hassan, Xinxin Cheng, Yiru Li, Huan Liu, Wuyun Fang, Qian Zhu, Shimei Wang
Summary: This study investigated the phenotypic data of multiple agronomic and physiological traits in 120 recombinant inbred lines (RILs) under drought stress. Genome-wide association study (GWAS) identified 9 quantitative trait loci (QTLs) associated with drought-related traits and predicted 10 candidate genes related to drought response. This study provides important information for understanding the drought tolerance mechanisms in rice and facilitates marker-assisted breeding of drought-tolerant rice varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Thierry Klanvi Tovignan, Yasmeen Basha, Steffen Windpassinger, Sruthy Maria Augustine, Rod Snowdon, Stjepan Vukasovic
Summary: Understanding sorghum response to water stress at different developmental stages is crucial for improving drought tolerance in sorghum varieties. This study aimed to characterize the agro-physiological responses and water use of sorghum under different drought scenarios. The experiment used a DroughtSpotter facility to track real-time water use. The results showed that DS2 had a greater impact on green leaf number and plant leaf area, but delayed flowering compared to DS1. Moreover, DS2 had taller plants and higher biomass production. However, DS1R and WW treatments outperformed both DS1 and DS2 in terms of grain yield. Transpiration and photosynthetic rates decreased concurrently with stomatal conductance, indicating stomatal down-regulation. However, the increase in intercellular CO2 concentration suggested a non-stomatal limitation of photosynthesis. Overall, DS2 had higher water use efficiency compared to WW and DS1 treatments, highlighting the importance of avoiding drought stress during the critical stage of growing point differentiation for better yield and water use efficiency.
Article
Biotechnology & Applied Microbiology
Rutwik Barmukh, Manish Roorkiwal, Vanika Garg, Aamir W. Khan, Liam German, Deepa Jaganathan, Annapurna Chitikineni, Jana Kholova, Himabindu Kudapa, Kaliamoorthy Sivasakthi, Srinivasan Samineni, Sandip M. Kale, Pooran M. Gaur, Someswar Rao Sagurthi, Yoselin Benitez-Alfonso, Rajeev K. Varshney
Summary: Chickpea production is susceptible to drought stress. A genetic region called 'QTL-hotspot' has been identified to control chickpea growth and improve crop production under drought. A non-synonymous substitution in the CaTIFY4b transcription factor has been found to regulate seed weight and organ size in chickpea, and ectopic expression of CaTIFY4b in a different plant species enhances root growth under water deficit. Gene expression analysis suggests that CaTIFY4b may regulate organ size under water deficit by modulating the expression of a transcriptional co-activator called GIF1. These findings provide new insights into the physiological and molecular mechanisms of chickpea growth and production under specific drought conditions.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Plant Sciences
Hongxu Dong, Techale Birhan, Nezif Abajebel, Misganu Wakjira, Tesfaye Mitiku, Cornelia Lemke, Vincent Vadez, Andrew H. Paterson, Kassahun Bantte
Summary: A backcross nested-association mapping population was used to study drought tolerance traits in an elite Ethiopian sorghum cultivar. The study identified QTLs for eight drought-responsive traits that are predictive of grain yield. The results show that the Ethiopian cultivar already possesses some favorable alleles for drought tolerance, but the exotic donors offer potential for further improving drought resilience. The selected traits were found to be significantly predictive of sorghum grain yield.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Rahul Chandnani, Changsoo Kim, Jinesh D. Patel, Hui Guo, Tariq Shehzad, Jason G. Wallace, Daohua He, Zhengsheng Zhang, Jeevan Adhikari, Sameer Khanal, Peng W. Chee, Andrew H. Paterson
Summary: This study investigated the genetic mapping of plant architecture, flowering time, and maturity traits in cotton, and identified a total of 27 QTLs associated with these traits. The findings suggest that this population structure can help reduce background noise and small effect QTLs, and the germplasm developed in this study may serve as potential pre-breeding material for improving cotton cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Jia Wang, Lin Mao, Zhaoqiong Zeng, Xiaobo Yu, Jianqiu Lian, Jun Feng, Wenying Yang, Jiangang An, Haiying Wu, Mingrong Zhang, Liezhao Liu
Summary: This study utilized QTL mapping, QTL-seq, and RNA sequencing to identify genes controlling protein content in soybean using the Nanxiadou 25 variety. Major QTLs on chromosome 20 were repeatedly detected across multiple environments, indicating potential candidate genes. Through gene expression analysis and clone sequencing, different SNPs and indels were identified as potentially responsible for changes in protein content.
Article
Plant Sciences
Fengqi Zhang, Jun Zhang, Zhiyan Ma, Laikun Xia, Xiangyang Wang, Lanxun Zhang, Yong Ding, Jianshuang Qi, Xinyuan Mu, Faxin Zhao, Tianhui Ji, Baojun Tang
Summary: This study identified four LRWC-related QTLs in maize seedlings under water deficit through QTL-seq analysis. Seven candidate genes that may control LRWC under water deficit at the seeding stage of maize were discovered using RNA-seq analysis, including ZmPrx64, ZmCIPK, HSP90, and ABCG34. These findings contribute to understanding the molecular basis of drought tolerance in maize seedlings and have implications for breeding drought-tolerant maize varieties.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Nutrition & Dietetics
Rajesh Kumar Rai, Sandhya S. Kumar, Sourav Sen Gupta, Devraj J. Parasannanavar, Thekkumkara Surendran Nair Anish, Anamitra Barik, Rajeev Kumar Varshney, Hemalatha Rajkumar
Summary: This article reviews the current burden of anaemia in India and argues that existing strategies to mitigate it are inadequate. It proposes a threefold strategy, including conducting a nationwide survey to estimate the burden of anaemia, further research on the dosage of iron supplementation in food fortification programs, and restraint in introducing new anaemia control programs.
BRITISH JOURNAL OF NUTRITION
(2023)
Review
Biotechnology & Applied Microbiology
Ali Raza, Javaria Tabassum, Ali Zeeshan Fakhar, Rahat Sharif, Hua Chen, Chong Zhang, Luo Ju, Vasileios Fotopoulos, Kadambot H. M. Siddique, Rakesh K. Singh, Weijian Zhuang, Rajeev K. Varshney
Summary: Climate change leads to various environmental stresses, including soil salinity, which negatively affects agricultural productivity. Plants respond to salinity stress by regulating ion homeostasis, inducing antioxidant defense systems, and producing phytohormones and osmoprotectants. Enhancing salt tolerance in plants is crucial for sustaining global agricultural productivity.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(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.
Article
Plant Sciences
Chong Zhang, Yuting Chen, Lihui Wang, Lu Liu, Xin Zhong, Panpan Chu, Meijia Gao, Hua Chen, Tiecheng Cai, Faqian Xiong, Xiurong Zhang, Ali Raza, Rong-long Pan, Rajeev K. Varshney, Fengzhen Liu, Weijian Zhuang
Summary: We identified and analyzed AhPLCP genes in cultivated peanut and confirmed the involvement of AhRD21B in chilling tolerance through experiments. We found 52 AhPLCP genes and grouped them into eight subfamilies. The promoters of AhPLCP genes contained stress responsive elements. AhPLCP genes were generally constitutively expressed, and many genes showed cold responsiveness. Heterologous expression of AhRD21B significantly enhanced cold tolerance in transgenic Arabidopsis by regulating cold-related genes. These findings provide important insights into the functions of AhPLCP genes in plant stress tolerance.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Yasir Sharif, Gandeka Mamadou, Qiang Yang, Tiecheng Cai, Yuhui Zhuang, Kun Chen, Ye Deng, Shahid Ali Khan, Niaz Ali, Chong Zhang, Ali Raza, Hua Chen, Rajeev K. Varshney, Weijian Zhuang
Summary: Peanut is an important food and feed crop that is affected by various stresses, and APYs play a crucial role in regulating cellular ATP levels under stress. In this study, we identified and characterized 17 APY homologs in peanut and studied their expression patterns and functional roles in different tissues and stress conditions. We found that the AhAPY2-1 gene showed abundant expression in the pericarp, and the functional characterization of AhAPY2-1 promoter in transgenic Arabidopsis plants suggested its potential use in enhancing the defensive abilities of the pericarp. These findings highlight the importance of APYs as a future research subject for peanut and other crops.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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)
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.
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)
Review
Plant Sciences
Ivica Djalovic, Sayanta Kundu, Rajeev Nayan Bahuguna, Ashwani Pareek, Ali Raza, Sneh L. Singla-Pareek, P. V. Vara Prasad, Rajeev K. Varshney
Summary: The global mean temperature is rapidly increasing due to anthropogenic practices, which leads to the emission of greenhouse gases. This temperature increase is predicted to reach 1.5°C above pre-industrial levels by 2050. The warming climate adversely impacts crop production, particularly maize, by affecting biochemical, physiological, and metabolic processes, resulting in poor growth and reduced yield. Heat stress tolerance in crops is regulated by various environmental factors, including humidity, vapor pressure deficit, soil moisture content, and solar radiation. Therefore, exploring genetic diversity in maize through landraces and wild accessions can help identify traits, genes, and QTLs that can enhance heat stress tolerance in elite cultivars.
Article
Plant Sciences
Vanika Garg, Aamir W. Khan, Kevin Fengler, Victor Llaca, Yuxuan Yuan, Tri D. Vuong, Charlotte Harris, Ting-Fung Chan, Hon Ming Lam, Rajeev K. Varshney, Henry T. Nguyen
Summary: Highly contiguous genome assemblies were generated for two economically important soybean cultivars, Williams 82 and Lee, using complementary genomics technologies and assembly algorithms. Centromeric and telomeric repeats were clearly annotated on all chromosomes of both cultivars. The complete reconstructions of several chromosomes without any gaps and the identification of protein-coding genes will greatly contribute to soybean research and improvement.
Article
Plant Sciences
Sejal Parmar, Pasupuleti Janila, Sunil S. Gangurde, Murali T. Variath, Vinay Sharma, Deekshitha Bomireddy, Surendra S. Manohar, Rajeev K. Varshney, Prashant Singam, Manish K. Pandey
Summary: This study identified genomic regions and candidate genes for high iron and zinc contents in groundnut through genetic mapping and quantitative trait locus analysis. The findings revealed that these candidate genes may play crucial roles in the accumulation of iron and zinc contents in groundnut seeds. The results of this study hold potential for further fine mapping and diagnostic marker development for high iron and zinc contents in groundnut.
Article
Plant Sciences
Cassandria G. Tay G. Fernandez, Philipp E. Bayer, Jakob Petereit, Rajeev Varshney, Jacqueline Batley, David Edwards
Summary: Many genome annotations contain false-positive gene models, which can lead to errors in phylogenetic and comparative studies. In this study, a method based on evolutionary conservation is proposed to predict gene models and identify potentially erroneous annotations. A set of 15,345 representative gene models from 12 legume assemblies is developed using this method, which can support genome annotations for other legumes.
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.