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Saavedra-Díaz C, Trujillo-Montenegro JH, Jaimes HA, Londoño A, Villareal FAS, López LO, Valens CAV, López-Gerena J, Riascos JJ, Quevedo YM, Aguilar FS. Genetic association analysis in sugarcane (Saccharum spp.) for sucrose accumulation in humid environments in Colombia. BMC PLANT BIOLOGY 2024; 24:570. [PMID: 38886648 PMCID: PMC11184777 DOI: 10.1186/s12870-024-05233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/31/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Sucrose accumulation in sugarcane is affected by several environmental and genetic factors, with plant moisture being of critical importance for its role in the synthesis and transport of sugars within the cane stalks, affecting the sucrose concentration. In general, rainfall and high soil humidity during the ripening stage promote plant growth, increasing the fresh weight and decreasing the sucrose yield in the humid region of Colombia. Therefore, this study aimed to identify markers associated with sucrose accumulation or production in the humid environment of Colombia through a genome-wide association study (GWAS). RESULTS Sucrose concentration measurements were taken in 220 genotypes from the Cenicaña's diverse panel at 10 (early maturity) and 13 (normal maturity) months after planting. For early maturity data was collected during plant cane and first ratoon, while at normal maturity it was during plant cane, first, and second ratoon. A total of 137,890 SNPs were selected after sequencing the 220 genotypes through GBS, RADSeq, and whole-genome sequencing. After GWAS analysis, a total of 77 markers were significantly associated with sucrose concentration at both ages, but only 39 were close to candidate genes previously reported for sucrose accumulation and/or production. Among the candidate genes, 18 were highlighted because they were involved in sucrose hydrolysis (SUS6, CIN3, CINV1, CINV2), sugar transport (i.e., MST1, MST2, PLT5, SUT4, ERD6 like), phosphorylation processes (TPS genes), glycolysis (PFP-ALPHA, HXK3, PHI1), and transcription factors (ERF12, ERF112). Similarly, 64 genes were associated with glycosyltransferases, glycosidases, and hormones. CONCLUSIONS These results provide new insights into the molecular mechanisms involved in sucrose accumulation in sugarcane and contribute with important genomic resources for future research in the humid environments of Colombia. Similarly, the markers identified will be validated for their potential application within Cenicaña's breeding program to assist the development of breeding populations.
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Affiliation(s)
- Carolina Saavedra-Díaz
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
- Pontificia Universidad Javeriana, Cali, Colombia
| | | | - Hugo Arley Jaimes
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | - Alejandra Londoño
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | | | - Luis Orlando López
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | | | - Jershon López-Gerena
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | - John J Riascos
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia
| | | | - Fernando S Aguilar
- Centro de Investigación de la Caña de Azúcar de Colombia (CENICAÑA), Cali, Colombia.
- Colombian Sugarcane Research Center (Cenicaña), km 26 Vía Cali-Florida, Valle del Cauca, Colombia.
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Kalairaj A, Rajendran S, Panda RC, Senthilvelan T. A study on waterlogging tolerance in sugarcane: a comprehensive review. Mol Biol Rep 2024; 51:747. [PMID: 38874798 DOI: 10.1007/s11033-024-09679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
Sugarcane (Saccharum officinarum) is an important crop, native to tropical and subtropical regions and it is a major source of sugar and Bioenergy in the world. Abiotic stress is defined as environmental conditions that reduce growth and yield below the optimum level. To tolerate these abiotic stresses, plants initiate several molecular, cellular, and physiological changes. These responses to abiotic stresses are dynamic and complex; they may be reversible or irreversible. Waterlogging is an abiotic stress phenomenon that drastically reduces the growth and survival of sugarcane, which leads to a 15-45% reduction in cane's yield. The extent of damage due to waterlogging depends on genotypes, environmental conditions, stage of development and duration of stress. An improved understanding of the physiological, biochemical, and molecular responses of sugarcane to waterlogging stress could help to develop new breeding strategies to sustain high yields against this situation. The present review offers a summary of recent findings on the adaptation of sugarcane to waterlogging stress in terms of growth and development, yield and quality, as well as biochemical and adaptive-molecular processes that may contribute to flooding tolerance.
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Affiliation(s)
- Ashmitha Kalairaj
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamilnadu, 602 105, India
| | - Swethashree Rajendran
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamilnadu, 602 105, India
| | - Rames C Panda
- Chemical Engineering Division, RajaLakshmi Engineering College, Thandalam, Chennai, Tamilnadu, 602 105, India
| | - T Senthilvelan
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, Tamilnadu, 602 105, India.
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Huang H, Wei Y, Huang S, Lu S, Su H, Ma L, Huang W. Integrated metabolomic and transcriptomic analyses provide insights into regulation mechanisms during bulbous stem development in the Chinese medicinal herb plant, Stephania kwangsiensis. BMC PLANT BIOLOGY 2024; 24:276. [PMID: 38605285 PMCID: PMC11007893 DOI: 10.1186/s12870-024-04956-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Stephania kwangsiensis Lo (Menispermaceae) is a well-known Chinese herbal medicine, and its bulbous stems are used medicinally. The storage stem of S. kwangsiensis originated from the hypocotyls. To date, there are no reports on the growth and development of S. kwangsiensis storage stems. RESULTS The bulbous stem of S. kwangsiensis, the starch diameter was larger at the stable expanding stage (S3T) than at the unexpanded stage (S1T) or the rapidly expanding stage (S2T) at the three different time points. We used ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and Illumina sequencing to identify key genes involved in bulbous stem development. A large number of differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified. Based on the differential expression profiles of the metabolites, alkaloids, lipids, and phenolic acids were the top three differentially expressed classes. Compared with S2T, significant changes in plant signal transduction and isoquinoline alkaloid biosynthesis pathways occurred at both the transcriptional and metabolic levels in S1T. In S2T compared with S3T, several metabolites involved in tyrosine metabolism were decreased. Temporal analysis of S1T to S3T indicated the downregulation of phenylpropanoid biosynthesis, including lignin biosynthesis. The annotation of key pathways showed an up-down trend for genes and metabolites involved in isoquinoline alkaloid biosynthesis, whereas phenylpropanoid biosynthesis was not completely consistent. CONCLUSIONS Downregulation of the phenylpropanoid biosynthesis pathway may be the result of carbon flow into alkaloid synthesis and storage of lipids and starch during the development of S. kwangsiensis bulbous stems. A decrease in the number of metabolites involved in tyrosine metabolism may also lead to a decrease in the upstream substrates of phenylpropane biosynthesis. Downregulation of lignin synthesis during phenylpropanoid biosynthesis may loosen restrictions on bulbous stem expansion. This study provides the first comprehensive analysis of the metabolome and transcriptome profiles of S. kwangsiensis bulbous stems. These data provide guidance for the cultivation, breeding, and harvesting of S. kwangsiensis.
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Affiliation(s)
- Hao Huang
- Guangxi Vocational University of Agriculture, Nanning, 530009, China.
| | - Ying Wei
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Shaojun Huang
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Shijian Lu
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Huasheng Su
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Liuhui Ma
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Weiping Huang
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
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Li C, Iqbal MA. Leveraging the sugarcane CRISPR/Cas9 technique for genetic improvement of non-cultivated grasses. FRONTIERS IN PLANT SCIENCE 2024; 15:1369416. [PMID: 38601306 PMCID: PMC11004347 DOI: 10.3389/fpls.2024.1369416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Under changing climatic scenarios, grassland conservation and development have become imperative to impart functional sustainability to their ecosystem services. These goals could be effectively and efficiently achieved with targeted genetic improvement of native grass species. To the best of our literature search, very scant research findings are available pertaining to gene editing of non-cultivated grass species (switch grass, wild sugarcane, Prairie cordgrass, Bermuda grass, Chinese silver grass, etc.) prevalent in natural and semi-natural grasslands. Thus, to explore this novel research aspect, this study purposes that gene editing techniques employed for improvement of cultivated grasses especially sugarcane might be used for non-cultivated grasses as well. Our hypothesis behind suggesting sugarcane as a model crop for genetic improvement of non-cultivated grasses is the intricacy of gene editing owing to polyploidy and aneuploidy compared to other cultivated grasses (rice, wheat, barley, maize, etc.). Another reason is that genome editing protocols in sugarcane (x = 10-13) have been developed and optimized, taking into consideration the high level of genetic redundancy. Thus, as per our knowledge, this review is the first study that objectively evaluates the concept and functioning of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 technique in sugarcane regarding high versatility, target specificity, efficiency, design simplicity, and multiplexing capacity in order to explore novel research perspectives for gene editing of non-cultivated grasses against biotic and abiotic stresses. Additionally, pronounced challenges confronting sugarcane gene editing have resulted in the development of different variants (Cas9, Cas12a, Cas12b, and SpRY) of the CRISPR tool, whose technicalities have also been critically assessed. Moreover, different limitations of this technique that could emerge during gene editing of non-cultivated grass species have also been highlighted.
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Affiliation(s)
- Chunjia Li
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, Yunnan, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, China
| | - Muhammad Aamir Iqbal
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, Yunnan, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, China
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5
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Li H, Gui Y, Zhu K, Wei J, Zhang R, Yang R, Tang L, Zhou H, Liu X. Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1243664. [PMID: 37885666 PMCID: PMC10598656 DOI: 10.3389/fpls.2023.1243664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.
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Affiliation(s)
- Haibi Li
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Yiyun Gui
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kai Zhu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jinju Wei
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ronghua Zhang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongzhong Yang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liqiu Tang
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Hui Zhou
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xihui Liu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
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6
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Corbion C, Smith-Ravin J, Marcelin O, Bouajila J. An Overview of Spirits Made from Sugarcane Juice. Molecules 2023; 28:6810. [PMID: 37836653 PMCID: PMC10574467 DOI: 10.3390/molecules28196810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/05/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Among the family of sugarcane spirits, those made from juice are diverse and often produced in a traditional way. They must be distinguished from other sugarcane spirits, which are more widely produced and made from other sugarcane derivatives, such as molasses. These alcoholic beverages contribute significantly to the socio-economic development of many countries. However, despite ancestral know-how, there is a lack of contemporary data required to characterize some sugarcane juice spirits (SCJSs) and to overcome the current and future threats that producers will have to face. While preserving their authenticity and specificity, SCJS producers expect to improve and ensure sufficient yield and a superior quality product. Even if the scientific knowledge on these spirits is not comparable, the available data could help identify the critical points to be improved in the making process. This review aims to present the main SCJSs encountered worldwide, defining their specific features through some important aspects with, notably, references to the complex notion of terroir. To continue, we discuss the main steps of the SCJS process from harvesting to aging. Finally, we expose an inventory of SCJS's chemical compositions and of their sensory description that define the specific organoleptic properties of these spirits.
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Affiliation(s)
- Claudine Corbion
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS-INPT-UPS, 31062 Toulouse, France;
| | - Juliette Smith-Ravin
- Groupe BIOSPHERES, Campus de Schoelcher, 97275 Schoelcher, Martinique, France; (J.S.-R.); (O.M.)
| | - Odile Marcelin
- Groupe BIOSPHERES, Campus de Schoelcher, 97275 Schoelcher, Martinique, France; (J.S.-R.); (O.M.)
| | - Jalloul Bouajila
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS-INPT-UPS, 31062 Toulouse, France;
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Niazi R, Parveen G, Noman M, Mukhtar N, Hadayat N, Sami A, Khaliq B, Shrestha J, Ullah I. Comparative expression analysis of sucrose phosphate synthase gene family in a low and high sucrose Pakistani sugarcane cultivars. PeerJ 2023; 11:e15832. [PMID: 37719124 PMCID: PMC10503496 DOI: 10.7717/peerj.15832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/11/2023] [Indexed: 09/19/2023] Open
Abstract
Sugarcane is the world's largest cultivated crop by biomass and is the main source of sugar and biofuel. Sucrose phosphate synthase (SPS) enzymes are directly involved in the synthesis of sucrose. Here, we analyzed and compared one of the important gene families involved in sucrose metabolism in a high and low sucrose sugarcane cultivar. A comprehensive in silico analysis of the SoSPS family displayed their phylogenetic relationship, gene and protein structure, miRNA targets, protein interaction network (PPI), gene ontology and collinearity. This was followed by a spatial expression analysis in two different sugarcane varieties. The phylogenetic reconstruction distributed AtSPS, ZmSPS, OsSPS, SoSPS and SbSPS into three main groups (A, B, C). The regulatory region of SoSPS genes carries ABRE, ARE, G-box, and MYC as the most dominant cis-regulatory elements. The PPI analysis predicted a total of 14 unique proteins interacting with SPS. The predominant expression of SPS in chloroplast clearly indicates that they are the most active in the organelle which is the hub of photosynthesis. Similarly, gene ontology attributed SPS to sucrose phosphate synthase and glucosyl transferase molecular functions, as well as sucrose biosynthetic and disaccharide biological processes. Overall, the expression of SPS in CPF252 (high sucrose variety) was higher in leaf and culm as compared to that of CPF 251 (low sucrose variety). In brief, this study adds to the present literature about sugarcane, sucrose metabolism and role of SPS in sucrose metabolism thereby opening up further avenues of research in crop improvement.
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Affiliation(s)
- Robi Niazi
- Department of Botany, Women University Swabi, Swabi, Khyber Pakhtun Khwa, Pakistan
| | - Gulnaz Parveen
- Department of Botany, Women University Swabi, Swabi, Khyber Pakhtun Khwa, Pakistan
| | - Muhammad Noman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center Islamabad Pakistan, Islamabad, Capital, Pakistan
| | - Naila Mukhtar
- Department of Botany, University of Okara, Okara, Punjab, Pakistan
| | - Naila Hadayat
- Department of Botany, Division of Science & Technology, University of Education, Lahor
| | - Amtul Sami
- Health Biotechnology, Women University Swabi, Swabi, Khyber Pakhtun Khwan, Pakistan
| | - Binish Khaliq
- Department of Botany, University of Okara, Okara, Punjab, Pakistan
| | - Jiban Shrestha
- Nepal Agricultural Research Council, National Plant Breeding and Genetics Research Centre, Khumaltar, Lalitpur, Nepal
| | - Irfan Ullah
- Department of Zoology, Karakaram International University, Ghizer, Gilgit, Pakistan
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Kumar R, Sagar V, Verma VC, Kumari M, Gujjar RS, Goswami SK, Kumar Jha S, Pandey H, Dubey AK, Srivastava S, Singh SP, Mall AK, Pathak AD, Singh H, Jha PK, Prasad PVV. Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1225234. [PMID: 37645467 PMCID: PMC10461627 DOI: 10.3389/fpls.2023.1225234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.
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Affiliation(s)
- Rajeev Kumar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Vidya Sagar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, India
| | | | - Mala Kumari
- Integral Institute of Agriculture Science and Technology, Integral University, Lucknow, India
| | - Ranjit Singh Gujjar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Sanjay K. Goswami
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Sudhir Kumar Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research, Kanpur, India
| | - Himanshu Pandey
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Abhishek Kumar Dubey
- Indian Council of Agricultural Research (ICAR)-Research Complex for Eastern Region, Patna, India
| | - Sangeeta Srivastava
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - S. P. Singh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Ashutosh K. Mall
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Ashwini Dutt Pathak
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Hemlata Singh
- Department of Botany, Plant Physiology & Biochemistry, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, India
| | - Prakash Kumar Jha
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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Sandhu KS, Shiv A, Kaur G, Meena MR, Raja AK, Vengavasi K, Mall AK, Kumar S, Singh PK, Singh J, Hemaprabha G, Pathak AD, Krishnappa G, Kumar S. Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane. PLANTS 2022; 11:plants11162139. [PMID: 36015442 PMCID: PMC9412483 DOI: 10.3390/plants11162139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.
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Affiliation(s)
- Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Aalok Shiv
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Mintu Ram Meena
- Regional Center, ICAR-Sugarcane Breeding Institute, Karnal 132001, India
| | - Arun Kumar Raja
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Krishnapriya Vengavasi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashutosh Kumar Mall
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Praveen Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Jyotsnendra Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashwini Dutt Pathak
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gopalareddy Krishnappa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
- Correspondence: (G.K.); (S.K.)
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
- Correspondence: (G.K.); (S.K.)
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10
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Meena MR, Appunu C, Arun Kumar R, Manimekalai R, Vasantha S, Krishnappa G, Kumar R, Pandey SK, Hemaprabha G. Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits. Front Genet 2022; 13:854936. [PMID: 35991570 PMCID: PMC9382102 DOI: 10.3389/fgene.2022.854936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in sugarcane breeding have contributed significantly to improvements in agronomic traits and crop yield. However, the growing global demand for sugar and biofuel in the context of climate change requires further improvements in cane and sugar yields. Attempts to achieve the desired rates of genetic gain in sugarcane by conventional breeding means are difficult as many agronomic traits are genetically complex and polygenic, with each gene exerting small effects. Unlike those of many other crops, the sugarcane genome is highly heterozygous due to its autopolyploid nature, which further hinders the development of a comprehensive genetic map. Despite these limitations, many superior agronomic traits/genes for higher cane yield, sugar production, and disease/pest resistance have been identified through the mapping of quantitative trait loci, genome-wide association studies, and transcriptome approaches. Improvements in traits controlled by one or two loci are relatively easy to achieve; however, this is not the case for traits governed by many genes. Many desirable phenotypic traits are controlled by quantitative trait nucleotides (QTNs) with small and variable effects. Assembling these desired QTNs by conventional breeding methods is time consuming and inefficient due to genetic drift. However, recent developments in genomics selection (GS) have allowed sugarcane researchers to select and accumulate desirable alleles imparting superior traits as GS is based on genomic estimated breeding values, which substantially increases the selection efficiency and genetic gain in sugarcane breeding programs. Next-generation sequencing techniques coupled with genome-editing technologies have provided new vistas in harnessing the sugarcane genome to look for desirable agronomic traits such as erect canopy, leaf angle, prolonged greening, high biomass, deep root system, and the non-flowering nature of the crop. Many desirable cane-yielding traits, such as single cane weight, numbers of tillers, numbers of millable canes, as well as cane quality traits, such as sucrose and sugar yield, have been explored using these recent biotechnological tools. This review will focus on the recent advances in sugarcane genomics related to genetic gain and the identification of favorable alleles for superior agronomic traits for further utilization in sugarcane breeding programs.
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Affiliation(s)
- Mintu Ram Meena
- Regional Centre, ICAR-Sugarcane Breeding Institute, Karnal, India
- *Correspondence: Mintu Ram Meena, ; Chinnaswamy Appunu,
| | - Chinnaswamy Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Mintu Ram Meena, ; Chinnaswamy Appunu,
| | - R. Arun Kumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - S. Vasantha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - Ravinder Kumar
- Regional Centre, ICAR-Sugarcane Breeding Institute, Karnal, India
| | - S. K. Pandey
- Regional Centre, ICAR-Sugarcane Breeding Institute, Karnal, India
| | - G. Hemaprabha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
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Shabbir R, Javed T, Afzal I, Sabagh AE, Ali A, Vicente O, Chen P. Modern Biotechnologies: Innovative and Sustainable Approaches for the Improvement of Sugarcane Tolerance to Environmental Stresses. AGRONOMY 2021; 11:1042. [DOI: 10.3390/agronomy11061042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Sugarcane (Saccharum spp.) is one of the most important industrial cash crops, contributing to the world sugar industry and biofuel production. It has been cultivated and improved from prehistoric times through natural selection and conventional breeding and, more recently, using the modern tools of genetic engineering and biotechnology. However, the heterogenicity, complex poly-aneuploid genome and susceptibility of sugarcane to different biotic and abiotic stresses represent impediments that require us to pay greater attention to the improvement of the sugarcane crop. Compared to traditional breeding, recent advances in breeding technologies (molecular marker-assisted breeding, sugarcane transformation, genome-editing and multiple omics technologies) can potentially improve sugarcane, especially against environmental stressors. This article will focus on efficient modern breeding technologies, which provide crucial clues for the engineering of sugarcane cultivars resistant to environmental stresses.
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