Recent advancements in legumes: Next generation sequencing and omics approaches


Abstract views: 602 / PDF downloads: 600

Authors

  • PUSHPIKA UDAWAT Amity University Madhya Pradesh, Maharajpura, Gwalior, Madhya Pradesh 474 005, India

https://doi.org/10.56093/ijas.v93i5.119566

Keywords:

Abiotic stress, Climate change, Grain, Legume, Technological advancements

Abstract

Legumes are important food crops in sustaining food security globally along with improving physio-chemical soil properties by mechanism of biological nitrogen (N2) fixation. Different types of abiotic stresses (especially their intensity, duration, and magnitude) such as drought, salt, cold and heat affect crop yield negatively and threaten overall food security. As the world population is expanding rapidly on the limited agricultural resources, sustainable management of the same is the need of the hour. Legumes are major nitrogen fixers that are enriched with metabolites, which provide second line of defence against several biotic as well as abiotic stresses. In past years genome sequence information of several grain legumes has been well documented. Due to genome sequencing, re-sequencing and RNA sequencing (RNA Seq.) of grain legumes, information associated to legume development, structural variation, differentially expressed genes and functional genomics was made available. Regulation of entire plant physiology and nitrogen fixation in grain legumes during abiotic stress is multifaceted and only some pathways have been revealed. This review is focussed on exploring the genetic variations analysed through omics approaches to enhance crop yield and productivity under drought, salt, cold and heat stress of grain legumes. Therefore this reviewis a compilation of recent biotechnological advancements on grain legumes using omics approaches for better understanding of their abiotic stress tolerance.

Downloads

Download data is not yet available.

References

Abdelrahman M, Jogaiah S, Burritt D and Phan Tran L. 2018. Legume genetic resources and transcriptome dynamics under abiotic stress conditions. Plant Cell Environment 41(9): 1972–83.

Agarwal G, Clevenger J, Pandey M K, Wang H, Shasidhar Y, Chu Y, Fountain J, Choudhary D, Culbreath A, Liu X, Huang G, Wang X, Deshmukh R, Holbrook C, Agbolade J, Olakunle T, Obiremi E, Busari T, Idowu J, IsiakaA and Aasa-Sadique A. 2020. Leaf anatomical evaluation of some minor legumes and their correlated genetic implications. Asian Journal of Research in Botany 4: 21–26.

Araujo S, Beebe S, Crespi M, Delbreil B, Gonzalez E, Gruber V, Lejeuene-Henaut I, Link W, Monteros M, Prats E, Rao I, Vadez V and VazPatto M. 2015. Abiotic stress responses in legumes: strategies used to cope with environmental challenges. Critical Reviews in Plant Sciences 34: 237–80.

Asfaw A, Blair M and Struik P. 2012. Multi-environment quantitative trait loci analysis for photosynthate acquisition, accumulation, and remobilization traits in common bean under drought stress. Gene Genome Genetics (Bethesda) 2(5): 579–95.

Brasileiro A, Morgante C, Araujo A, Leal Bertioli S, Silva A, Martins A and Guimaraes P. 2015. Transcriptome profiling of wild Arachis from water-limited environments uncovers drought tolerance candidate genes. Plant Molecular Biology Reporter 33: 1876–92.

Cai Y, Chen L, Liu X, Guo C, Sun S, Wu C and Hou W. 2018. CRISPR/Cas9- mediated targeted mutagenesis of GmFT2a delays flowering time in soya bean. Plant Biotechnology Journal 16(1): 176–85.

Chen X, Li H, Pandey M, Yang Q, Wang X, Garg V, L H, Chi X, Doddamani D, Hong Y, Upadhyaya H, Guo H, Khan A, Zhu F, Zhang X, Pan L, Pierce G, Zhou G, Krishnamohan K, Chen M, Zhong N, Agarwal G, Li S, Chitikineni A, Zhang G, Sharma S, Chen N, Liu N, Janila P, Li S, Wang M, Wang T, Sun J, Li X, Li C, Wang M, Yu L, Wen S, Singh S, Yang Z, Zhao J, Zhang C, Yu Y, Bi J, Zhang X, Liu Z, Paterson A, Wang S, Liang X, Varshney R and Yu S. 2016. Draft genome of the peanut a genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proceedings of National Academy of Sciences USA 113: 6785–90.

Cortes A and Blair M. 2018. Genotyping by sequencing and genome environment associations in wild common bean predict widespread divergent adaptation to drought. Frontiers in Plant Science 9: 128.

Curtin S, Xiong Y, Michno J, Campbell B, Stec A, Cermak T and Stupar R. 2018. CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. Plant Biotechnology Journal 16(6): 1125–37.

Dhanapal A, Ray J, Singh S, HoyosVillegas V, Smith J, Purcell L and Fritschi F. 2015. Genome- wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes. Theoretical and Applied Genetics 128(1): 73–91.

Ding H, Zhang Z, Qin F, Dai L, Li C, Ci D and Song W. 2014. Isolation and characterization of drought-responsive genes from peanut roots by suppression subtractive hybridization. Electronic Journal of Biotechnology 17(6): 304–10.

Du H, Zeng X, Zhao M, Cui X, Wang Q, Yang H and Yu D. 2016. Efficient targeted mutagenesis in soybean by TALENs and CRISPR/ Cas9. Journal of Biotechnology 217: 90–97.

Dwivedi S, Siddique K, Farooq M, Thornton P and Ortiz R. 2018. Using biotechnology led approaches to uplift cereal and food legume yields in dryland environments. Frontiers in Plant Sciences 9: 1249.

Dwivedi S, Upadhyaya H, Balaji J, Buhariwalla H, Blair M and Ortiz R. 2006. Using genomics to exploit grain legume biodiversity in crop improvement. Plant Breeding Review 26: 171–57.

Foyer C and Nguyen Hand Lam H. 2019. Legumes – The art and science of environmentally sustainable agriculture. Plant Cell Environment 42: 1–5.

Furlan A, Bianucci E, Castro S and Dietz K. 2017. Metabolic features involved in drought stress tolerance mechanisms in peanut nodules and their contribution to biological nitrogen fixation. Plant Science 263: 12–22.

Gao R, Feyissa B, Croft M and Hannoufa A. 2018. Gene editing by CRISPR/Cas9 in the obligatory outcrossing Medicago sativa. Planta 247(4): 1043–50.

Garg R, Bhattacharjee A and Jain M. 2015. Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Molecular Biology Reporter 33(3): 388–400.

Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N and Jain M. 2016. Transcriptome analyses reveal genotype and developmental stagespecific molecular responses to drought and salinity stresses in chickpea. Scientific Reports 6: 19228.

Gayen D, Gayali S, Barua P, Lande N, Varshney S, Sengupta S and Chakraborty N. 2019. Dehydration- induced proteomic landscape of mitochondria in chickpea reveals large scale coordination of key biological processes. Journal of Proteomics 192: 267–79.

Gerland P, Raftery A E, Seveikova H, Li N, Gu D and Spoorenberg T. 2014. World population stabilization unlikely this century. Science 346: 234–37.

Girdthai T, Jogloy S, Akkasaeng C, Vorasoot N, Wongkaew S, Holbrook C and Patanothai A. 2010. Heritability of, and geno-typic correlations between, aflatoxin traits and physiological traits for drought tolerance under end of season drought in peanut (Arachis hypogaea L.). Field Crops Research 118(2): 169–76.

Govind G, Harshavardhan V, Patricia J, Dhanalakshmi R, Senthil K, Sreenivasulu N and Udayakumar M. 2009. Identification and functional validation of a unique set of drought induced genes preferentially expressed in response to gradual water stress inpeanut. Molecular Genetics and Genomics 281(6): 591–605.

Gruber V, Blanchet S, Diet A, Zahaf O, Boualem A, Kakar K, Alunni B, Udvardi M, Frugier F and Crespi M. 2009. Identification of transcription factors involved in root apex responses to salt stress in Medicago truncatula. Molecular genetics and genomics 281: 55–66.

Handa N, Arora U, Arora N, Kaur P, Kapoor D and Bhardwaj R. 2021. Role of metabolites in abiotic stress tolerance in legumes. Abiotic Stress and Legumes, pp. 245–76. Singh V P, Singh S, Tripathi D K, Prasad S M, Bhardwaj and Chauhan D K (Eds). Academic Press.

HoyosVillegas V, Song Q, Wright E, Beebe S and Kelly J. 2016. Joint linkage QTL mapping for yield and agronomic traits in a composite map of three common bean RIL populations. Crop Science 56: 2546–63.

Hwang S, King C, Ray J, Cregan P, Chen P, Carter T and Purcell L. 2015. Confirmation of delayed canopy wilting QTLs from multiple soybean mapping populations. Theoretical and Applied Genetics 128(10): 2047–65.

Kale S, Jaganathan J, Ruperao P, Chen C, Punna R, Kudapa H, Thudi M, Roorkiwal M, Mohan A, Doddamani D, Garg V, KaviKishor P, Gaur P, Nguyen H, Batley J, Edwards D, Sutton T and Varshney R. 2015. Prioritization of candidate genes in QTL hotspot region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports 5: 15296

Kaler A, Ray J, Schapaugh W, Asebedo A, King C, Gbur E and Purcell L. 2018. Association mapping identifies loci for canopy temperature under drought in diverse soybean genotypes. Euphytica 214(8): 135.

Katam R, Sakata K, Suravajhala P, Pechan T, Kambiranda D, Naik K and Basha S. 2016. Comparative leaf proteomics of drought tolerant and susceptible peanut in response to water stress. Journal of Proteomics 143: 209–26.

Kaushal N, Awasthi A, Gupta K, Gaur P, Siddique K and Nayar H. 2013. Heat stressinduced reproductive failures in chickpea (Cicer arietinum) are associated with impaired sucrose metabolism in leaves and anthers. Functional Plant Biology 40: 1334–49.

Kaushal N, Bhandari K, Siddique K and Nayyar H. 2016. Food crops face rising temperatures: an overview of responses, adaptive mechanisms, and approaches to improve heat tolerance. Cogent Food and Agriculture 2: 1134380.

Khan N, Bano A, Rathinasabapathi B and Babar M. 2018. UPLCHRMS based untargeted metabolic profiling reveals changes in chickpea (Cicer arietinum) metabolome following long term drought stress. Plant Cell Environment 42(1): 115–32.

Kumar M, Chauhan A, Kumar M, Yusuf M, Sanyal A and Chauhan P. 2019. Transcriptome sequencing of chickpea (Cicer arietinum L.) genotypes for identification of drought responsive genes under drought stress condition. Plant Molecular Biology Reporter 17: 186–203.

Li H, Rasheed A, Hickey L and He Z. 2018. Fast forwarding genetic gain. Trends in Plant Science 23(3): 183–86.

Li M, Xin D, Gao Y, Li K, Fan K, Munoz N and Lam H. 2017. Using genomic information to improve soybean adaptability to climate change. Journal of Experimental Botany 68(8): 1823–34.

Li Y, Ruperao P, Batley J, Edwards D, Khan T, Colmer T and Sutton T. 2018. Investigating drought tolerance in chickpea using genome wide association mapping and genomic selection based on whole-genome resequencing data. Frontiers in Plant Science 9: 190.

Ma H, Song L, Shu Y, Wang S, Niu J, Wang Z, Yu T, Gu W and Ma H. 2012. Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes. Journal of Proteomics 75: 1529–46.

Mahdavi Mashaki K, Garg V, Nasrollahnezhad Ghomi A, Kudapa H, Chitikineni A, Zaynali Nezhad K and Thudi M. 2018. RNA Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.). PLoS ONE 13 (6): e0199774.

Manavalan L, Prince S, Musket T, Chaky J, Deshmukh R, Vuong T and Nguyen H. 2015. Identification of novel QTL governing root architectural traits in an interspecific soybean population. PLoS ONE 10 (3): e0120490.

Matamoros M and Manuel B. 2021. Molecular responses of legumes to abiotic stress: post-translational modifications of proteins and redox signaling. Journal of Experimental Botany 72: 5876–92.

Min X, Jin X, Zhang Z, Wei X, Ndayambaza B, Wang Y and Liu W. 2020. Genome wide identification of NAC transcription factor family and functional analysis of the abiotic stress responsive genes in Medicago sativa L. Journal of Plant Growth Regulation 39: 324–37.

Mir R, ZamanAllah M, Sreenivasulu N, Trethowan R and Varshney R. 2012. Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops. Theoretical and Applied Genetics 125(4): 625–45.

Muchero W, Roberts P, Diop N, Drabo I, Cisse N, Close T and Ehlers J. 2013. Genetic architecture of delayed senescence, biomass, and grain yield under drought stress in cowpea. PLoS ONE 8(7): e70041.

Mukeshimana G, Butare L, Cregan P, Blair M and Kelly J. 2014. Quantitative trait loci associated with drought tolerance in common bean. Crop Science 54(3): 923–38.

Myers S, Smith M, Guth S, Golden C, Vaitla B and Mueller N. 2017. Climate change and global food systems: potential impacts on food security and under nutrition. Annual Review of Public Health 38: 259–77.

Pang J, Turner N, Khan T, Du Y, Xiong J, Colmer T and Siddique K. 2017. Response of chickpea (Cicer arietinum L.) to terminal drought: Leaf stomatal conductance, pod abscisic acid concentration, and seed set. Journal of Experimental Botany 68(8): 1973–85.

Qi X, Li M, Xie M, Liu X, Ni M, Shao G and Lam H. 2014. Identification of a novel salt tolerance gene in wild soybean by whole genome sequencing. Nature Communications 5: 4340.

Ravi K, Vadez V, Isobe S, Mir R, Guo Y, Nigam S and Varshney R. 2011. Identification of several small maineffect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theoretical and Applied Genetics 122(6): 1119–32.

Ray D, Mueller N, West P and Foley J. 2013. Yield trends are insufficient to double global crop production by 2050. PLoS One 8: e66428.

Rehman A, Malhotra R, Bett K, Taran B, Bueckert R and Warkentin T. 2011. Mapping QTL associated with traits affecting grain yield in chickpea (Cicer arietinum L.) under terminal drought stress. Crop Science 51(2): 450–63.

Rodrigues F, Fuganti- Pagliarini R, Marcolino Gomes J, Nakayama T, Molinari H, Lobo F and Nepomuceno A. 2015. Daytime soybean transcriptome fluctuations during water deficit stress. BMC Genomics 16: 505.

Sabaghpour S, Mahmodi A, Kamel S and Malhotra R. 2006. Studyon chickpea drought tolerance lines under dryland condition of Iran. Indian Journal of Crop Science 1(1–2): 70–73.

Saxena R, Kumar M and Tomar R 2021. Seed priming: An effective approach to improve seed germination and abiotic stress tolerance. Indian Journal of Natural Sciences 12(66): 32346–35.

Saxena R, Kumar M and Tomar R. 2019. Plant Responses and Resilience toward Drought and Salinity Stress. Plant Archives 19(2): 50–58.

Silvente S, Sobolev A and Lara M. 2012. Metabolite adjustments in drought tolerant and sensitive soybean genotypes in response to water stress. PLoS ONE 7(6): e38554.

Singh D, Singh C, Taunk J, Tomar R, Chaturvedi A, Gaikwad K and Pal M. 2017. Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress. BMC Genomics 18: 206.

Singh V, Khan A, Saxena R, Sinha P, Kale S, Parupalli S, Kumar V, Chitikineni A, Vechalapu S, Kumar S, Sharma M, Ghanta A, Yamini K, Muniswamy S and Varshney R. 2017. Indelseq: a fast-forward genetics approach for identification of trait associated putative candidate genomic regions and its application in pigeon pea (Cajanus cajan). Plant Biotechnology Journal 15: 906–14.

Sita K, Sehgal A, Rao B, Nair R, Prasad P and Kumar S. 2017. Food legumes and rising temperatures: effects, adaptive functional mechanisms specific to reproductive growth stage and strategies to improve heat tolerance. Frontiers in Plant Science 8: 1658.

Sivasakthi K, Thudi M, Tharanya M, Kale S, Kholova J, Halime M and Vadez V. 2018. Plant vigour QTLs comap with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome. BMC Plant Biology 18: 29.

Subba P, Kumar R, Gayali S, Shekhar S, Parveen S, Pandey A, Datta A, Chakraborty S and Chakraborty N. 2013. Characterisation of the nuclear proteome of a dehydration-sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar. Proteomics 13: 1973–92.

Thangella P, Pasumarti S, Pullakhandam R, Geereddy B and Daggu M. 2018. Differential expression of leaf proteins in four cultivars of peanut (Arachis hypogaea L.) under water stress. Biotechnology 8(3): 15.

Udawat P, Jha R, Mishra A and Jha B. 2017. Overexpression of a plasma membrane-localized SbSRP-like protein enhances salinity and osmotic stress tolerance in transgenic tobacco. Frontiers in Plant Sciences (Plant Biotechnology) 20(8): 582.

Udawat P, Jha R, Sinha D, Mishra A and Jha B. 2016. Overexpression of a cytosolic abiotic stress responsive universal stress protein (SbUSP) mitigates salt and osmotic stress in transgenic tobacco plants. Frontiers in Plant Sciences (Plant Physiology) 7: 518.

Udawat P, Mishra A and Jha B. 2014. Heterologous expression of an uncharacterized universal stress protein gene (SbUSP) from the extreme halophyte, Salicornia brachiata, which confers salt and osmotic tolerance to E. coli. Gene 536(1): 163–70.

Ullah N, Yuce M, Gokce Z and Budak H. 2017. Comparative metabolite profiling of drought stress in roots and leaves of seven Triticeae species. BMC Genomics 18: 969.

Varshney R, Hiremath P, Lekha P, Kashiwagi J, Balaji J, Deokar A and Hoisington D. 2009. A comprehensive resource of drought- and salinity responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10: 523.

Varshney R, Chen W, Li Y, Bharti A, Saxena R, Schlueter J, Donoghue M, Azam S, Fan G, Whaley A, Farmer A, Sheridan J, Iwata A, Tuteja R, Penmetsa R, Wu W, Upadhyaya H, Yang S, Shah T, Saxena K, Michael T, McCombie W, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook D, May G, Xu X and Jackson S. 2012. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30: 83–89.

Varshney R, Murali Mohan S, Gaur P, Gangarao N, Pandey M, Bohra A, Sawargaonkar S, Chitikineni A, Kimurto P, Janila P, Saxena K, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi S, Mallikarjuna N, Anuradha G, Babbar A, Choudhary A, Mhase M, Bharadwaj C, Mannur D, Harer P, Guo B, Liang X, Nadarajan N and Gowda C. 2013. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnology Advances 31: 1120–34.

Varshney R, Thudi M, Nayak S, Gaur P, Kashiwagi J, Krishnamurthy L and Viswanatha K. P. 2014. Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 127(2): 445–62.

Varshney R, Thudi M, Pandey M, Tardieu F, Ojiewo C, Vadez V, Whitbread A, Siddique K, Nguyen H, Carberry P and Bergvinson D. 2018. Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy. Journal of Experimental Botany 69: 3293–3312.

Varshney R, Pandey M, Bohra A, Singh V, Thudi M and Saxena R. 2019. Toward the sequence based breeding in legumes in the post genome sequencing era. Theoretical and AppliedGenetics 132: 797–816.

Vu H, Kilian A, James A, Bielig L and Lawn R. 2015. Use of DArT molecular markers for QTL analysis of drought-stress responses in soybean. II. Marker identification and QTL analyses. Crop and Pasture Science 66: 817–30.

Wang J, Chu S, Zhang H, Zhu Y, Cheng H and Yu D. 2016. Development and application of a novel genome wide SNP array reveals domestication history in soybean. Scientific Reports 6: 20728.

Wang X, Khodadadi E, Fakheri B and Komatsu S. 2017. Organ specific proteomics of soybean seedlings under flooding and drought stresses. Journal of Proteomics 162: 62–72.

Watson A, Ghosh S, Williams M, Cuddy W, Simmonds J and Hickey L. 2018. Speed breeding is a powerful tool to accelerate crop research and breeding. Nature Plants 4: 23–29.

Wu J, Wang L and Wang S. 2016. Comprehensive analysis and discovery of drought related NAC transcription factors in common bean. BMC Plant Biology 16(1): 193.

Xu C, Xia C, Xia Z, Zhou X, Huang J, Huang Z and Zhang C. 2018. Physiological and transcriptomic responses of reproductive stage soybean to drought stress. Plant Cell Report 37(12): 1611–24.

Xu P, Wu X, Munoz A, Wang B, Wu X, Hu Y and Li G. 2017. Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp). Plant Biotechnology Journal 15(5): 547–57.

Ye H, Roorkiwal M, Valliyodan B, Zhou L, Chen P, Varshney R and Nguyen H. 2018. Genetic diversity of root system architecture in response to drought stress in grain legumes. Journal of Experimental Botany 69(13): 3267–77.

Downloads

Submitted

2021-12-29

Published

2023-06-06

Issue

Section

Review Article

How to Cite

UDAWAT, P. (2023). Recent advancements in legumes: Next generation sequencing and omics approaches. The Indian Journal of Agricultural Sciences, 93(5), 467–474. https://doi.org/10.56093/ijas.v93i5.119566
Citation