Legume Pangenome: Status and Scope for Crop Improvement

Article

Jha, Uday Chand, Nayyar, Harsh, von Wettberg, Eric J. B., Naik, Yogesh Dashrath, Thudi, Mahendar and Siddique, Kadambot H. M.. 2022. "Legume Pangenome: Status and Scope for Crop Improvement." Plants. 11 (22). https://doi.org/10.3390/plants11223041
Article Title

Legume Pangenome: Status and Scope for Crop Improvement

ERA Journal ID213962
Article CategoryArticle
AuthorsJha, Uday Chand, Nayyar, Harsh, von Wettberg, Eric J. B., Naik, Yogesh Dashrath, Thudi, Mahendar and Siddique, Kadambot H. M.
Journal TitlePlants
Journal Citation11 (22)
Article Number3041
Number of Pages14
Year2022
PublisherMDPI AG
Place of PublicationSwitzerland
ISSN2223-7747
Digital Object Identifier (DOI)https://doi.org/10.3390/plants11223041
Web Address (URL)https://www.mdpi.com/2223-7747/11/22/3041
Abstract

In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using ‘pangenome analysis.’ This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.

Keywordspangenome; structural variation; genome sequence; gene; crop domestication; legumes
Byline AffiliationsIndian Institute of Pulses Research, India
Panjab University, India
University of Vermont, United States
Dr. Rajendra Prasad Central Agricultural University, India
Shandong Academy of Agricultural Sciences, China
University of Southern Queensland
University of Western Australia
Permalink -

https://research.usq.edu.au/item/z0227/legume-pangenome-status-and-scope-for-crop-improvement

Log in to edit

Download files

Published Version
plants-11-03041.pdf
License: CC BY 4.0
File access level: Anyone

  • 72
    total views
  • 68
    total downloads
  • 1
    views this month
  • 3
    downloads this month

Export as

Related outputs

Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection
Kumar, Ashish, Naik, Yogesh Dashrath, Gautam, Vedant, Patil, Sunanda, Valluri, Vinod, Channale, Sonal, Bhatt, Jayant, Sharma, Stuti, Ramakrishnan, R. S., Sharma, Radheshyam, Kudapa, Himabindu, Zwart, Rebecca S., Punnuri, Somashekhar M., Varshney, Rajeev K. and Thudi, Mahendar. 2025. "Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection." The Plant Genome. 18 (1). https://doi.org/10.1002/tpg2.20508
Major abiotic stresses on quality parameters in grain legumes: Impacts and various strategies for improving quality traits
Jha, Uday Chand, Priya, Manu, Naik, Yogesh Dashrath, Nayyar, Harsh, Thudi, Mahendar, Punnuri, Somashekhar M., Siddique, Kadambot H.M. and Prasad, P.V. Vara. 2024. "Major abiotic stresses on quality parameters in grain legumes: Impacts and various strategies for improving quality traits." Environmental and Experimental Botany. 228. https://doi.org/10.1016/j.envexpbot.2024.105978
Uncovering key genomic regions for agronomical traits and stress tolerance in sorghum [Sorghum bicolor (L.) Moench] through meta-QTL analysis
Verma, Shruti, Quaiyum, Zeba, Prasad, Bishun Deo, Sahni, Sangita, Naik, Yogesh Dashrath, Mane, Rushikesh Sanjay, Eerapagula, Ramesh, Mahato, Ajay Kumar, Jha, Sonam, Rangari, Sagar Krushnaji, Mishra, Soumya, Sharma, V. K., Bhutia, K. L. and Thudi, Mahendar. 2024. "Uncovering key genomic regions for agronomical traits and stress tolerance in sorghum [Sorghum bicolor (L.) Moench] through meta-QTL analysis." Cereal Research Communications. https://doi.org/10.1007/s42976-024-00585-5
Invasive sorghum aphid: A decade of research on deciphering plant resistance mechanisms and novel approaches in breeding for sorghum resistance to aphids
Thudi, Mahendar, Reddy, M. S. Sai, Naik, Yogesh Dashrath Naik, Cheruku, Varun Kumar Reddy, Sangireddy, Manoj Kumar Reddy, Cuevas, Hugo E., Knoll, Joseph E., Louis, Joe, Kousik, Chandrasekar S., Toews, Michael D., Ni, Xinzhi and Punnuri, Somashekhar M.. 2024. "Invasive sorghum aphid: A decade of research on deciphering plant resistance mechanisms and novel approaches in breeding for sorghum resistance to aphids." Crop Science: a journal serving the international community of crop scientists. 64 (5), pp. 2436-2458. https://doi.org/10.1002/csc2.21301
Transforming waste to wealth: Impact of food waste-derived soil amendments and synthetic nitrogen fertilizer on soil dynamics
O'Connor, James, Mickan, Bede S., Gurung, Sun K., Siddique, Kadambot H. M., Leopold, Matthias, Bühlmann, Christopher H. and Bolan, Nanthi S.. 2024. "Transforming waste to wealth: Impact of food waste-derived soil amendments and synthetic nitrogen fertilizer on soil dynamics." Soil Use and Management. 40 (3). https://doi.org/10.1111/sum.13093
Value of food waste-derived fertilisers on soil chemistry, microbial function and crop productivity
O'Connor, James, Mickan, Bede S., Gurung, Sun K., Buhlmann, Christopher H., Jenkins, Sasha N., Siddique, Kadambot H.M., Leopold, Matthias and Bolan, Nanthi S.. 2024. "Value of food waste-derived fertilisers on soil chemistry, microbial function and crop productivity." Applied Soil Ecology. 198. https://doi.org/10.1016/j.apsoil.2024.105380
Development and evaluation of Fusarium wilt-resistant and high-yielding chickpea advanced breeding line, KCD 11
Laxuman, C., Naik, Yogesh Dashrath, Desai, B. K., Kenganal, Mallikarjun, Patil, Bharat, Reddy, B. S., Patil, D. H., Chakurte, Sidramappa, Kuchanur, P. H., Kumar K, Shiva, Gaddi, Ashok Kumar, Yogesh, L. N., Nidagundi, Jayaprakash, Dodamani, B. M., Sunkad, Gururaj, Thudi, Mahendar and Varshney, Rajeev K.. 2024. "Development and evaluation of Fusarium wilt-resistant and high-yielding chickpea advanced breeding line, KCD 11." The Plant Genome. 17 (2). https://doi.org/10.1002/tpg2.20460
Meta-QTL analysis reveals the important genomics regions for biotic stresses, nutritional quality and yield related traits in pearl millet
Gupta, Shreshth, Rangari, Sagar Krushnaji, Sahu, Aakash, Naik, Yogesh Dashrath, Satayavathi, C. Tara, Punnuri, Somashekhar and Thudi, Mahendar. 2024. "Meta-QTL analysis reveals the important genomics regions for biotic stresses, nutritional quality and yield related traits in pearl millet." CABI Agriculture and Bioscience. 5 (1). https://doi.org/10.1186/s43170-024-00230-5
Phenotypic profiling of lentil (Lens culinaris Medikus) accessions enabled identification of promising lines for use in breeding for high yield, early flowering and desirable traits
Naik, Yogesh Dashrath, Sharma, Vinay Kumar, Ask, Muraleedhar Sidaram, Rangari, Sagar Krushnaji, Kumar, Raj, Dikshit, Harsh Kumar, Sangita, Sahani, Kant, Ravi, Mishra, Gyan, Mir, Reyazul Rouf, Kudapa, Himabindu, Elango, Dinakaran, Zwart, Rebecca S., Varshney, Rajeev Kumar and Thudi, Mahendar. 2024. "Phenotypic profiling of lentil (Lens culinaris Medikus) accessions enabled identification of promising lines for use in breeding for high yield, early flowering and desirable traits ." Plant Genetic Resources: Characterization and Utilization. 22 (2), pp. 69-77. https://doi.org/10.1017/S1479262124000042
Meta-QTL analysis enabled identification of candidate genes and haplotypes for enhancing biotic stress resistance in chickpea
Isha, Ishita, Singh, Sarvjeet, Jha, Uday, Laxuman, C., Kudapa, Himabindu, Varshney, Rajeev K. V and Thudi, Mahendar. 2024. "Meta-QTL analysis enabled identification of candidate genes and haplotypes for enhancing biotic stress resistance in chickpea." Journal of Plant Biochemistry and Biotechnology. https://doi.org/10.1007/s13562-024-00873-5
Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration
Jha, Uday Chand, Nayyar, Harsh, Chattopadhyay, Anirudha, Beena, Radha, Lone, Ajaz A., Naik, Yogesh Dashrath, Thudi, Mahendar, Prasad, Pagadala Venkata Vara, Gupta, Sanjeev, Dixit, Girish Prasad and Siddique, Kadambot H. M.. 2023. "Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration." Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1183505
Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance
Channale, Sonal, Thompson, John P., Varshney, Rajeev K., Thudi, Mahendar and Zwart, Rebecca S.. 2023. "Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance." Frontiers in Plant Science. 14. https://doi.org/10.3389/fpls.2023.1139574
Genomic resources in plant breeding for sustainable agriculture
Thudi, Mahendar, Palakurthi, Ramesh, Schnable, James C., Chitikineni, Annapurna, Dreisigacker, Susanne, Mace, Emma, Srivastava, Rakesh K., Satyavathi, C. Tara, Odeny, Damaris, Tiwari, Vijay K., Lam, Hon-Ming, Hong, Yan Bin, Singh, Vikas K., Li, Guowei, Xu, Yunbi, Chen, Xiaoping, Kaila, Sanjay, Nguyen, Henry, Sivasankar, Sobhana, ..., Varshney, Rajeev K.. 2021. "Genomic resources in plant breeding for sustainable agriculture." Journal of Plant Physiology. 257, pp. 1-18. https://doi.org/10.1016/j.jplph.2020.153351
Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea (Cicer arietinum L.)
Jha, Uday Chand, Nayyar, Harsh, Palakurthi, Ramesh, Jha, Rintu, Valluri, Vinod, Bajaj, Prasad, Chitikineni, Annapurna, Singh, Narendra P., Varshney, Rajeev K. and Thudi, Mahendar. 2021. "Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea (Cicer arietinum L.)." Frontiers in Plant Science. 12, pp. 1-16. https://doi.org/10.3389/fpls.2021.655103
MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)
Manchikatla, Praveen Kumar, Kalavikatte, Danamma, Mallikarjuna, Bingi Pujari, Palakurthi, Ramesh, Khan, Aamir W., Jha, Uday Chand, Bajaj, Prasad, Singam, Prashant, Chitikineni, Annapurna, Varshney, Rajeev K. and Thudi, Mahandar. 2021. "MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)." Frontiers in Plant Science. 12, pp. 1-11. https://doi.org/10.3389/fpls.2021.688694
Integrated breeding approaches to enhance the nutritional quality of food legumes
Jha, Rintu, Yadav, Hemant Kumar, Raiya, Rahul, Singh, Rajesh Kumar, Jha, Uday Chand, Sathee, Lekshmy, Singh, Prashant, Thudi, Mahendar, Singh, Anshuman, Chaturvedi, Sushil Kumar and Tripathi, Shailesh. 2022. "Integrated breeding approaches to enhance the nutritional quality of food legumes." Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.984700
Two decades of association mapping: Insights on disease resistance in major crops
Gangurde, Sunil S., Xavier, Alencar, Naik, Yogesh Dashrath, Jha, Uday Chand, Rangari, Sagar Krushnaji, Kumar, Raj, Reddy, M. S. Sai, Channale, Sonal, Elango, Dinakaran, Mir, Reyazul Rouf, Zwart, Rebecca, Laxuman, C., Sudini, Hari Kishan, Pandey, Manish K., Punnuri, Somashekhar, Mendu, Venugopal, Reddy, Umesh K., Guo, Baozhu, Gangarao, N. V. P. R., ..., Thudi, Mahendar. 2022. "Two decades of association mapping: Insights on disease resistance in major crops." Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.1064059
Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)
Fayaz, Humara, Tyagi, Sandhya, Wani, Aijaz A., Pandey, Renu, Akhtar, Sabina, Bhat, Mohd Ashraf, Chitikineni, Annapurna, Varshney, Rajeev Kumar, Thudi, Mahendar, Kumar, Upendra and Mir, Reyazul Rouf. 2022. "Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)." Scientific Reports. 12 (1). https://doi.org/10.1038/s41598-022-14487-1
Genome-wide association mapping of seed oligosaccharides in chickpea
Elango, Dinakaran, Wang, Wanyan, Thudi, Mahender, Sebastiar, Sheelamary, Ramadoss, Bharathi Raja and Varshney, Rajeev K.. 2022. "Genome-wide association mapping of seed oligosaccharides in chickpea." Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.1024543
Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?
Elango, Dinakaran, Rajendran, Karthika, der Laan, Liza Van, Sebastiar, Sheelamary, Raigne, Joscif, Thaiparambil, Naveen A., Hadda, Noureddine, Raja, Bharath, Wang, Wanyan, Ferela, Antonella, Chiteri, Kevin O., Thudi, Mahendar, Varshney, Rajeev K., Chopra, Surinder, Sing, Arti and Singh, Asheesh K.. 2022. "Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health?" Frontiers in Plant Science. 13. https://doi.org/10.3389/fpls.2022.829118
Publisher Correction: Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea
Channale Sonal, Kalavikatte, Danamma, Thompson J.P., Kudapa, Himabindu, Bajaj, Prasad, Varshney, Rajeev K., Zwart, Rebecca S. and Thudi, Mahendar. 2022. "Publisher Correction: Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea ." Scientific Reports. 12 (1). https://doi.org/10.1038/s41598-022-08495-4
A Scintillating Journey of Genomics in Simplifying Complex Traits and Development of Abiotic Stress Resilient Chickpeas
Jaganathan, Deepa, Mallikarjuna, Bingi Pujari, Palakurthi, Ramesh, Samineni, Srinivasan, Laxuman, C., Bharadwaj, Chellapilla, Zwart, Rebecca, Fikre, Asnake, Gaur, Pooran, Varshney, Rajeev K. and Thudi, Mahendar. 2022. "A Scintillating Journey of Genomics in Simplifying Complex Traits and Development of Abiotic Stress Resilient Chickpeas." Kole, Chittaranjan (ed.) Genomic Designing for Abiotic Stress Resistant Pulse Crops. Cham, Switzerland. Springer. pp. 15-43
Transcriptome analysis reveals key genes associated with root‑lesion nematode Pratylenchus thornei resistance in chickpea
Channale, Sonal, Kalavikatte, Danamma, Thompson, John P., Kudapa, Himabindu, Bajaj, Prasad, Varshney, Rajeev K., Zwart, Rebecca S. and Thudi, Manhendar. 2021. "Transcriptome analysis reveals key genes associated with root‑lesion nematode Pratylenchus thornei resistance in chickpea." Scientific Reports. 11 (1), pp. 1-11. https://doi.org/10.1038/s41598-021-96906-3
Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits
Varshney, Rajeev K., Thudi, Mahendar, Roorkiwal, Manish, He, Weiming, Upadhyaya, Hari D., Yang, Wei, Bajaj, Prasad, Cubry, Philippe, Rathore, Abhishek, Jian, Jianbo, Doddamani, Dadakhalandar, Khan, Aamir W., Garg, Vanika, Chitikineni, Annapurna, Xu, Dawen, Gaur, Pooran M., Singh, Narendra P., Chaturvedi, Sushil K., Nadigatla, Gangarao V. P. R., ..., Liu, Xin. 2019. "Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits." Nature Genetics. 51, pp. 857-864. https://doi.org/10.1038/s41588-019-0401-3
Resistance to plant-parasitic nematodes in chickpea: current status and future perspectives
Zwart, Rebecca S., Thudi, Mahendar, Channale, Sonal, Manchikatla, Praveen K., Varshney, Rajeev K. and Thompson, John P.. 2019. "Resistance to plant-parasitic nematodes in chickpea: current status and future perspectives." Frontiers in Plant Science. 10, pp. 1-14. https://doi.org/10.3389/fpls.2019.00966