Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

Article

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
Article Title

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

ERA Journal ID16629
Article CategoryArticle
AuthorsVarshney, Rajeev K. (Author), Thudi, Mahendar (Author), Roorkiwal, Manish (Author), He, Weiming (Author), Upadhyaya, Hari D. (Author), Yang, Wei (Author), Bajaj, Prasad (Author), Cubry, Philippe (Author), Rathore, Abhishek (Author), Jian, Jianbo (Author), Doddamani, Dadakhalandar (Author), Khan, Aamir W. (Author), Garg, Vanika (Author), Chitikineni, Annapurna (Author), Xu, Dawen (Author), Gaur, Pooran M. (Author), Singh, Narendra P. (Author), Chaturvedi, Sushil K. (Author), Nadigatla, Gangarao V. P. R. (Author), Krishnamurthy, Lakshmanan (Author), Dixit, G. P. (Author), Fikre, Asnake (Author), Kimurto, Paul K. (Author), Sreeman, Sheshshayee M. (Author), Bharadwaj, Chellapilla (Author), Tripathi, Shailesh (Author), Wang, Jun (Author), Lee, Suk-Ha (Author), Edwards, David (Author), Polavarapu, Kavi Kishor Bilhan (Author), Penmetsa, R. Varma (Author), Crossa, Jose (Author), Nguyen, Henry T. (Author), Siddique, Kadambot H. M. (Author), Colmer, Timothy D. (Author), Sutton, Tim (Author), von Wettberg, Eric (Author), Vigouroux, Yves (Author), Xu, Xun (Author) and Liu, Xin (Author)
Journal TitleNature Genetics
Journal Citation51, pp. 857-864
Number of Pages8
Year2019
Place of PublicationUnited States
ISSN1061-4036
1546-1718
Digital Object Identifier (DOI)https://doi.org/10.1038/s41588-019-0401-3
Web Address (URL)https://www.nature.com/articles/s41588-019-0401-3
Abstract

We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

Keywordschickpea, Genome-wide association studies, whole-genome resequencing
Contains Sensitive ContentDoes not contain sensitive content
ANZSRC Field of Research 2020300406. Crop and pasture improvement (incl. selection and breeding)
Public Notes

Files associated with this item cannot be displayed due to copyright restrictions.

Institution of OriginUniversity of Southern Queensland
Byline AffiliationsInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Centre for Crop Health (Operations)
BGI Group, China
University of Montpellier, France
Indian Council of Agricultural Research, India
Rani Lakshmi Bai Central Agricultural University, India
International Crops Research Institute for the Semi-Arid Tropics, Kenya
International Crops Research Institute for the Semi-Arid Tropics, Ethiopia
Egerton University, Kenya
University of Agricultural Sciences Bangalore, India
iCarbonX, China
Seoul National University, Korea
University of Western Australia
Osmania University, India
University of California, United States
International Maize and Wheat Improvement Center, Mexico
University of Missouri, United States
Department of Primary Industries and Regions, South Australia
University of Vermont, United States
Permalink -

https://research.usq.edu.au/item/q58q9/resequencing-of-429-chickpea-accessions-from-45-countries-provides-insights-into-genome-diversity-domestication-and-agronomic-traits

Log in to edit
  • 231
    total views
  • 8
    total downloads
  • 3
    views this month
  • 0
    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. 2024. "Genome-wide association mapping reveals novel genes and genomic regions controlling root-lesion nematode resistance in chickpea mini core collection." The Plant Genome. https://doi.org/10.1002/tpg2.20508
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
Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat
Bhoite, Roopali, Han, Yong, Alamuru, Alamuru Krishna, Varshney, Rajeev K. and Sharma, Darshan Lal. 2024. "Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat." The Plant Genome. 17 (1). https://doi.org/10.1002/tpg2.20358
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
Translational genomics for achieving higher genetic gains in groundnut
Pandey, Manish K., Pandey, Arun K., Kumar, Rakesh, Nwosu, Chogozie Victor, Guo, Baozhu, Wright, Graeme C., Bhat, Ramesh S., Chen, Xiaoping, Bera, Sandip K., Yuan, Mei, Jiang, Huifang, Faye, Issa, Radhakrishnan, Thankappan, Wang, Xingjun, Liang, Xuanquiang, Liao, Boshou, Zhang, Xinyou, Varshney, Rajeev K. and Zhuang, Weijian. 2020. "Translational genomics for achieving higher genetic gains in groundnut." Theoretical and Applied Genetics: international journal of plant breeding research. 133, pp. 1679-1702. https://doi.org/10.1007/s00122-020-03592-2
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
A QTL on the Ca7 chromosome of chickpea affects resistance to the root‑lesion nematode Pratylenchus thornei
Khoo, Kelvin H. P., Sheedy, Jason G., Taylor, Julian D., Croser, Janine S., Hayes, Julie E., Sutton, Tim, Thompson, John P. and Mather, Diane E.. 2021. "A QTL on the Ca7 chromosome of chickpea affects resistance to the root‑lesion nematode Pratylenchus thornei." Molecular Breeding: new strategies in plant improvement. 41 (12), pp. 1-13. https://doi.org/10.1007/s11032-021-01271-8
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
Legume Pangenome: Status and Scope for Crop Improvement
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
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
Engineering MXene surface with POSS for reducing fire hazards of polystyrene with enhanced thermal stability
Yu, Bin, Yuen, Anthony Chun Yin, Xu, Xiaodong, Zhang, Zhen-Cheng, Yang, Wei, Lu, Hongdian, Fei, Bin, Yeoh, Guan Heng, Song, Pingan and Wang, Hao. 2021. "Engineering MXene surface with POSS for reducing fire hazards of polystyrene with enhanced thermal stability." Journal of Hazardous Materials. 401, pp. 1-13. https://doi.org/10.1016/j.jhazmat.2020.123342
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
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
The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers
Yang, Shi Ying, Saxena, Rachit K., Kulwal, Pawan L., Ash, Gavin J., Dubey, Anuja, Harper, John D. I., Upadhyaya, Hari D., Gothalwal, Ragini, Kilian, Andrzej and Varshney, Rajeev K.. 2011. "The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers." Journal of Genetics. 90 (1), pp. 103-109. https://doi.org/10.1007/s12041-011-0050-5
The preparation, structures, and properties of poly (vinylidene fluoride)/multiwall carbon nanotubes nanocomposites
Tang, Xue‐Gang, Hou, Meng, Ge, Lei, Zou, Jin, Truss, Rowan, Yang, Wei, Yang, Ming‐Bo, Zhu, Zhong-Hua and Bao, Rui‐Ying. 2012. "The preparation, structures, and properties of poly (vinylidene fluoride)/multiwall carbon nanotubes nanocomposites." Journal of Applied Polymer Science. 125 (S1), pp. E592-E600. https://doi.org/10.1002/app.36671
Identification of multiple root disease resistant wheat germplasm against cereal nematodes and dryland root rot and their validation in regions of economic importance
Nicol, J. M., Sahin, E., Wallwork, H., Chakraborty, S., Lu, M., O'Brien, L., Sutherland, M., Horne, M., Simpfendorfer, S., Herde, D., Ogbonnaya, F., Duvellier, E., Bolat, N., Yahyaoui, A., Buerstmayr, H., Lewis, J., Crossa, J., Singh, A. K., Bishnoi, S. P., ..., Gargouri, S.. 2008. "Identification of multiple root disease resistant wheat germplasm against cereal nematodes and dryland root rot and their validation in regions of economic importance." Appels, Rudi (ed.) 11th International Wheat Genetics Symposium 2008 (IWGS 2008). Brisbane, Australia 24 - 29 Aug 2008 Sydney, Australia.