Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications

Punna Ramu; Rakesh K. Srivastava; Abhijit Sanyal; Kevin Fengler; Jun Cao; Yun Zhang; Mitali Nimkar; Justin Gerke; Sriram Shreedharan; Victor Llaca; Gregory May; Brooke Peterson-Burch; Haining Lin; Matthew King; Sayan Das; Vaid Bhupesh; Ajin Mandaokar; Karunakaran Maruthachalam; Pobbathi Krishnamurthy; Harish Gandhi; Abhishek Rathore; Rajeev Gupta; Annapurna Chitikineni; Prasad Bajaj; S. K. Gupta; C. Tara Satyavathi; Anand Pandravada; Rajeev K. Varshney; Raman Babu

doi:10.1038/s42003-023-05258-3

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Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications

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Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications

Punna Ramu, Rakesh K. Srivastava, Abhijit Sanyal, Kevin Fengler, Jun Cao, Yun Zhang, Mitali Nimkar, Justin Gerke, Sriram Shreedharan, Victor Llaca, …

Communications biology, Vol.6(1), 902

2023

DOI: https://doi.org/10.1038/s42003-023-05258-3

PMID: 37667032

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Abstract

High-quality reference genome assemblies, representative of global heterotic patterns, offer an ideal platform to accurately characterize and utilize genetic variation in the primary gene pool of hybrid crops. Here we report three platinum grade de-novo, near gap-free, chromosome-level reference genome assemblies from the active breeding germplasm in pearl millet with a high degree of contiguity, completeness, and accuracy. An improved Tift genome (Tift23D2B1-P1-P5) assembly has a contig N50 ~ 7,000-fold (126 Mb) compared to the previous version and better alignment in centromeric regions. Comparative genome analyses of these three lines clearly demonstrate a high level of collinearity and multiple structural variations, including inversions greater than 1 Mb. Differential genes in improved Tift genome are enriched for serine O-acetyltransferase and glycerol-3-phosphate metabolic process which play an important role in improving the nutritional quality of seed protein and disease resistance in plants, respectively. Multiple marker-trait associations are identified for a range of agronomic traits, including grain yield through genome-wide association study. Improved genome assemblies and marker resources developed in this study provide a comprehensive framework/platform for future applications such as marker-assisted selection of mono/oligogenic traits as well as whole-genome prediction and haplotype-based breeding of complex traits.

Details

Title: Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications
Authors/Creators: Punna Ramu - Corteva (United States)
Rakesh K. Srivastava - International Crops Research Institute for the Semi-Arid Tropics
Abhijit Sanyal - Corteva (United States)
Kevin Fengler - Corteva (United States)
Jun Cao - Corteva (United States)
Yun Zhang - Corteva (United States)
Mitali Nimkar - Corteva (United States)
Justin Gerke - Corteva (United States)
Sriram Shreedharan - Corteva (United States)
Victor Llaca - Corteva (United States)
Gregory May - Corteva (United States)
Brooke Peterson-Burch - Corteva (United States)
Haining Lin - Corteva (United States)
Matthew King - Natera (United States)
Sayan Das - Corteva (United States)
Vaid Bhupesh - Corteva (United States)
Ajin Mandaokar - Corteva (United States)
Karunakaran Maruthachalam - Corteva (United States)
Pobbathi Krishnamurthy - Corteva (United States)
Harish Gandhi - International Crops Research Institute for the Semi-Arid Tropics
Abhishek Rathore - International Maize and Wheat Improvement Center
Rajeev Gupta - Edward T. Schafer Agricultural Research Center
Annapurna Chitikineni - International Crops Research Institute for the Semi-Arid Tropics
Prasad Bajaj - International Crops Research Institute for the Semi-Arid Tropics
S. K. Gupta - International Crops Research Institute for the Semi-Arid Tropics
C. Tara Satyavathi - Indian Council of Agricultural Research – All India Coordinated Research Project on Pearl Millet, Jodhpur, India
Anand Pandravada - Corteva (United States)
Rajeev K. Varshney - Murdoch University, Food Futures Institute
Raman Babu - Corteva (United States)
Publication Details: Communications biology, Vol.6(1), 902
Publisher: Nature Publishing Group UK
Identifiers: 991005602264007891
Copyright: © 2023 The Author(s)
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

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Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1543 Flow Cytometry
Web Of Science research areas: Biology
ESI research areas: Biology & Biochemistry