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

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Relation http://oar.icrisat.org/12172/
https://www.nature.com/articles/s42003-023-05258-3
https://doi.org/10.1038/s42003-023-05258-3
 
Title Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications
 
Creator Ramu, P
Srivastava, R K
Sanyal, A
Fengler, K
Cao, J
Zhang, Y
Nimkar, M
Gerke, J
Shreedharan, S
Llaca, V
May, G
Peterson-Burch, B
Lin, H
King, M
Das, S
Bhupesh, V
Mandaokar, A
Maruthachalam, K
Krishnamurthy, P
Gandhi, H
Rathore, A
Gupta, R
Chitikineni, A
Bajaj, P
Gupta, S K
Satyavathi, C T
Pandravada, A
Varshney, R K
Babu, R
 
Subject Millets
Pearl Millet
Genetics and Genomics
 
Description 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.
 
Publisher Nature Research
 
Date 2023-09-04
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12172/1/Communications%20biology_6_01-11_2023.pdf
Ramu, P and Srivastava, R K and Sanyal, A and Fengler, K and Cao, J and Zhang, Y and Nimkar, M and Gerke, J and Shreedharan, S and Llaca, V and May, G and Peterson-Burch, B and Lin, H and King, M and Das, S and Bhupesh, V and Mandaokar, A and Maruthachalam, K and Krishnamurthy, P and Gandhi, H and Rathore, A and Gupta, R and Chitikineni, A and Bajaj, P and Gupta, S K and Satyavathi, C T and Pandravada, A and Varshney, R K and Babu, R (2023) Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications. Communications Biology, 6. 01-11. ISSN 2399-3642