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

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

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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.

Item Type:	Article
Divisions:	Center of Excellence in Genomics and Systems Biology Research Program : Asia Statistics, Bio-Informatics & Data Management
CRP:	UNSPECIFIED
Uncontrolled Keywords:	pearl millet, molecular breeding applications, haplotype-based breeding, Tift genome
Subjects:	Mandate crops > Millets Mandate crops > Millets > Pearl Millet Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	05 Sep 2023 05:25
Last Modified:	05 Sep 2023 05:25
URI:	http://oar.icrisat.org/id/eprint/12172
Official URL:	https://www.nature.com/articles/s42003-023-05258-3
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We acknowledge the Research and Development division of Corteva AgriscienceTM for supporting this study. The funding support from the CGIAR Research Program on Grain Legumes and Dryland Cereals (CRP-GLDC) and the ICRISAT-Pearl Millet Hybrid Parents Research Consortium (PMHPRC) is gratefully acknowledged. This study has been published as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals.
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