Platinum-standard reference genome assemblies representing global heterotic gene pools provide a reliable genomic resource for molecular breeding applications in pearl millet

Authors: RAMU, PUNNA - Corteva Agriscience; SRIVASTAVA, RAKESH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SANYAL, ABHIJIT - Corteva Agriscience; FENGLER, KEVIN - Corteva Agriscience; CAO, JUN - Corteva Agriscience; ZHANG, YUN - Corteva Agriscience; NIMKAR, MITALI - Corteva Agriscience; GERKE, JUSTIN - Corteva Agriscience; SHREEDHARAN, SRIRAM - Corteva Agriscience; LLACA, VICTOR - Corteva Agriscience; BHUPESH, VAID - Corteva Agriscience; Gupta, Rajeev; BABU, RAMAN - Corteva Agriscience

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/18/2023
Publication Date: 9/4/2023
Citation: Ramu, P., Srivastava, R., Sanyal, A., Fengler, K., Cao, J., Zhang, Y., Nimkar, M., Gerke, J., Shreedharan, S., Llaca, V., Bhupesh, V., Gupta, R., Babu, R. 2023. Platinum-standard reference genome assemblies representing global heterotic gene pools provide a reliable genomic resource for molecular breeding applications in pearl millet. Communications Biology. 6:Article 902. https://doi.org/10.1038/s42003-023-05258-3.
DOI: https://doi.org/10.1038/s42003-023-05258-3

Interpretive Summary: Ensuring food security for the burgeoning world population, especially in the wake of climate change and associated adverse effects, is a major challenge that necessitates approaches including crop diversification and targeted crop improvement. Among major cereals, pearl millet is adapted to harsher environments in the arid and semi-arid regions of the world, accounts for roughly 50% of the world’s millet production and is considered a boon to geographies that are vulnerable to climate change and prone to depleting water resources and widespread malnutrition. In this study we report three platinum grade de-novo, near gap-free, chromosome-level reference genome assemblies representing the active breeding germplasm in pearl millet. Improved genome assemblies and marker resources developed in this study provide a comprehensive platform for future molecular breeding applications with a huge potential of enhancing rate of genetic gains in pearl millet and avenues for translational genomics in crop improvement program in other cereals.

Technical Abstract: High-quality reference genome assemblies, representatives 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 representing the active breeding germplasm in pearl millet with a high degree of contiguity, completeness, and accuracy. An improved Tift genome (Tift23D2B1-P1-P5) assembly had a contig N50 ~7,000-fold (126 Mb) in relation to the previous version including significantly better alignment in centromeric regions. Pangenome analyses of the three lines clearly demonstrated a high level of collinearity and multiple structural variations, including inversions greater than 1Mb. Novel genes identified in the improved Tift genome are enriched for serine O-acetyltransferase and glycerol-3-phosphate metabolic process which play a significant role in improving the nutritional quality of protein in seed and disease resistance in plants, respectively. Genome-wide association studies (GWAS) uncovered multiple marker-trait associations for a range of agronomic traits, including grain yield. Improved genome assemblies and marker resources developed in this study provide a comprehensive platform for future applications such as marker-assisted selection (MAS) of mono/oligogenic traits as well as whole-genome prediction (WGP)/genomic selection (GS) and haplotype-based breeding of complex traits.