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Designing of a mini-core that effectively represents 3004 diverse accessions of rice

View ORCID ProfileAngad Kumar, Shivendra Kumar, View ORCID ProfileManoj Prasad, Jitendra K. Thakur
doi: https://doi.org/10.1101/762070
Angad Kumar
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Shivendra Kumar
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Manoj Prasad
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Jitendra K. Thakur
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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  • For correspondence: jthakur@nipgr.ac.in
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ABSTRACT

Genetic diversity provides foundation for plant breeding and genetic research. As part of the 3K Rice Genome Project, over 3000 rice genomes were recently sequenced. We added four Indian rice accessions to it and made original panel of 3004 accessions. However, large set of germplasms are difficult to preserve and evaluate. Construction of core and mini-core collections is an efficient method for managing genetic resources. This study aims to designing of mini-core comprised of 520 accessions representing original panel. The designed mini-core captured most of the SNPs and represented all phenotypes and geographical regions. The mini-core was validated using different statistical analyses and had representation from all major groups including japonica, indica, aus/boro and aromatic/basmati. GWAS analyses with mini-core panel efficiently reproduced the marker-traits association identified among original 3004 panel. Expression analysis of trait-associated genes highlights the relevance of such mini-core panel. Haplotype analysis could also validate our mini-core panel. Apart from mini-core, we identified few regional and varietal specific marker-trait associations which were not evident in original panel. In this era of large-scale sequencing projects, such a strategy of designing mini-core will be very useful.

One-sentence summary Designing of mini-core as manageable association panel that efficiently mirroring the large and diverse collection of 3004 rice accessions.

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Posted September 09, 2019.
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Designing of a mini-core that effectively represents 3004 diverse accessions of rice
Angad Kumar, Shivendra Kumar, Manoj Prasad, Jitendra K. Thakur
bioRxiv 762070; doi: https://doi.org/10.1101/762070
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Designing of a mini-core that effectively represents 3004 diverse accessions of rice
Angad Kumar, Shivendra Kumar, Manoj Prasad, Jitendra K. Thakur
bioRxiv 762070; doi: https://doi.org/10.1101/762070

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