Abstract
As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated Asian rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to map resequencing data to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice.
Highlights
Background & SummaryAsian cultivated rice is a staple food for half of the world population
To better understand the full-range of genetic diversity that is stored in rice germplasm banks around the world, several studies have been conducted using microarrays[8,9] and low coverage skim sequencing[10,11]
IRGSP reference genome sequences (RefSeqs)), showed how the high genetic diversity present in domesticated rice populations provides a solid base for the improvement of rice cultivars[12]
Summary
With the planet’s population expected to reach 10 billion by 2050, farmers must increase production by at least 100 million metric tons per year[1,2] To address this need, future rice cultivars should provide higher yields, be more nutritious, be resilient to multiple abiotic and biotic stresses, and have less of an environmental footprint[3,4]. Future rice cultivars should provide higher yields, be more nutritious, be resilient to multiple abiotic and biotic stresses, and have less of an environmental footprint[3,4] To achieve this goal, a comprehensive and more in-depth understanding of the full range of genetic diversity of the pan-cultivated rice genome and its wild relatives will be needed[5].
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