Genotyping-By-Sequence and SNP Discovery in Brazilian Rice Cultivars

A wide range of naturally occurring variation, likely to be agronomically relevant, exists in rice cultivars. The knowledge of information about drought tolerance in rice together with increase of yield, are important aspects for Brazilian rice breeding programs, especially when rice is known to be one of the most drought-susceptible crops. Rice is a staple food for over half the people in the world, and water scarcity resulting from rising demand for water for competing uses indicates the need for finding polymorphisms linked to drought-tolerant varieties of rice.

Single-nucleotide polymorphism (SNPs) are considered an effective way of acessing such polymorphism. To explore the existing biodiversity of rice in Brazil, a collection of 94 rice accessions was selected from the Embrapa Rice Core Collection based on diversity, utility in breeding, and geographical representation in Brazil and worldwide.

In this study, we use a 96-plex Genotyping-by-sequence (GBS) protocol to detect polymorphism in this collection. An initial analysis identified 13,167 SNPs distributed along the 12 rice chromosomes when filtering sites for at least 95% of taxa with data.