Tools for using the International Rice Genebank to breed for climate-resilient varieties

Abstract

Traditional rice varieties have been critical for developing improved stress-tolerant rice varieties. Tools to analyze the genome sequences of traditional varieties are accelerating the identification and deployment of genes conferring climate change resilience.

Fig 1. Traditional rice varieties are adapted to a wide range of climate conditions.

An illustration of the range of stress-prone agro-ecosystems to which traditional rice varieties are adapted: upland (left), comprising aerobic soils that are often drought prone, nutrient deficient, and low input; rainfed lowland (center), comprising nonirrigated systems that are prone to drought, submergence, and salinity; and deepwater (right), in which water levels continuously rise during the growing season, often necessitating harvesting by boat. This large range of environmental adaptation is unique to rice, and these traditional varieties, which are maintained by Genebanks, serve as important genetic resources in breeding for climate change.

Fig 2. Using SNP-Seek to identify haplotypes for climate adaptation–related genes.

Single nucleotide polymorphism (SNP) haplotypes for OsSTL1 (LOC_Os04g02000; a gene identified by Yuan and colleagues [5] to improve rice salt tolerance) in the 3K RG using SNP-Seek. (a) Across the 3K RG, 162 SNPs were found in the 4.8 M filtered SNP set that group into 3 major and 2 minor haplotypes. (b) Haplotype patterns across the 3K RG. Red arrow indicates position 619903 on Chr 4 where a nonsynonymous CDS SNP occurs. (c) Screening of germplasm for seedling stage salinity tolerance by Yuan and colleagues (image kindly provided by Prof. Zichao Li, China Agricultural University, Beijing, China). Breeding lines with improved salinity tolerance could be identified by screening for the haplotype carrying the favorable allele.