Spike-Stalk Injection Method Causes Extensive Phenotypic And Genotypic Variations For Rice Germplasm

Genetic diversities or favorable genes within distantly related species are the important resources for crop genetic improvement and germplasm innovation. Spike-Stalk injection method (SSI) has long been applied in rice genetic improvement by directly introducing genetic materials from non-mating donor species, while its inheritance patterns and the underlying mechanisms are poorly elucidated. In this study, a rice variantERV1with improved yield-related traits was screened out in the way of introducing genomic DNA ofOryza eichingeri(2n=24, CC genome) intoRH78(Oryza sativa L. 2n=24, AA genome) using SSI method. Genome-wide comparison revealed that the genomic heterozygosity ofERV1was approximately 8-fold higher thanRH78. Restriction-site associated DNA sequencing technology (RAD-seq) and association analysis of theERV1inbred F2 population identified 5 quantitative trait loci (QTLs) regions responsible for these yield-related traits, and found that genomic heterozygosity ofERV1inbred lines was significantly lower thanERV1, while spontaneous mutation rate of theERV1inbred lines was significantly higher thanERV1. Our results preliminarily uncovered the inheritance patterns of SSI variant rice, and the potential genomic regions for traits changes, which yielded novel insights into the mechanisms of SSI method, and may accelerate our understanding of plant genome evolution, domestication, and speciation in nature.