Traces of introgression from cAus into tropical Japonica observed in African upland rice varieties

Abstract

Abstract Background Asian rice Oryza sativa, first domesticated in China, is having considerable success in African fields. While the timing and location of this introduction remain unclear, rice of Asian origin may have evolved specifically during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. Methods We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions of both origins, revealing higher similarity with accessions from Indonesia and Madagascar. Peculiarities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. Key results Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms for this adaptation to harsh upland cultivation conditions.