Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication

Abstract

African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.

Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

“…Rice is one of the most anthropogenically and economically essential crops globally, and improvements of grain yield and disease resistance are the primary goals of crop genetic improvement [ 36 ]. In recent years, the improvement and enhancement of rice nutritional quality has received wide attention [ 37 ].…”

Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication

“…Thailand et al have reported that the expression of the BADH1 gene in Indica correlates with salt stress and other environmental stresses, such as plasmolysis, temperature, and light [ 15 ]. Rice and its major trait domestication have been independent of two different species, African rice ( Oryza glaberrima Steud) and Asian rice ( Oryza sativa L.) [ 20 ], although there could be a third domestication event by recent archeological evidence in the Amazon [ 21 ]. Genomics has produced unprecedented amounts of datasets for deeper insights into domestication studies [ 20 ], and whole-genome resequencing of rice DNA could result in tracing back the details of its domestication history by population genomic analysis [ 22 ].…”

“…Rice and its major trait domestication have been independent of two different species, African rice ( Oryza glaberrima Steud) and Asian rice ( Oryza sativa L.) [ 20 ], although there could be a third domestication event by recent archeological evidence in the Amazon [ 21 ]. Genomics has produced unprecedented amounts of datasets for deeper insights into domestication studies [ 20 ], and whole-genome resequencing of rice DNA could result in tracing back the details of its domestication history by population genomic analysis [ 22 ]. Resequencing our previous whole-genome data also revealed different domestication patterns of BADH1 and BADH2 [ 19 ].…”

Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies

“…Genomics presents tools, resources and knowledge to accelerate domestication of new species thus potentially enhancing food and nutritional security (Brozynska et al, 2015 ). Genomics has enabled identification of various domestication genes and provided knowledge on functional importance of their allelic variation (Wambugu et al, 2021 ). These genomic advances are providing insights on genetic histories of important crops and the geographical spread of traits that may have been selected during domestication (Tripodi et al, 2021 ).…”