Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)

Abstract

African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.

Endophytes from African Rice (Oryza glaberrima L.) Efficiently Colonize Asian Rice (Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll

“…Furthermore, it is increasingly evident that environmental conditions such as soil nutrition, moisture, and temperature have a direct influence on endophere communities [ 64 ]. O. glaberrima and O. sativa have adapted to growth in very different climatic conditions: O. glaberrima is adapted to harsh African climate and presents resistance or tolerance to viruses, nematode, bacteria, drought, iron toxicity and high salinity [ 65 , 66 ], while O. sativa cv. Baldo plants are grown through a submersion technique in regions of Italy characterized by temperate climate with more than 30 °C of excursion between winter and summer.…”

Water stress resilient cereal crops: Lessons from wild relatives

“…Traits could also be introgressed from the African O. glaberrima drought‐tolerant rice to the Asian O. sativa (Wambugu et al, 2019). Some accessions of African rice have the capacity to retain more transpirable water via early stomatal closure at the start of the drought period (Figure 2) (Bimpong et al, 2011a).…”

Out of Africa: characterizing the natural variation in dynamic photosynthetic traits in a diverse population of African rice (Oryza glaberrima)

“…However, the resilience to a range of abiotic and biotic stresses makes O. glaberrima an attractive target for gene mining and translation ( Fig. 1 ; Sarla and Swamy, 2005 ), which was one of the motivations for the interspecific New Rice for Africa (NERICA) breeding programme ( Wambugu et al , 2019 ). This underlying genetic diversity might allow commercial rice to tolerate increasingly unpredictable climatic conditions.…”

“…Variation in photosynthetic, NPQ, and stomatal traits have been examined in O. sativa ; however, there is no comprehensive analysis which compares both induction and decline. We hypothesize that due to the origins within the diverse African climates, substantial variation for dynamic photosynthesis traits may exist within the genome of O. glaberrima and we have used a new, whole-genome re-sequenced, resource of 155 O. glaberrima accessions ( Wambugu et al , 2019 ; Cubry et al , 2020 ) to characterize 58 phenotypic traits for photosynthesis and leaf WUE. This includes the use of automated machine learning to describe SD and gas exchange methods to facilitate the modelling of A , NPQ, and g s induction and decline dynamics across a large population of individuals.…”