Characterization of Selected Rice Varieties Adapted in Africa

Abstract

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Rice varieties developed through the inter-specific crosses between Asian (Oryza sativa L.) and African cultivated rice (O. glaberrima Steud.) have contributed to yield enhancement of African rice. However, the genetic diversity and genetic structure of the African varieties have rarely been reported. In this study, we characterized 40 rice varieties including rice released in Africa based on eleven yield related agronomic traits and 96 single nucleotide polymorphism (SNP) markers. They were grouped into three categories based on the cluster analysis using agronomic traits. Meanwhile, they were grouped into two distinct clusters, indica-and japonica-type, based on the genetic distance using 96 SNP markers. CG14, which belongs to O. glaberrima, was found to be an admixture type between indica and japonica. The number of secondary branches (SBs) was the only agronomic trait which was significantly different between two groups. The results of this study provide basic agronomic and genomic information of cultivated and tested rice varieties for Africa, that would be helpful for further rice varietal improvement in Africa.

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

“…Previously, our genetic diversity analysis of rice varieties adapted to the environmental conditions in Africa using indica-japonica SNP set 1 revealed that CG14 (Oryza glaberrima) is genetically closely related to japonica, whereas NERICA (New Rice for Africa) varieties, developed from a cross between O. glaberrima and O. sativa, are closely related to indica (Megersa et al 2016). After the development of indica-japonica SNP set 2, we genotyped 83 diverse germplasms using both SNP sets.…”

QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line

“…The Fluidigm SNP genotyping system has automated polymerase chain reaction (PCR) and integrated fluidic circuit (IFC) technology, which automatically mixes PCR reagents through microfluidic channel networks. The indica-japonica SNP assays, based on the Fluidigm system developed in the previous study [16], have been applied to various genetic analyses and molecular breeding, such as bulked segregant analysis (BSA) [17], genetic diversity analysis [18,19], QTL analysis [20][21][22][23], and background profiling [24][25][26]. This Fluidigm SNP marker set has provided a faster and more cost-effective tool than other high-throughput SNP genotyping systems for primary analysis during molecular breeding using inter-subspecific populations, to date.…”