Abstract
Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.
Highlights
In Africa, rice is a staple food for millions of people and constitutes a major part of the diet in the continent (Maclean et al, 2002; Atera et al, 2011)
We found out that (i) only 14% (3,834 of 27,560) of the Single nucleotide polymorphism (SNP) were polymorphic across the whole O. glaberrima collection, which is much lower than diversity reported in other Oryza species; and (ii) a subset of 350 accessions selected to represent a mini-core collection captured 97% of the SNP polymorphism and most alleles observed in the whole O. glaberrima collection available at the AfricaRice genebank (Ndjiondjop et al, 2017)
The germplasm used in the present study includes 234 O. sativa genotypes (172 indica, and 62 japonica) that are either widely grown by farmers in sub Saharan Africa, and/or extensively used as trait donors by rice breeders in the region; and 96 genotypes developed by AfricaRice breeders since the 1990s
Summary
In Africa, rice is a staple food for millions of people and constitutes a major part of the diet in the continent (Maclean et al, 2002; Atera et al, 2011). Rice belongs to the genus Oryza, which consists of several wild and two cultivated species. (African rice) are the two cultivated rice species in Asia and Africa, respectively (Chang, 1976). Several African rice accessions have adaptive or protective mechanisms of resistance/tolerance to major abiotic and biotic stresses, including drought, iron toxicity, weed competitiveness, nematodes, African rice gall midge, and bacterial blight (Jones et al, 1997b; Linares, 2002; Vikal et al, 2007). The Asian rice was probably introduced into West Africa at the beginning of the 16th century and adopted by farmers living in the Upper Guinea Coast who had previous experience in growing the African rice (Linares, 2002). Most Asian rice varieties have limited resistance/tolerance to locally endemic abiotic and biotic stresses in Africa (Jones et al, 1997a)
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