Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10−4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10−2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use

Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

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

Genetic Variation and Population Structure of Oryza sativa Accessions in the AfricaRice Collection and Development of the AfricaRice O. sativa Core Collection

Genetic diversity studies provide an increased understanding of genebank collections and enhance their use for improving global food security. This study explores the genetic variation and population structure of 5,738 rice (Oryza sativa L.) accessions representing 39.6% of the O. sativa collection conserved in the AfricaRice genebank of which 74.0% originated from African countries. These accessions were genotyped with 25,904 polymorphic DArTseq based single nucleotide polymorphisms (SNPs). Genetic distances between pairs of accessions indicate high variability, with 21.0% of pairs being moderately distant and 78.2% highly distant from each other. The genotyped accessions are traditionally grown in six different agro-ecologies from 73 countries. Using neighbor-joining tree, principal component and model-based population structure analyses, the accessions were divided into four genotypic groups representing the two O. sativa subspecies, Japonica (787 accessions) and Indica, which were further divided into landraces (1,879 accessions), and improved cultivars (3,027 accessions), and a fourth small group of admixed accessions. Subclusters identifying a specific agro-ecology (upland, lowland, mangrove swamp) or originating country were noted. Using the maximum length sub-tree method, we selected 10% of the total accessions to form the “AfricaRice O. sativa Core Collection” (AROSCC). The subset of 600 O. sativa accessions captures more than 95% of the SNP polymorphisms in the entire collection. The AROSCC is an important resource to support pre-breeding and rice improvement programs around the world