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Title: Assessment of genetic variation and population structure of diverse rice genotypes adapted to lowland and upland ecologies in Africa using SNPs

Author
item NDJIONDJOP, MARIE-NOELLE - Africa Rice Center (AFRICARICE)
item SEMAGN, KASSA - University Of Alberta
item SOW, MOUNIROU - Africa Rice Center (AFRICARICE)
item MANNEH, BABOUCARR - Africa Rice Center (AFRICARICE)
item GOUDA, ARNAUD - Africa Rice Center (AFRICARICE)
item KPEKI, SÈDJRO - Africa Rice Center (AFRICARICE)
item PEGALEPO, ESTHER - Africa Rice Center (AFRICARICE)
item WAMBUGU, PETERSON - Kenya Agricultural And Livestock Research Organization
item SIÉ, MOUSSA - Africa Rice Center (AFRICARICE)
item Warburton, Marilyn

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2018
Publication Date: 4/9/2018
Citation: Ndjiondjop, M., Semagn, K., Sow, M., Manneh, B., Gouda, A.C., Kpeki, S.B., Pegalepo, E., Wambugu, P., Sié, M., Warburton, M.L. 2018. Assessment of genetic variation and population structure of diverse rice genotypes adapted to lowland and upland ecologies in Africa using SNPs. Frontiers in Plant Science. 9(446):1-13. https://doi.org/10.3389/fpls.2018.00446.
DOI: https://doi.org/10.3389/fpls.2018.00446

Interpretive Summary: Rice, along with maize and wheat, provide the majority of food calories to people around the world. The conservation of genetic sequence diversity present in the many different improved varieties, farmer’s varieties, and wild and weedy relatives of rice, can be used to find new gene variants to improve any trait of interest. These varieties are stored in different gene banks around the world. The AfricaRice gene bank has 22,000 registered rice samples. Of these, the varieties belonging to the species Oryza glaberrima represent one of the two cultivated species grown in Africa, and has many important traits for rice farmers. Rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ and ‘Advanced Rice for Africa (ARICA)’ improved varieties by crossing Oryza glaberrima to cultivated rice, and selecting offspring with useful traits such as resistance to insects, disease, drought, flooding, or salty water. The NERICA and ARICA rice varieties were all characterized via genetic fingerprinting and compared to other popular African rice varieties and representative populations of three rice species. The results show that a few of the NERICA cultivars are very similar to each other, but most are genetically different, and will be good sources of new genetic variation. NERICA and ARICA rice varieties are more related to each other depending on what environment they were bred to be cultivated under (lowland, upland, irrigated or rainfed). This will allow breeders to target new genetic variation from these or future inter-species crosses to the correct rice growing ecologies, and make their work more efficient.

Technical Abstract: Background: 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)’. Here, we studied the genetic variation, relatedness, and population structure of 331 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNP). Results: A sample of 1 aus, 11 ARICAs, 85 NERICAs, 62 japonica, and 172 indica genotypes were genotyped with 26,260 SNPs, of which 15,020 SNPs were polymorphic. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA and NERICA varied from 0.015 to 0.624, from 0.020 to 0.661, 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 japonica (22.6%), ARICAs (18.2%), and indica (7.8%). 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 polymorphic 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. Conclusions: 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. Results from this study aid breeders in selecting genetically divergent genotypes as the best parental combinations for future breeding programs.