Genome wide association study pinpoints key agronomic QTLs in African riceOryza glaberrima

Abstract

18Background 19 African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and 20 abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has 21 colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of 22 quantitative traits and adaptive variation of agricultural interest for this species. 23 Results 24Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study 25 carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and 26 resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association 27 methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes 28 from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied 29 our pipeline to panicle-and resistance-related traits, highlighting some interesting QTLs and candidate genes (including 30Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution 31 climate database, we performed an association analysis based on climatic variables, searching for genomic regions that 32 might be involved in adaptation to climatic variations. 33 Conclusion 34Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity 35 within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might 36 be useful to the rice breeding community. 37 38

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

“…We focused our analysis on two climate variables that were the most pertinent to annual species, i.e., mean temperature of the wettest quarter (bio8) and mean precipitation of the wettest quarter (bio 16), respectively. A GWAS with these climate variables has been performed 106 . Briefly, we first used the impute method from the R package LEA v2.0 101 to fill the gaps in the genotypic matrix in order to achieve greater power.…”

Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

“…In the same study, several single nucleotide polymorphisms (SNPs) close to two major resistance genes RYMV1 and RYMV3 were identified. However, the SNPs associated with resistance conferred by RYMV1 and RYMV3 were not found in regions flanking any of the identified partial resistance QTLs indicating differences in genes and pathways of resistance ( Cubry et al, 2020 ) suggesting the complex mechanism of partial resistance to RYMV in rice.…”

“…For example, Orjuela et al (2013) reported on the co-localization of QTL1 in a 151-kb interval of the RYMV2 gene, hence this QTL may combine complete and partial resistance. Genome-wide association analysis study (GWAS) involving various accessions of O. glaberrima also revealed considerable relationships between quantitative resistance and two known major resistance genes ( Cubry et al, 2020 ). In the same study, several single nucleotide polymorphisms (SNPs) close to two major resistance genes RYMV1 and RYMV3 were identified.…”

“…Improvements in high-throughput genotyping have enhanced the identification of QTLs through GWAS. For instance, Cubry et al (2020) observed a total of 2,199 SNPs, close to chromosomes 4 and 11 associated with RYMV1 and RYMV3 resistance, respectively. However, adoption and utilization of genomics-selection approaches in many breeding programs has remained low due to less know-how on genomic tools, and the cost involved in MAS ( Ndjiondjop et al, 2013 ).…”

High-throughput phenotyping reveals a link between transpiration efficiency and transpiration restriction under high evaporative demand and new loci controlling water use-related traits in African rice,Oryza glaberrimaSteud

“…This panel was further used to identify QTLs associated with flowering time, panicle architecture and resistance to Rice yellow mottle virus, providing insights into the adaptive variation of African rice as compared to Asian rice (Cubry et al, 2020). Due to its adaptation to contrasted environments, we hypothesized that O. glaberrima could also be a source of interesting alleles for improving TE.…”