Abstract
BackgroundIncreasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties. However, the molecular basis of the traits in NU varieties is largely unknown.ResultsWhole genome re-sequencing was performed of four NU lines (3, 4, 5, and 7) and for the parental Oryza sativa WAB56–104 and Oryza glaberrima CG14. The k-mer analysis predicted large genomes for the four NU lines, most likely inherited from WAB56–104. Approximately 3.1, 0.10, and 0.40 million single nucleotide polymorphisms, multi nucleotide polymorphisms, and short insertions/deletions were mined between the parental lines, respectively. Integrated analysis with another four NU lines (1, 2, 8, and 9) showed that the ratios of the donor CG14 allelic sites in the NU lines ranged from 1.3 to 9.8%. High resolution graphical genotype indicated genome-level similarities and common genetic events during the breeding process: five xyloglucan fucosyltransferase from O. glaberrima were introgressed in common. Segregation of genic segments revealed potential causal genes for some agronomic traits including grain shattering, awnness, susceptibility to bacterial leaf bright, and salt tolerance. Analysis of unmapped sequences against the reference cultivar Nipponbare indicated existence of unique genes for pathogen and abiotic stress resistance in the NU varieties.ConclusionsThe results provide understanding of NU genomes for rice improvement for Africa reinforcing local capacity for food security and insights into molecular events in breeding of interspecific hybrid crops.
Highlights
Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries
Genome sizes were predicted using the k-mer distributions; CG14 genome exhibited the smallest size of 399.8 Mbp, WAB56–104, NU3 and NU7 exhibited larger sizes ranging from 444.9 to 455.4 Mbp, and NU4 and NU5 genome sizes were intermediate between the parental lines (Table 1)
The present study provided a draft whole picture of the Upland New Rice for Africa (NU) genomes, including polymorphisms, introgression from the donor parent, some potential introgression segments by outcross and de novo mutations
Summary
Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. One of the first subsets of NU varieties (NU 1 to 11), derived from an upland tropical japonica cultivar WAB56–104,developed by WARDA as the recurrent parent, and the O. glaberrima accession CG14 as the donor parent, were released in 2000s (Sié et al 2012). These NUs were adapted into the upland rice ecosystems in West African countries, exhibiting good yield potential (4–5 t/ha), short duration, no grain shattering and tolerance to lodging (Africa Rice Center 2008; Somado et al 2008). The NU rice grains exhibit high protein content (~ 10%) which makes for better nutritious value for the African consumers (Somado et al 2008)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
