Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

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.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0224-3) contains supplementary material, which is available to authorized users.

Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups

“…To test the latter possibility, we predicted the genome size of AG-1 IA by a k -mer analysis using the two sets of genomic DNA sequencing data with the 173 bp and 5.6 kb inserts 10 using the method of Yamamoto et al . 24 .The estimated genome size ranged from 41.4 to 49.3 Mb at the k -mer length of 17. These values are 11.2 to 33.4% larger than the total length of the genome assembly.…”

Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice

“…In recent years, genome comparison based on high depth next generation sequencing data has been used to identify inherited chromosome blocks and key trait loci in several studies (Zhou et al 2016;Huang et al 2018;Yamamoto et al 2018). The newly developed NTRs showed remarkable improvement in yield performance especially in fertility than their parental ATR lines.…”

“…Whole genome sequencing of 30 cultivars revealed 28 chromosomal blocks inherited from ancestral lines that shared by all high-yielding cultivars (Huang et al 2018). High resolution graphical genotype map was constructed for new upland African rice, which indicated similar genome constitution and common genetic events, and showed potential genes related to important agronomic traits by genome resequencing (Yamamoto et al 2018).…”

Dry matter partitioning to leaves differentiates African and Asian rice genotypes exposed to elevated CO2

“…Nonetheless, the 17 genotypes we chose represent a vanishingly small proportion of the thousands of the accessions that are available in the gene banks (McCouch, McNally, Wang, & Hamilton, 2012). Additionally, NERICA, as a newly developed resource (the New Rice for Africa), produced by crossing African rice and Asian rice (Jones, Dingkuhn, Aluko/snm, & Semon, 1997; Saito et al., 2012) and introduced of African allele by 1~9% to Asian rice (Yamamoto et al., 2018), might be good candidates for eCO 2 responsive genotypes, but no studies are available for testing NERICA for eCO 2 responsiveness. To discover candidate genotypes with high responsiveness to eCO 2 , a large‐scale study should screen hundreds of genotypes collected from many regions.…”