Genomic characterization of elite diversity in rice: the example of IRRI [International Rice Research Institute, Philippines] breeding program for irrigated ecosystems

Genetic diversity is now accessible through unprecedented precision thanks advances in DNA sequencing technologies. While a wealth of genomic resources is available for a broad collection of rice (Oryza sativa L.) elite rice germplasm resulting from intensive breeding efforts remains to be systematically characterized with the view to mobilizing genomic information to expedite varietal development. Authors re-sequenced 124 elite lines representing the diversity of the IRRI [[International Rice Research Institute, Philippines] breeding program for irrigated ecosystems and analyzed nucleotide diversity at a 100 kb scale. Authors could highlight 630 regions (100 kb to 1.42 Mb) with low diversity, which include genes of proven agronomical impact. Authors represent one-fifth of the genome and deserve specific attention for managing diversity in the long term. Comparing elite lines with 254 accessions representative of the diversity of O. sativa unexpectedly revealed their general similarity with Xian/Indica group, but analyses based on principal components revealed differentiation along the genome between the two groups. Eighty-three genomic regions were identified, which differentiate between the elite and landrace Indica groups. Authors ranged from few kilobases to several mega-bases, spanning approximately 10% of the whole genome. Some highlighted historical introgression from the circum-Aus and Geng/Japonica varietal groups. In other cases, elite line possessed haplotypes not commonly found in other groups. In other cases, elite lines possessed haplotypes not commonly found in other groups. Their origin remains to be identified in relation to past hybridization aimed at incorporating particular traits or genes. These fractions of the genome may be rich in exotic alleles underlying important traits. Results and the associated dataset provide important resources for managing breeding program diversity and exploring genetic factors involved in crop adaptation and performance.