Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

Key message The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic...

Full description

Saved in:
Bibliographic Details
Published in:Theoretical and applied genetics 2019-04, Vol.132 (4), p.1145-1158
Main Authors: Ndjiondjop, Marie Noelle, Alachiotis, Nikolaos, Pavlidis, Pavlos, Goungoulou, Alphonse, Kpeki, Sèdjro Bienvenu, Zhao, Dule, Semagn, Kassa
Format: Article
Language:English
Subjects:
Agriculture
Analysis
Asia
Biochemistry
Biomedical and Life Sciences
Biotechnology
Chromosomes
Chromosomes, Plant - genetics
Comparative analysis
Diversity indices
Gene polymorphism
Genetic aspects
Genetic Association Studies
Genetic distance
Genetic diversity
Genetic Markers
Genetic polymorphisms
Genetic research
Genetic Variation
Genetics, Population
Genomes
Germplasm
Life Sciences
Original
Original Article
Oryza - genetics
Oryza barthii
Oryza sativa
Phylogeny
Physical Chromosome Mapping
Plant Biochemistry
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Polymorphism
Polymorphism, Single Nucleotide - genetics
Population structure
Principal Component Analysis
Rice
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Key message The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice ( Oryza glaberrima Steud.) as compared to its wild progenitor ( O. barthii A. Chev.) and to Asian rice ( O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii , respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10 −4 , which is not only 20-fold smaller than the value estimated from all genomewide SNPs ( π  = 1.6 × 10 −2 ), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii , lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
ISSN:0040-5752
1432-2242
DOI:10.1007/s00122-018-3268-2