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

Abstract

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. Abstract 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. Electronic supplementary material The online version of this article (10.1007/s00122-018-3268-2) contains supplementary material, which is available to authorized users.

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing

“…Most genebanks minimize such high levels of intra-accession variation by purifying seed lots to make them acceptable for genetic and pre-breeding studies 68 . In a recent example, our group at the AfricaRice genotyped 3,245 accessions belonging to O. barthii (115), O. sativa (772) and O. glaberrima (2,358) with 26,073 physically mapped SNPs 21 , with each accession represented by a single plant after seed purification 25 . There are, however, concerns regarding the development of purified seed lots and/or use of a single individual to represent a genebank collection, especially in landraces and wild accessions.…”

“…Values for θ and π estimated from Set-2, Set-11 and Set-12 within 90 accessions were highly correlated (0.967 ≤ r ≤ 0.996) and very low, with 81 of the 90 accessions showing < 0.06 θ and π values (19), O. sativa subsp. japonica (18), improved interspecific genotypes (14), lowland O. sativa (30), and upland O. sativa (21). See Supplementary Table S1 for germplasm summary and Table S2 for details on the number of polymorphic SNPs for all datasets.…”

“…The DArTseq-based SNPs were highly useful for a wide range of purposes, including (1) understanding the genetic diversity, population structure, and genetic differentiation among African rice ( Oryza glaberrima Steud.) collections, and developing core and minicore sets 25 ; (2) developing species- and subspecies-diagnostic SNP markers to minimize misclassification, misidentification and mislabeling errors during germplasm acquisition and routine genebank operations 26 ; (3) identifying candidate genes using selective sweep analysis 21 ; and (4) comparing the extent of genetic variation and relatedness among various landraces and improved intraspecific and interspecific rice varieties developed by AfricaRice breeders with those developed by other institutions 29 . Based on the pilot study, we aim to genotype the entire rice collection conserved at AfricaRice using DArTseq and use the data to improve our germplasm curation.…”

“…SSR markers are codominant and more reproducible, with better genome coverage than Methods plant materials and genotyping. This study was conducted using a total of 1,527 DNA samples from 90 accessions and varieties (all referred here as accessions) that represented a wild O. barthii (18), landraces of cultivated species of O. glaberrima (21), O. sativa subsp. indica (19), O. sativa subsp.…”

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

“…Other important tests include the XP-CLR test ( Chen et al, 2010 ) and the μ statistic ( Alachiotis and Pavlidis, 2018 ) which implement multiple signatures to detect selective sweeps ( Supplementary Table S1 ) and have been used to detect candidate loci in maize and African rice, respectively ( Hufford et al, 2012 ; Ndjiondjop et al, 2019 ).…”