Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.) (original) (raw)
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Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
Proceedings of the National Academy of Sciences, 2009
Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.
Scientific Reports
Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cu...
Molecular Breeding, 2017
Oryza nivara is the ancestral species of cultivated rice (Oryza sativa). It has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as yield improvement, lost during the course of domestication. To determine the molecular changes that occurred during domestication, the O. sativa ssp. japonica variety, Nipponbare, from which a reference sequence (RefSeq) was developed, was crossed with the O. nivara accession (IRGC100897), from which BACend sequences (BES) were derived. The mapping population composed of 279 F 2 progeny lines derived from this cross was phenotyped for 19 traits important to domestication and yield improvement, including basal sheath and culm color, culm angle, days to heading, plant height, seed shattering, flag leaf length and width, panicle type and length, awn length and color, pericarp color, and seed color, length, width, length to width ratio, volume and surface area. The population was genotyped using 95 SSR markers and 114 single nucleotide variation (SNV) markers, selected by comparing the Nipponbare RefSeq and O. nivara BES. At least one major QTL was identified for each trait evaluated, and for 28 of the 46 QTL, the trait increase was attributed to the allele contributed by the O. nivara parent. Candidate genes were identified in 37 of the QTL regions. This study validated SNV markers that can be used for mapping in populations with a wild species parent. In the future, SNVs could be used for marker-assisted selection to incorporate desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara into elite, adapted O. sativa varieties.
Marker-assisted selection can enable more precise and rapid breeding strategies, but limitations in genotyping techniques have prevented markers from being integrated into mainstream breeding programs. Multiplexed single nucleotide polymorphism (SNP) markers have the potential to increase the speed, efficiency and costeffectiveness of genotyping, provided that an optimal SNP density is used for each application. To test the usefulness of multiplexed SNP genotyping in rice, we designed four GoldenGate VeraCode oligo pool assay (OPA) sets for the Illumina BeadXpress Reader. Validated markers from existing 1536 Illumina SNPs and 44K Affymetrix SNP chips developed at Cornell University were used to select subsets of SNPs for maximum information and even distribution for each application. A 96-plex OPA was developed for assigning a sample into one of the five Oryza sativa population subgroups. One 384-plex OPA was designed to have evenly spaced polymorphic markers for QTL mapping and background selection for indica indica crosses, two additional 384-plex OPAs were selected for use in indica japonica crosses, while all of them can be used for genetic diversity analysis and DNA fingerprinting. More research is required to identify relevant SNPs for African rice germplasm, including O. glaberrima and NERICA varieties, and wild Oryza species to provide cost-effective and robust SNP genotyping assays for breeding programs focused on improving rice for Africa. The availability of optimized SNP sets will help increase the efficiency of genetic mapping and marker-assisted selection to meet the challenges of rice improvement in the future.
Plant Genetic Resources, 2012
Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivatedindicarice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties w...
Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice
PLOS Genetics, 2007
Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation. Citation: Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, et al. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3(9): e163.
PLOS ONE
Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 traitspecific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the
Genetic Resources and Crop Evolution, 2016
Insertion/deletion (InDel) polymorphisms are generally irreversible and, thus, are useful for evaluating the genetic relationships within the genus Oryza. Moreover, subspecies-specific (SS) InDel markers linked to conserved genomic regions specific to the indica and japonica subspecies of Oryza sativa can provide insight into the genetic relationships between cultivated and wild rice. The evolutionary relationship among Oryza species in respect to their indica and japonica alleles was investigated using 67 selected indica-japonica InDel SS-STS primers across 290 accessions, including 61 Asian cultivated rice (O. sativa) cultivars, 27 African cultivated rice (O. glaberrima) accessions, and 202 accessions of wild Joong Hyoun Chin and Yoo-Jin Lee have contributed equally to this paper.
2020
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve yield potential in temperate rice. In this study, a comparative study of the genomic regions in the eight high yielding varieties (HYVs) was conducted with those of the four non-HYV varieties. NGS mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared the japonica-originated genomic regions on the nine chromosomes, although they were developed from different breeding programs. A panel of 94 varieties was classified into four varietal groups with the 39 SNP markers from 39 genes residing the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica originated genomic regions were present only in JAP and HYV groups with exceptions for Chr4-1 and Chr4-2. The Wx gene located within Chr6-1 was present in HYV and JAP variety groups, while the ...