Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes

Abstract

BackgroundThe development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes.ResultsThe panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel.ConclusionsThis publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0371-7) contains supplementary material, which is available to authorized users.

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

“…Compared with the whole population, LD dropped much faster in Q3-1 and Q3-3 but more slowly in Q3-2. The effect of population structure on LD pattern has been widely reported [52,[60][61][62]. Varying patterns of LD decay in different subpopulations were likely reflecting their breeding histories and the origins of accessions in subpopulations [63] and may influence the QTL mapping resolution of the panel.…”

Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

“…For example, Jarquín et al (2014) detected 52,349 SNPs and after filtering used 16,502 SNPs obtained from 301 elite soybean breeding lines, and Nimmakayala et al (2014) detected 23,693 SNPs and after filtering used 11,485 in a genetic analysis of watermelon germplasm. Likewise, Phuong Phung et al (2014) characterized 182 rice accessions with 25,971 markers after a data-cleaning step. Valdisser et al (2016) identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping.…”

“…In common bean, SNP detection can be validated by several methods (Galeano et al, 2009;Hyten et al, 2010;Zhao et al, 2010) that each has advantages and disadvantages (Cortes et al, 2011). Recently, a new method was introduced based on a hybridization approach known as Diversity Arrays Technology (DArTseq) (Mace et al, 2008) using a method of genotyping by sequencing (GBS) that combines DArT complexity reduction methods with next-generation sequencing platforms (Phuong Phung et al, 2014). A DArTseq complexity reduction approach in combination with Illumina short read sequencing (Hiseq2000) was also applied (Kilian et al, 2016).…”

“…The many advantages of DArTseq include no prior knowledge about sequencing of the plant genome and the capacity to produce high-density results, scoring thousands of unique genomic-wide DNA fragments in one single experiment with low-cost genotype information (Jaccoud et al, 2001;Kilian et al, 2016). The DArTseq method is used to discriminate diverse species for population studies, genetic diversity studies, germplasm characterization (Cruz et al, 2013), association studies (Courtois et al, 2013;Phuong Phung et al, 2014), and genetic mapping (Ren et al, 2015). To date, DArTseq genotyping has also been used for genetic analysis in species genomes, including Sorghum bicolor (Mace et al, 2008), rye (Bolibok-Brągoszewska et al, 2009), Lesquerella and related species (Cruz et al, 2013), japonica rice (Courtois et al, 2013), watermelon (Ren et al, 2015), and pineapple (Kilian et al, 2016).…”

DArTseq Genotyping Reveals High Genetic Diversity of Polish Rye Inbred Lines

“…Recently, a new highly informative and high-throughput technology of genomewide markers called DArT genotyping by sequencing (DArTseq) has been developed. ; Cruz et al, 2013) and Vietnamese rice (Phung et al, 2014). So far, DArTseq has been successfully applied in evaluation of genetic diversity in lesquerella (Physaria spp.…”