The application of DArTseq technology to pineapple

Kilian, Andrzej; Sanewski, Garth M.; Ko, L.

doi:10.17660/actahortic.2016.1111.27

Cited by 37 publications

(25 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The company developed a method named DArTseq. DArTseq combines genome complexity reduction methods and next-generation sequencing platforms (Courtois et al, 2013;Cruz et al, 2013;Raman et al, 2014;Kilian et al, 2016). Therefore, DArTseq represents a new implementation of sequencing of complexity-reduced representations (Huang et al, 2014) and more recent applications of this concept on the nextgeneration sequencing platforms (Sonah et al, 2013;Bastien et al, 2014).…”

Section: Snp Discovery By Dartseqmentioning

confidence: 99%

“…The DArTseq method has several advantages, including rapid sequencing, low cost per sample, and the ability to handle high-density genomewide marker scans. Moreover, the technical simplicity of this technique facilitated its successful use in the genetic analysis of diverse germplasm resources (Jaccoud et al, 2001;Cruz et al, 2013;Schmutz et al, 2014;Kilian et al, 2016). Genetic variations are lower in cultivated common bean than ancestor genotypes (Gepts et al, 1986;McClean et al, 2004).…”

Section: Snp Discovery By Dartseqmentioning

confidence: 99%

“…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). DArTseq has been developed to generate genome-wide SNPs that overcome some of the previous disadvantages (Degner et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…DArTseq has been developed to generate genome-wide SNPs that overcome some of the previous disadvantages (Degner et al, 2014). 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).…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

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

Nemli¹,

Aşçioğul²,

Ateş³

et al. 2017

Turk J Agric For

View full text Add to dashboard Cite

The common bean (Phaseolus vulgaris L.) is the most consumed food legume in the world and is a major source of dietary protein, carbohydrates, and valuable micronutrients, especially in developing countries. Diversity Arrays Technology (DArTseq), based on genome reduction with restriction enzymes, provides a rapid, high-throughput, and cost-effective tool capable of generating thousands of genotyped single nucleotide polymorphisms (SNPs) for a genome-wide analysis of genetic diversity. In this study, we aimed to characterize common bean accessions using SNPs detected by a DArTseq approach. A total of 43,018 SNPs were identified from 173 common bean accessions, including Andean and Mesoamerican genotypes. After filtering raw and redundant data, a total of 16,366 SNPs were considered for further analyses. According to population structure analysis, the genotypes were roughly divided into 2 gene pools of Andean and Mesoamerican types. Pairwise fixation index (Fst) values were calculated to resolve the differentiation between populations. This study demonstrated that discovering SNPs from the whole genome is a potential resource for identifying naturally diverse accessions and also the information could be used in breeding programs to develop new common bean varieties.

show abstract

Section: Snp Discovery By Dartseqmentioning

confidence: 99%

Section: Snp Discovery By Dartseqmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

Nemli¹,

Aşçioğul²,

Ateş³

et al. 2017

Turk J Agric For

View full text Add to dashboard Cite

show abstract

Genetic diversity and population structure among Ugandan shea tree (Vitellaria paradoxa subsp. nilotica) accessions based on DarTSeq markers

et al. 2023

View full text Add to dashboard Cite

Molecular markers such as single nucleotide polymorphisms (SNPs) and SilicoDArT are important in dissecting the genetic diversity of a population at DNA level. The two marker types were analyzed using the same genotyping platform. Although the two marker types were analyzed using the same genotyping platform, they were filtered using a different marker stringency. We determined the genetic diversity of 623 half-sibs of shea tree (Vitellaria paradoxa a C. F. Gaertn. nilotica) assembled from five geographical locations (Katakwi, Otuke, Amuru, Moyo, and Arua) in Uganda's shea parklands. A total of 27,063 Diversity Arrays Technology (DArT) SNP and 9018 SilicoDArT markers were used to assess genetic diversity and population structure.The populations showed a low genetic diversity (Gst = 0.21), very low population differentiation (FST = 0.02), low-to-moderate linkage disequilibrium (r = 0.2), and Hardy-Weinberg Equilibrium (HWE = 0.1982). The study further revealed a higher genetic diversity within population (0.26) than among the population (0.21).A high level of heterozygosity was observed within individuals (0.26) and markers (0.32) revealing a high non-random association of alleles at different loci that offer

show abstract

Assessment of genetic diversity and heterotic alignment of CIMMYT and IITA maize inbred lines adapted to sub‐Saharan Africa

Gonhi,

Odong,

Dramadri

et al. 2024

Crop Science

View full text Add to dashboard Cite

Despite the breeding efforts by many institutions, maize (Zea mays L.) productivity in sub‐Saharan Africa is still low. A limited number of productive maize hybrids have been developed partly due to a lack of knowledge on the diversity and heterotic relationship of the germplasm, especially in public breeding programs. Understanding the extent of diversity, structure, and heterotic grouping of available maize germplasm originating from different breeding programs is important to enhance long‐term genetic gain in hybrid maize breeding programs by optimizing heterotic pools using modern breeding tools. Information about the genetic structure of the available germplasm could help breeders design effective breeding strategies to improve yield. This study was conducted to determine the genetic diversity, population structure, and heterotic alignment among 187 elite maize inbred lines from the IITA (International Institute of Tropical Agriculture) and CIMMYT (International Maize and Wheat Improvement Center) maize breeding programs. The inbred lines were genotyped with 9857 Diversity Array Technology sequencing based single nucleotide polymorphism markers. Hierarchical clustering revealed three major groups, with some subgroups consistent with the selection history, and pedigree of the inbred lines. Three broad groups were detected: two consisting of CIMMYT lines and a mixed group consisting of both CIMMYT and IITA inbred lines. The STRUCTURE analysis revealed six subpopulations (fixation index value = 0.58), which depicts a moderate genetic diversity among the materials. Population 2 comprises the highest number of genotypes (102) from both programs. More than 89% of the elite lines had homozygosity exceeding 95%, with the remaining lines requiring further inbreeding through repeated self‐pollination. There was inconsistency in the predetermined heterotic groups' alignment between CIMMYT and IITA elite inbred lines. Analysis of molecular variance revealed that 96% of the total variation was accounted for by differences within groups, with the remaining 4% representing the variation between groups. This suggests that the two programs can benefit from germplasm exchange for the improvement of maize productivity.

show abstract

The application of DArTseq technology to pineapple

Cited by 37 publications

References 12 publications

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

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

Genetic diversity and population structure among Ugandan shea tree (Vitellaria paradoxa subsp. nilotica) accessions based on DarTSeq markers

Assessment of genetic diversity and heterotic alignment of CIMMYT and IITA maize inbred lines adapted to sub‐Saharan Africa

Contact Info

Product

Resources

About