Genotyping-by-sequencing: a promising tool for plant genetics research and breeding

Chung, Yong Suk; Choi, Sang Chul; Jun, Tae-Hwan; Kim, Changsoo

doi:10.1007/s13580-017-0297-8

Cited by 100 publications

(77 citation statements)

References 60 publications

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“…Genotyping by sequencing (GBS), using next-generation sequencing (NGS), is becoming an increasingly useful technique in the fields of biology and agronomy [1][2][3]. In recent years, the cost of sequencing per base has drastically reduced, although the library preparation cost and time involved still remain high.…”

Section: Introductionmentioning

confidence: 99%

Miniaturization technologies for cost-effective AmpliSeq library preparation for next generation sequencing

Ogiso‐Tanaka

Kaga

Hajika

2018

Preprint

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Purpose: AmpliSeq technology, the target enrichment method for next-generation sequencing (NGS), enables quick and easy detection of the genomic "hot spot" region frequently mutated in species. Even though the cost of NGS has decreased, library preparation cost accounts for a more significant proportion of the total cost. If AmpliSeq library can be prepared at a lower cost, large-scale precision oncology can be more easily carried out. Furthermore, this technology can be widely applied not only to medical research, but also to polymorphism detection in biology. This study aimed to reduce the cost of AmpliSeq library preparation by adopting miniaturization technology. Methods:We used approximately 10 ng of genomic DNA for ultra-multiplex PCR of 384, 768, 1152, 1920, and 3072 amplicons. Multiplex PCR was performed in a total volume of 1.6, 2.0, and 2.4 µL, using a nano-liter liquid handler, for library preparation. Results:The success rate of library construction decreased with decreasing total multiplex PCR reaction volume. Using 1.6-, 2.0-, and 2.4-µL reactions, the success rates of ultra-multiplex PCR were 25%, 95%, and 100%, respectively. We could stably create libraries of the correct amplicon size, with an amplicon number of approximately 1500 or less. As a result of NGS, uniformity of PCR amplification and read length of quality-checked libraries were hardly affected by the number of amplicons. Conclusion:Here, we show that the minimum volume for a stable reaction was 2.4 µL and the maximum number of amplicons obtained was approximately 1500. The protocol saved 86.8% in reagent usage and reduced handling time by 85% compared to that required by the manual protocol. Therefore, miniaturization technologies could reduce the cost of AmpliSeq library preparation through minimization of reagents.

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Section: Introductionmentioning

confidence: 99%

Miniaturization technologies for cost-effective AmpliSeq library preparation for next generation sequencing

Ogiso‐Tanaka

Kaga

Hajika

2018

Preprint

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“…Online-only Table 2 gives statistics about the variants called (SNPs) for individual genotypes. Studies of genetic diversity, population genetics, phylogenetics [51][52][53][54] , association mapping and genome-wide association studies 15,[55][56][57][58] , linkage map and quantitative trait loci (QTL) mapping [59][60][61][62][63] , marker-assisted and genomic selection 35,63 have used GBS data for the advancement of breeding in various plant species including wheat. Together with agromorphological and yield data, GBS data generated for wheat genotypes in this study will be extremely useful in future crop breeding programs.…”

Section: Data Recordsmentioning

confidence: 99%

Agro-morphological, yield, and genotyping-by-sequencing data of selected wheat germplasm

Islam

Abdullah

Zubaida

et al. 2020

Preprint

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Wheat (Triticum aestivum) is the most important staple food in Pakistan. Knowledge of its genetic diversity is critical for designing effective crop breeding programs. Here we report agro-morphological and yield data for 112 genotypes (including 7 duplicates) of wheat (Triticum aestivum) cultivars, advance lines, landraces and wild relatives, collected from several research institutes and breeders across Pakistan. We also report genotyping-by-sequencing (GBS) data for a selected sub-set of 52 genotypes. Sequencing was performed using Illumina HiSeq 2500 platform using the PE150 run. Data generated per sample ranged from 1.01 to 2.5 Gb; 90% of the short reads exhibited quality scores above 99.9%. TGACv1 wheat genome was used as a reference to map short reads from individual genotypes and to filter single nucleotide polymorphic loci (SNPs). On average,up to 364,074 SNPs per genotype were recorded. The sequencing data has been submitted to the SRA database of NCBI (accession number SRP179096). The agro-morphological and yield data, along with the sequence data and SNPs will be invaluable resources for wheat breeding programs in future.

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“…Specifically, in oil palm the GBS technique has been used for identifying candidate genes related to oil bunch [37], bunch weight [20,37], stem height [21] and oil quality traits studies [38] with the enzymes ApeKI and PstI-MspI. Here, we used the enzyme PstI for the library construction, allowing us to identify relatively high number of SNPs with probably novel genetics variants, which according to Chung et al [39] is one of the most important advantages of…”

Section: Association Analysismentioning

confidence: 99%

Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

Osorio

Garzón

Delgadillo

et al. 2019

Preprint

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Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. The work presented herein provides, to our knowledge, the first association mapping study in an interspecific OxG hybrid population of oil palm which presents tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrids for 10 agronomic traits. Twelve genomic regions were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on candidate genes that mapped on genomic regions involved in plant architecture and yield; however, these potential candidate genes need to be confirmed for future targeted functional analysis. The associated markers may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis, Elaeis oleifera, genotyping-by-sequencing, plant architecture, yield.

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Genotyping-by-sequencing: a promising tool for plant genetics research and breeding

Cited by 100 publications

References 60 publications

Miniaturization technologies for cost-effective AmpliSeq library preparation for next generation sequencing

Miniaturization technologies for cost-effective AmpliSeq library preparation for next generation sequencing

Agro-morphological, yield, and genotyping-by-sequencing data of selected wheat germplasm

Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

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