ArticlePlant biotechnology journal2018
Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels.
Article in Plant biotechnology journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence.Scientific reports · 2020Pooled it
- Article
- Machine learning solutions for integrating partially overlapping genetic datasets and modelling host-endophyte effects in ryegrass (Frontiers in plant science · 2025Article
- Review
- Developing an integrated genomic selection approach beyond biomass for varietal protection and nutritive traits in perennial ryegrass (Lolium perenne L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Advances in lentil production through heterosis: Evaluating generations and breeding systems.PloS one · 2022Article
- Genotyping by Sequencing Advancements in Barley.Frontiers in plant science · 2022Review
- Combining NDVI and Bacterial Blight Score to Predict Grain Yield in Field Pea.Frontiers in plant science · 2022Article
- VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset.PLoS computational biology · 2021Article
- Article
- Article
- Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus.BMC plant biology · 2020Article
- Making the most of all data: Combining non-genotyped and genotyped potato individuals with HBLUP.The plant genome · 2020Article
- Article
- Genomic Prediction and Genetic Correlation of Agronomic, Blackleg Disease, and Seed Quality Traits in Canola (Plants (Basel, Switzerland) · 2020Article
- Characterization of Genetic and Allelic Diversity Amongst Cultivated and Wild Lentil Accessions for Germplasm Enhancement.Frontiers in genetics · 2020Article
- Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).Scientific reports · 2019Article
- Validation of Genotyping by Sequencing Using Transcriptomics for Diversity and Application of Genomic Selection in Tetraploid Potato.Frontiers in plant science · 2019Article
- Exploitation of data from breeding programs supports rapid implementation of genomic selection for key agronomic traits in perennial ryegrass.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Genomic Prediction Using Prior Quantitative Trait Loci Information Reveals a Large Reservoir of Underutilised Blackleg Resistance in Diverse Canola (The plant genome · 2018Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The application of genomics in crops has the ability to significantly improve genetic gain for agriculture. Many marker-dense tools have been developed, but few have seen broad adoption in plant genomics due to issues of significant variations of genome size, levels of ploidy, single nucleotide polymorphism (SNP) frequency and reproductive habit. When combined with limited breeding activities, small research communities and scant sequence resources, the suitability of popular systems is often suboptimal and routinely fails to effectively balance cost-effectiveness and sample throughput. Genotyping-by-sequencing (GBS) encompasses a range of protocols including resequencing of the transcriptome. This study describes a skim GBS-transcriptomics (GBS-t) approach developed to be broadly applicable, cost-effective and high-throughput while still assaying a significant number of SNP loci. A range of crop species with differing levels of ploidy and degree of inbreeding/outbreeding were chosen, including perennial ryegrass, a diploid outbreeding forage grass; phalaris, a putative segmental allotetraploid outbreeding forage grass; lentil, a diploid inbreeding grain legume; and canola, an allotetraploid partially outbreeding oilseed. GBS-t was validated as a simple and largely automated, cost-effective method which generates sufficient SNPs (from 89 738 to 231 977) with acceptable levels of missing data and even genome coverage from c. 3 million sequence reads per sample. GBS-t is therefore a broadly applicable system suitable for many crops, offering advantages over other systems. The correct choice of subsequent sequence analysis software is important, and the bioinformatics process should be iterative and tailored to the specific challenges posed by ploidy variation and extent of heterozygosity.
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