The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences

Russell, Joanne; Hackett, Christine A.; Hedley, Pete E.; Liu, Hui; Milne, Linda; Bayer, Micha; Marshall, David; Jorgensen, Linzi; Gordon, Sandra; Brennan, Rex

doi:10.1007/s11032-013-9996-8

Cited by 47 publications

(38 citation statements)

References 31 publications

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“…sequencing and sequence alignment (Sonah et al, 2013). Molecular breeders are rapidly adapting GBS for classical uses such as genetic diversity estimation (Fu et al, 2014), trait mapping (Liu et al, 2014), QTL mapping and development of high resolution linkage maps (Russell et al, 2014). GBS is also being used for other classical uses of molecular markers like population and evolutionary studies (Larson et al, 2014).…”

Section: Genotyping By Sequencingmentioning

confidence: 99%

Development and use of molecular markers: past and present

Grover

Sharma

2014

Critical Reviews in Biotechnology

269

149

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Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications.

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Section: Genotyping By Sequencingmentioning

confidence: 99%

Development and use of molecular markers: past and present

Grover

Sharma

2014

Critical Reviews in Biotechnology

269

149

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“…Therefore, if gene/QTL mapping is intended, it is necessary to utilize novel approaches that allow simultaneous polymorphism identification and genotyping in experimental sesame populations. GBS has been demonstrated as a versatile approach for large-scale SNP identification and genotyping with work on a wide range of plant taxa (Elshire et al 2011;Poland et al 2012aPoland et al , 2012bHuang et al 2014;Jarquín et al 2014;Russell et al 2014;Hart and Griffiths 2015;Islam et al 2015;Jaganathan et al 2015). In this work, a GBS approach (Elshire et al 2011) was employed for high-throughput SNP marker development and genotyping in a F 6 -RIL mapping population.…”

Section: Resultsmentioning

confidence: 99%

High-throughput single nucleotide polymorphism (SNP) identification and mapping in the sesame (Sesamum indicum L.) genome with genotyping by sequencing (GBS) analysis

et al. 2016

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Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is considered to be the first oil seed crop known to man. Despite its versatile use as an oil seed and a leafy vegetable, sesame is a neglected crop and has not been a subject of molecular genetic research until the last decade. There is thus limited knowledge regarding genome-specific molecular markers that are indispensible for germplasm enhancement, gene identification, and marker-assisted breeding in sesame. In this study, we employed a genotyping by sequencing (GBS) approach to a sesame recombinant inbred line (RIL) population for high-throughput single nucleotide polymorphism (SNP) identification and genotyping. A total of 15,521 SNPs were identified with 14,786 SNPs (95.26 %) located along sesame genome assembly pseudomolecules. By incorporating sesame-specific simple sequence repeat (SSR) markers developed in our previous work, 230.73 megabases (99 %) of sequence from the genome assembly were saturated with markers. This large number of markers will be available for sesame geneticists as a resource for candidate polymorphisms located along the physical chromosomes of sesame. Defining SNP loci in genome assembly sequences provides the flexibility to utilize any genotyping strategy to survey any sesame population. SNPs selected through a high stringency filtering protocol (770 SNPs) for improved map accuracy were used in conjunction with SSR markers (50 SSRs) in linkage analysis, resulting in 13 linkage groups that encompass a total genetic distance of 914 cM with 432 markers (420 SNPs, 12 SSRs). The genetic linkage map constitutes the basis for future work that will involve quantitative trait locus (QTL) analyses of metabolic and agronomic traits in the segregating RIL population.

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“…Several reference-based SNP calling pipelines are available so far [78]. Although a reference genome can facilitate GBS data analysis, several reference-independent SNP calling pipeline (e.g., Stacks and TASSEL-UNEAK) have been developed [79,80] and successfully applied for PGR diversity studies [81,82].…”

Section: Ngs-based Genotyping For Genetic Diversity Evaluationmentioning

confidence: 99%

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

D’Agostino¹,

Tripodi²

2017

Diversity

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Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore "gene space" and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding.

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The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences

Cited by 47 publications

References 31 publications

Development and use of molecular markers: past and present

Development and use of molecular markers: past and present

High-throughput single nucleotide polymorphism (SNP) identification and mapping in the sesame (Sesamum indicum L.) genome with genotyping by sequencing (GBS) analysis

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

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