Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives.

@article{Rasheed2017CropBC,
  title={Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives.},
  author={Awais Rasheed and Yuanfeng Hao and Xianchun Xia and Awais Khan and Yunbi Xu and Rajeev Kumar Varshney and Zhonghu He},
  journal={Molecular plant},
  year={2017},
  volume={10 8},
  pages={
          1047-1064
        }
}

Figures and Tables from this paper

High-Throughput Genotyping for Cereal Research and Breeding

Efficient genome-wide genotyping strategies and data integration in crop plants

This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration of NGS-based genotyping methods.

Editorial: Genome Wide Association Studies and Genomic Selection for Crop Improvement in the Era of Big Data

This Research Topic sought high-quality contributions, covering various aspects of genomics-assisted-breeding: increase in yield, improvement of nutritional content and end-use quality of crops, climate-smart agriculture, cropping systems in agriculture.

Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize

Highly consistent marker genotypes were obtained and highly consistent phylogenetic relationships were generated by using four marker panels and two genotype panels, providing strong evidence for the reliability of SNP markers and GBTS genotyping platform.

Genotyping by Sequencing Advancements in Barley

Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges and a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium.

Molecular Marker Development and Application for Improving Qualities in Bread Wheat

This chapter summarizes progress in gene cloning, gene specific marker (functional marker) development and validation, establishment of high-throughput platform in genotyping, as well as integration of molecular marker technology with conventional quality testing and traditional breeding since 2000.

Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes

The latest developments in genome sequencing and genotyping are described along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops to develop high-yielding and climate-resilient crops.

Fine mapping and gene cloning in the post-NGS era: advances and prospects

This review compares the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era, and discusses how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping.

Toward the sequence-based breeding in legumes in the post-genome sequencing era

A sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies is proposed.

Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane

This work comprehensively discusses the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, and integrated GS, high-throughput phenotyping (HTP), high- throughput genotypes (HTG), machine learning, and speed breeding followed by its prospective applications in Sugarcane improvement.
...

References

SHOWING 1-10 OF 189 REFERENCES

High-Throughput SNP Genotyping to Accelerate Crop Improvement

The range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities are discussed, and an example of SNP deployment for rice research and breeding is provided as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.

Array-based high-throughput DNA markers for crop improvement

These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money.

A whole-genome SNP array (RICE6K) for genomic breeding in rice.

Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection, and suggests that RICE 6K provides an efficient and reliable genotypesing tool for rice genomic breeding.

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

The most common genotyping methods used today are reviewed and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker‐assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity.

Development of a maize 55 K SNP array with improved genome coverage for molecular breeding

This maize 55 K SNP array is a potentially powerful tool for germplasm evaluation, marker-assisted breeding, and primary quantitative trait loci mapping and genome-wide association study (GWAS) for both tropical and temperate maize.

Development of genome-wide SNP assays for rice

Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation in eukaryotic genomes. SNPs may be functionally responsible for specific traits or phenotypes, or they may be

Application of genotyping by sequencing technology to a variety of crop breeding programs.

SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

The development of a SNP genotyping resource for use in sunflower revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability, as well as patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower.

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

The SBG approach presented provides users with the utmost flexibility in garnering high quality markers that can be directly used for genotyping and downstream applications, and it is shown that sequence-based genotypes technologies such as SBG will be essential for genotypesing of model and non-model genomes alike.

Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat

The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat and fully verified the genotype calls of 23 markers.
...