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
        }
}
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the… Expand
View on PubMed
cell.com
198 Citations
Highly Influential Citations
5
Background Citations
51
Methods Citations
12
Results Citations
1

198 Citations

Citation Type

Citation Type

Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array
TLDR
This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes. Expand
Efficient genome-wide genotyping strategies and data integration in crop plants
TLDR
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. Expand
Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize
TLDR
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. Expand
Molecular Marker Development and Application for Improving Qualities in Bread Wheat
TLDR
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. Expand
Fine mapping and gene cloning in the post-NGS era: advances and prospects
TLDR
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. Expand
Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip
  • Zifeng Guo, Quannv Yang, +11 authors Yunbi Xu
  • Biology
  • Plant Communications
  • 2021
TLDR
The technologies, protocols, and application scenarios developed for maize will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals, plants, and microorganisms. Expand
Toward the sequence-based breeding in legumes in the post-genome sequencing era
TLDR
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. Expand
Role of NGS and SNP genotyping methods in sugarcane improvement programs
TLDR
The NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods are reviewed to increase the accuracy of genomic selection and marker-assisted breeding. Expand
Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies
TLDR
This work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS, and provides recommendations to perform QC in crop species, and delivers an overview of bioinformatics tools that can be used to accomplish all needed tasks. Expand
Genomic Selection in Cereal Crops: Methods and Applications
TLDR
This chapter will explore the factors affecting the selection of superior genotype, how to design a suitable breeding pipeline along with the concept of statistical model, advantages, and applications, and how genomic selection is a remarkable approach for genetic gain. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 252 REFERENCES
High-Throughput SNP Genotyping to Accelerate Crop Improvement
TLDR
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. Expand
Array-based high-throughput DNA markers for crop improvement
TLDR
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. Expand
A whole-genome SNP array (RICE6K) for genomic breeding in rice.
TLDR
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. Expand
Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application
TLDR
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. Expand
A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array
TLDR
The high density Affymetrix® Axiom® Maize Genotyping Array is optimized for European and American temperate maize and was developed based on a diverse sample panel by applying stringent quality filter criteria to ensure its suitability for a broad range of applications. Expand
Development of a maize 55 K SNP array with improved genome coverage for molecular breeding
TLDR
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. Expand
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… Expand
Application of genotyping by sequencing technology to a variety of crop breeding programs.
TLDR
Current genotyping methods using next-generation sequencing (NGS) technologies are reviewed and case studies of genotypes-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system are explored. Expand
SNP Discovery and Development of a High-Density Genotyping Array for Sunflower
TLDR
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. Expand
Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations
TLDR
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. Expand
...
1
2
3
4
5
...