iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: http://pubmed.ncbi.nlm.nih.gov/32065714/
The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat - PubMed Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2020 Jun;18(6):1354-1360.
doi: 10.1111/pbi.13361. Epub 2020 Mar 10.

The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat

Congwei Sun  1 , Zhongdong Dong  1 , Lei Zhao  1 , Yan Ren  1 , Ning Zhang  1 , Feng Chen  1
Affiliations
Review

The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat

Congwei Sun et al. Plant Biotechnol J. 2020 Jun.

Erratum in

  • Corrigendum.
    [No authors listed] [No authors listed] Plant Biotechnol J. 2020 Jul;18(7):1635. doi: 10.1111/pbi.13423. Plant Biotechnol J. 2020. PMID: 32531141 Free PMC article. No abstract available.

Abstract

The rapid development and application of molecular marker assays have facilitated genomic selection and genome-wide linkage and association studies in wheat breeding. Although PCR-based markers (e.g. simple sequence repeats and functional markers) and genotyping by sequencing have contributed greatly to gene discovery and marker-assisted selection, the release of a more accurate and complete bread wheat reference genome has resulted in the design of single-nucleotide polymorphism (SNP) arrays based on different densities or application targets. Here, we evaluated seven types of wheat SNP arrays in terms of their SNP number, distribution, density, associated genes, heterozygosity and application. The results suggested that the Wheat 660K SNP array contained the highest percentage (99.05%) of genome-specific SNPs with reliable physical positions. SNP density analysis indicated that the SNPs were almost evenly distributed across the whole genome. In addition, 229 266 SNPs in the Wheat 660K SNP array were located in 66 834 annotated gene or promoter intervals. The annotated genes revealed by the Wheat 660K SNP array almost covered all genes revealed by the Wheat 35K (97.44%), 55K (99.73%), 90K (86.9%) and 820K (85.3%) SNP arrays. Therefore, the Wheat 660K SNP array could act as a substitute for other 6 arrays and shows promise for a wide range of possible applications. In summary, the Wheat 660K SNP array is reliable and cost-effective and may be the best choice for targeted genotyping and marker-assisted selection in wheat genetic improvement.

Keywords: Axiom® Wheat 660K SNP array; Illumina Wheat 90K iSelect SNP genotyping array; marker-assisted breeding; single-nucleotide polymorphisms; wheat.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1
Figure 1
Available genotyping platforms and their application in marker‐assisted selection.
Figure 2
Figure 2
Chromosomal distribution of the SNPs with unique reliable physical positions in the five arrays.
Figure 3
Figure 3
Heatmap display of SNP numbers along a window size of 1 Mb in each chromosome in the Wheat 35K, 55K, 90K, 660K and 820K arrays.
Figure 4
Figure 4
Numbers of overlapping SNP‐associated annotated genes derived from the five arrays.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Allen, A.M. , Winfield, M.O. , Burridge, A.J. , Downie, R.C. , Benbow, H.R. , Barker, G.L. , Wilkinson, P.A. et al (2017) Characterization of a Wheat Breeders’ Array suitable for high‐throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol. J. 15, 390–401. - PMC - PubMed
    1. Appels, R. , Eversole, K. , Feuillet, C. , Keller, B. , Rogers, J. , Stein, N. , Choulet, F. et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361, eaar7191. - PubMed
    1. Bevan, M.W. and Uauy, C. (2013) Genomics reveals new landscapes for crop improvement. Genome Biol. 14, 206. - PMC - PubMed
    1. Boeven, P.H. , Longin, C.F.H. , Leiser, W.L. , Kollers, S. , Ebmeyer, E. and Würschum, T. (2016) Genetic architecture of male floral traits required for hybrid wheat breeding. Theor. Appl. Genet. 129, 2343–2357. - PubMed
    1. Cavanagh, C.R. , Chao, S. , Wang, S. , Huang, B.E. , Stephen, S. , Kiani, S. , Forrest, K. et al (2013) Genome‐wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc. Natl Acad. Sci. USA, 110, 8057–8062. - PMC - PubMed

Publication types

LinkOut - more resources