Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Singh, Nisha ^a,b   Jayaswal, Pawan Kumar ^a   Panda, Kabita ^a   Mandal, Paritra ^a   Kumar, Vinod ^a   Singh, Balwant ^a   Mishra, Shefali ^a   Singh, Yashi ^a   Singh, Renu ^a   Rai, Vandna ^a   Gupta, Anita ^b   Raj Sharma, Tilak ^a   Singh, Nagendra Kumar ^a  

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b I K GUJRAL PUNJAB TECHNICAL UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT PROTEIN;

CHROMOSOMAL MAPPING; CLASSIFICATION; DNA MICROARRAY; GENE DOSAGE; GENETIC VARIATION; GENETICS; GENOTYPE; GENOTYPING TECHNIQUE; HAPLOTYPE; ORYZA; PHYLOGENY; PLANT BREEDING; PLANT CHROMOSOME; PLANT GENE; PLANT GENOME; PROCEDURES; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENE DOSAGE; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; GENOTYPING TECHNIQUES; HAPLOTYPES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA; PHYLOGENY; PLANT BREEDING; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 84933055390     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep11600     Document Type: Article

References (43)

1. Liu, L., Lee, G. A., Jiang, L. & Zhang, J. The earliest rice domestication in China. Antiquity 81, 313 (2007).
2. Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).
3. International Rice Genome Sequencing Project: The Map-Based Sequence of the Rice Genome. Nature 436, 793-800 (2005).
4. Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967 (2010).
5. Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497-501 (2012).
6. Huang, X. et al. Genome-wide association study of flowering time and grain yield traits in a world wide collection of rice germplasm. Nat. Genet. 44, 32-39 (2012).
7. Xu, X. et al. Re-sequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30, 105-111 (2012).
8. Krishnan, S. G. et al. Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnol. J. 10, 623-634 (2012).
9. Michael, J. T. High-throughput SNP genotyping to accelerate crop improvement. Plant Breed. Biotechnol. 2, 195-212 (2014).
10. McCouch, S. R. et al. Development of genome-wide SNP assays for rice. Breed. Sci. 60, 524-535 (2010).
11. Zhao, K. et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2, 467 (2011).
12. Tung, C. W. et al. Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice 3, 205-217 (2010).
13. Chen, H. et al. A high density SNP genotyping array for rice biology and molecular breeding. Mol.Plant. 7, 541-553 (2013).
14. Ganal, M. W. et al. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One 6, e28334 (2011).
15. Bachlava, E. et al. SNP discovery and development of a high-density genotyping array for sunflower. PLoS One 7, e29814 (2012).
16. Gibbs, R. A. et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528-532 (2009).
17. Matukumalli, L. K. et al. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4, e5350 (2009).
18. Ramos, A. M. et al. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4, e6524 (2009).
19. Wu, F., Mueller, L. A., Crouzillat, D., Petiard, V. & Tanksley, S. D. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174, 1407-1420 (2006).
20. Singh, N. K. et al. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes Funct. Integr. Genomics 7, 17-35 (2007).
21. Armisen, D., Lecharny, A. & Aubourg, S. Unique genes in plants: Specificities and conserved features throughout evolution. BMC Evol. Biol. 8, 280 (2008).
22. Duarte, J. M. et al. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol. Biol. 10, 61 (2010).
23. Waterhouse, R. M., Zdobnov, E. M. & Kriventseva, E. V. Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. Genome Biol. Evol. 3, 75-86 (2011).
24. De Smet, R. et al. Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. PNAS 110, 2898-2903 (2013).
25. Han, F., Peng, Y., Xu, L. & Xiao, P. Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes. BMC Genomics 15, 504 (2014).
26. BRLMM-P: a Genotype Calling Method for the SNP 5.0 Array http://media.affymetrix.com/support/technical/whitepapers/brlmmp-whitepaper.pdf (2007) 13-02-2007.
27. Neeraja, C. et al. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor. Appl. Genet. 115, 767-76 (2007).
28. Sarkar R. K. et al. Performance of submergence tolerant rice genotypes carrying the Sub1 QTL under stressed and non-stressed natural field conditions. Indian J. Agric. Sci. 79, 876-83 (2009).
29. Singh, S., Mackill, D. J. & Ismail, A. M. Responses of SUB1 rice introgression lines to submergence in the field: yield and grain quality. Field Crop Res. 113, 12-23 (2009).
30. Steemers, F. J. & Gunderson, K. L. Whole genome genotyping technologies on the Bead Array platform. Biotechnol. J. 2, 41-49 (2007).
31. Springer, N. M. et al. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5, e1000734 (2009).
32. Alkan, C., Coe, B. P. & Eichler, E. E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363-376 (2011).
33. Bernardo, A. N. et al. Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays. BMC Genomics 10, 251 (2009).
34. Paterson, A. H., Bowers, J. E. & Chapman, B. A. Ancient polyploidization predating divergence of the cereals and consequences for comparative genomics. PNAS 101, 9903-9908 (2004).
35. Singh, N. K. et al. Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct. Integr. Genomics 4, 102-17 (2004).
36. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
37. Marco, C. & Roberta, B. BLAST Parser. BITS Conference. Societa di Bioinformatica Italiana. Bologna, Italy. 5, 28-29, (2006).
38. Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acid Symp. Ser. 41, 95-98 (1999).
39. Thompson, D. J., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
40. Doyle, J. J. & Doyle, J. L. Isolation of plant DNA from fresh tissue. Focus 12, 13-15 (1990).
41. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 8 1, 559-575 (2007).
42. Bradbury, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635(2007).
43. Rambaut, A. Molecular evolution, phylogenetics and epidemiology http://tree.bio.ed.ac.uk/software/figtree/(2009) 05-12-2012.