High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Gaur, Rashmi ^a   Jeena, Ganga ^a   Shah, Niraj ^a   Gupta, Shefali ^a   Pradhan, Seema ^a   Tyagi, Akhilesh K ^a   Jain, Mukesh ^a   Chattopadhyay, Debasis ^a   Bhatia, Sabhyata ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL; CHROMOSOMAL MAPPING; CICER; DNA MUTATIONAL ANALYSIS; GENE LINKAGE DISEQUILIBRIUM; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENOME; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CICER; DNA MUTATIONAL ANALYSIS; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SYNTENY; TRANSCRIPTOME;

EID: 84940063561     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep13387     Document Type: Article

References (64)

1. van Os, H. et al. A 10,000 marker ultra-dense genetic recombination map as a new tool for anchoring a physical map and fast gene cloning in potato. Genetics. 173, 1075-1087 (2006).
2. Sun, Z. et al. An ultra dense genetic recombination map for Brassica napus, consisting of 13551 SRAP markers. Theor. Appl. Genet. 114, 1305-1317 (2007).
3. Blenda, A., Fang, D. D., Rami, J. F., Garsmeur, O., Luo, F., Lacape, J. M. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS One. 7, e45739 (2012).
4. Bowers, J. E. et al. Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3 (Bethesda) 2, 721-729 (2012).
5. Truco, M. J. et al. An ultra-high-density, transcript-based, genetic map of lettuce. G3 (Bethesda). 3, 617-631 (2013).
6. Wu, X., Ren, C., Joshi, T., Vuong, T., Xu, D. & Nguyen, H. T. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 11, 469 (2010).
7. Yamamoto, T. et al. Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics. 11, 267 (2010).
8. Branca, A. et al. Whole genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc. Natl Acad. Sci. USA 108, 864-870 (2011).
9. Maughan, P. J. et al. Single nucleotide polymorphism identification, characterization, and linkage mapping in quinoa. Plant Genome 5, 114-125 (2012).
10. Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967 (2010).
11. Chagné, D. et al. Genome-wide SNP detection, validation, and development of an 8k SNP array for apple. PLoS One. 7, e31745 (2012).
12. Verde, I. et al. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One. 7, e35668 (2012).
13. Peace, C. et al. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One. 7, e48305 (2012).
14. Troggio, M. et al. A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics. 176, 2637-2650 (2007).
15. Close, T. J. et al. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics. 10, 582 (2009).
16. Hyten, D. L. et al. High throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics. 11, 38 (2010).
17. Wang, J. et al. Integration of linkage maps for the amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. BMC Genomics. 12, 101 (2011).
18. Ren, Y. et al. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS One. 7, e29453 (2012).
19. D'Hont, A. et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature. 488, 213-217 (2012).
20. Muchero, W. et al. A consensus genetic map of cowpea [Vigna unguiculata (L)Walp.] and synteny based on EST-derived SNPs. Proc. Natl Acad. Sci. USA 106, 18159-18164 (2009).
21. Lucas, M. R., Diop, N.-N., Wanamaker, S. et al. 2011, Cowpea-soybean synteny clarified through an improved genetic map. Plant Genome 4, 218-225.
22. Sethy, N. K., Shokeen, B., Edwards, K. J. & Bhatia, S. Development of microsatellite markers and analysis of intra-specific genetic variability in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 112, 1416-1428 (2006).
23. Aryamanesh, N. et al. Mapping a major gene for growth habit and QTLs for aschochyta blight resistance and flowering time in a population between chickpea and Cicer reticulatum. Euphytica. 173, 307-319 (2010).
24. Winter, P. et al. A linkage map of chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinumx C. reticulatum cross: localization of resistance genes for Fusarium wilt races 4 and 5. Theor. Appl. Genet. 101, 1155-63 (2000).
25. Nayak, S. N. et al. Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theor. Appl. Genet. 120, 1415-1441 (2010).
26. Gaur, R. et al. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics. 12, 117 (2011).
27. Thudi, M. et al. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1291 marker loci for chickpea (Cicer arietinum L.). PLoS One. 6, e27275 (2011).
28. Choudhary, S., Gaur, R., Gupta, S. & Bhatia, S. EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor. Appl. Genet. 124, 1449-1462 (2012).
29. Gaur, R. et al. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res. 19, 357-373 (2012).
30. Hiremath, P. J. et al. Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotech. J 10, 716-732 (2012).
31. Deokar, A. A. et al. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics. 15, 708 (2014).
32. Jain, M. et al. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J 74, 715-729 (2013).
33. Varshney, R. K. et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31, 240-246 (2013).
34. Arumuganathan, K. & Earle, E. D. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218 (1991)
35. Jhanwar, S. et al. Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. J. 10, 690-702 (2012).
36. Khajuria, Y. P. et al. Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea. PloS ONE 10(5), e0125583. doi: 10.1371/journal.pone.0125583. (2015).
37. Van Deynze, A. et al. Diversity in conserved genes in tomato. BMC Genomics. 8, 465 (2007).
38. Kumar, S., You, F. M. & Cloutier, S. Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries. BMC Genomics. 13, 684 (2012).
39. Simko, I., Haynes, K. G. & Jones, R. W. Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics 173, 2237-2245 (2006).
40. Barker, G. L. & Edwards, K. J. A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops. Plant Biotechnol. J 7, 318-325 (2009).
41. Subbaiyan, G. K. et al. Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotech. J 10, 623-34 (2012).
42. Yang, Z. & Yoder, A. D. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 48, 274 (1999).
43. Rostoks, N. et al. Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc. Natl Acad. Sci. USA 103, 18656-18661 (2006).
44. Hyten, D. L. et al. High-throughput genotyping with the Golden Gate assay in the complex genome of soybean. Theor. Appl. Genet. 116, 945-952 (2008).
45. Yan, J. B. et al. High-throughput SNP genotyping with the Golden Gate assay in maize. Mol. Breed 25, 441-451 (2010).
46. Pavy, N. et al. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics. 9, 21 (2008).
47. Eckert, A. et al. High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet. Genomes. 5, 225-234 (2009).
48. van Os, H., Stam, P., Visser, R. G. F. & van Eck, H. J. RECORD: a novel method for ordering loci on a genetic linkage map. Theor. Appl. Genet. 112, 30-40 (2005).
49. Sim, S. et al. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE 7, e40563 (2012).
50. Frary, A., Presting, G. G. & Tanksley, S. D. Molecular mapping of the centromeres of tomato chromosomes 7 and 9. Mol. Gen. Genet. 250, 295-304 (1996).
51. Wenzl, P. et al. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics. 7, 206 (2006).
52. Yin, T. M., DiFazio, S. P., Gunter, L. E., Riemenschneider, D. & Tuskan, A. Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theor. Appl. Genet. 109, 451-463 (2004).
53. Liebhard, R., Loller, B., Gianfranceschi, L. & Gessler, C. Greating a saturated reference map for the apple (Malus domestica Borkh.) genome. Theor. Appl. Genet. 106, 1497-1508 (2003).
54. Woolbright, S. A. et al. A dense linkage map of hybrid cottonwood (Populus fremontii × P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree. Heredity. 100, 59-70 (2008).
55. Wang, Y. et al. A genetic linkage map of Populus adenopoda Maxim. × P. alba L. hybrid based on SSR and SRAP markers. Euphytica. 173, 193-205 (2010).
56. Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 449, 463-467 (2007).
57. Huang, S. et al. The genome of the cucumber, Cucumis sativus L. Nat. Genet. 41, 1275-1281 (2009).
58. Velasco, R. et al. The genome of the domesticated apple (Malus domestica Borkh.). Nat. Genet. 42, 833-839 (2010).
59. Ruperao, P. et al. A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotech. J 12, 778-786 (2014).
60. Fan, J. B. et al. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69-78 (2003).
61. Van Ooijen, J. Join Map version 4.0: Software for the calculation of genetic linkage maps in experimental population. Kyazma B.V. Wageningen, Netherlands. (2006).
62. Kosambi, D. The estimation of map distances from recombination values. Ann. Eugenics. 12, 172-175 (1994).
63. Voorrips, R. E. Map Chart: software for the graphical presentation of linkage maps and QTLs. J. Heredity. 93, 77-78 (2002).
64. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).