First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations

Plant Biotechnology Journal

Volumn 14, Issue 8, 2016, Pages 1673-1681

  Kumar, Vinay ^a   Khan, Aamir W ^a   Saxena, Rachit K ^a   Garg, Vanika ^a   Varshney, Rajeev K ^a,b  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

deletions; insertions; next generation sequencing; pigeonpea; single nucleotide polymorphism; whole genome re sequencing

Indexed keywords

CAJANUS; COPY NUMBER VARIATION; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPE; PLANT GENOME; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

CAJANUS; DNA COPY NUMBER VARIATIONS; GENETIC VARIATION; GENETICS, POPULATION; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84956659769     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/pbi.12528     Document Type: Article

References (51)

1. Abyzov, A., Urban, A.E., Snyder, M. and Gerstein, M. (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974–984.
2. Arai-Kichise, Y., Shiwa, Y., Nagasaki, H., Ebana, K., Yoshikawa, H., Yano, M. and Wakasa, K. (2011) Discovery of genome-wide DNA polymorphisms in a landrace cultivar of japonica rice by whole-genome sequencing. Plant Cell Physiol. 52, 274–282.
3. Arai-Kichise, Y., Shiwa, Y., Ebana, K., Shibata-Hatta, M., Yoshikawa, H., Yano, M. and Wakasa, K. (2014) Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. PLoS ONE, 9, e86312.
4. Bajaj, D., Das, S., Badoni, S., Kumar, V., Singh, M., Bansal, K.C., Tyagi, A.K. et al. (2015) Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. Sci. Rep. 5, 12468; doi: 10.1038/srep12468.
5. Bevan, M.W. and Uauy, C. (2013) Genomics reveals new landscapes for crop improvement. Genome Biol. 14, 206.
6. Bohra, A., Saxena, R.K., Saxena, K.B., Sameerkumar, C.V. and Varshney, R.K. (2014) Advances in pigeonpea genomics. In Legumes in the Omic Era (Gupta, S., Nadarajan, N., Gupta, D. S., eds.), pp. 95–110. New York: Springer.
7. Causse, M., Desplat, N., Pascual, L., Le Paslier, M.C., Sauvage, C., Bauchet, G., Berard, A. et al. (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genom. 14, 791.
8. Chen, H., Xie, W., He, H., Yu, H., Chen, W., Li, J., Yu, R. et al. (2014) A high-density SNP genotyping array for rice biology and molecular breeding. Mol. Plant, 7, 541–553.
9. Cingolani, P., Platts, A., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X. et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6, 80–92.
10. Dubey, A., Farmer, A., Schlueter, J., Cannon, S.B., Abernathy, B., Tuteja, R., Woodward, J. et al. (2011) Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Res. 18, 153–164.
11. Dutta, S., Kumawat, G., Singh, B.P., Gupta, D.K., Singh, S., Dogra, V., Gaikwad, K. et al. (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol. 11, 17.
12. Ganal, M.W., Durstewitz, G., Polley, A., Bérard, A., Buckler, E.S., Charcosset, A., Clarke, J.D. et al. (2011) 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.
13. Huang, X., Kurata, N., Wei, X., Wang, Z.-X., Wang, A., Zhao, Q., Zhao, Y. et al. (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature, 490, 497–501.
14. Hufford, M.B., Xu, X., Heerwaarden, J.V., Pyhäjärvi, T., Chia, J.-M., Cartwright, R.A., Elshire, R.J. et al. (2012) Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808–811.
15. Huntley, R.P., Sawford, T., Martin, M.J. and O'Donovan, C. (2014) Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. GigaScience, 3, 4.
16. Kassa, M.T., Penmetsa, R.V., Carrasquilla-Garcia, N., Sarma, B.K., Datta, S., Upadhyaya, H.D., Varshney, R.K. et al. (2012) Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives. PLoS ONE, 7, e39563.
17. Katta, M.A.V.S.K., Khan, A.W., Doddamani, D., Thudi, M. and Varshney, R.K. (2015) NGS-QCbox and Raspberry for parallel, automated and rapid quality control analysis of large-scale next generation sequencing (Illumina) data. PLoS ONE, 10, e0139868.
18. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645.
19. Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Mulaosmanovic, B., Kramer, R., Bohra, A. et al. (2012) A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms. Mol. Plant, 5, 1020–1028.
20. Kumawat, G., Raje, R.S., Bhutani, S., Pal, J.K., Mithra, A.S.V.C.R., Gaikwad, K., Sharma, T.R. et al. (2012) Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.). BMC Genet. 13, 84.
21. Lam, H.-M., Xu, X., Liu, X., Chen, W., Yang, G., Wong, F.-L., Li, M.-W. et al. (2010) Resequencing of 31 wild and cultivated soybean genomes iden-tifies patterns of genetic diversity and selection. Nat. Genet. 42, 1053–1059.
22. Langmead, B. and Salzberg, S. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357–359.
23. Lee, T.-H., Guo, H., Wang, X., Kim, C. and Paterson, A.H. (2014) SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genom. 15, 162.
24. Li, Y.H., Liu, Y.L., Reif, J.C., Liu, Z.X., Liu, B., Mette, M.F., Chang, R.Z. et al. (2014) Biparental resequencing coupled with SNP genotyping of a segregating population offers insights into the landscape of recombination and fixed genomic regions in elite soybean. G3 (Bethesda), 4, 553–560.
25. Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Zhang, Z. et al. (2014) Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46, 1220–1226.
26. Mace, E.S., Tai, S., Gilding, E.K., Li, Y., Prentis, P.J., Bian, L. and Wang, J. (2013) Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nat. Commun. 4, 2320.
27. Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448–3449.
28. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K. et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303.
29. McNally, K.L., Childs, K.L., Bohert, R., Davidson, R.M., Zhao, K., Ulat, B.J., Zeller, G. et al. (2009) Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl Acad. Sci. USA, 106, 12273–12278.
30. Michael, T.P. and Jackson, S. (2013) The first 50 plant genomes. The Plant Genome, 6, 1–7.
31. Pazhamala, L., Saxena, R.K., Singh, V.K., Sameerkumar, C.V., Kumar, V., Sinha, P., Patel, K. et al. (2015) Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan). Front. Plant Sci. 6, 50.
32. Salathia, N., Lee, H.N., Sangster, T.A., Morneau, K., Landry, C.R., Schellenberg, K., Behere, A.S. et al. (2007) Indel arrays: an affordable alternative for genotyping. Plant J. 51, 727–737.
33. Saxena, R.K., Saxena, K.B., Kumar, R.V., Hoisington, D.A. and Varshney, R.K. (2010) Simple sequence repeat-based diversity in elite pigeonpea genotypes for developing mapping populations to map resistance to Fusarium wilt and sterility mosaic disease. Plant Breed. 129, 135–141.
34. Saxena, R.K., Penmetsa, R.V., Upadhyaya, H.D., Kumar, A., Carrasquilla-Garcia, N., Schlueter, J.A., Farmer, A. et al. (2012) Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res. 19, 449–461.
35. Saxena, R.K., von Wettberg, E., Upadhyaya, H.D., Sanchez, V., Songok, S., Saxena, K.B., Kimurto, P. et al. (2014) Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS ONE, 9, e88568.
36. Singh, N.K., Gupta, D.K., Jayaswal, P.K., Mahato, A.K., Dutta, S., Singh, S., Bhutani, S. et al. (2011) The first draft of the pigeonpea genome sequence. J. Plant Biochem. Biotechnol. 21, 98–112.
37. Song, Q., Hyten, D.L., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L. and Cregan, P.B. (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE, 8, e54985.
38. Stanton-Geddes, J., Paape, T., Epstein, B., Briskine, R., Yoder, J., Mudge, J., Bharti, A.K. et al. (2013) Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula. PLoS ONE, 8, e65688.
39. Subbaiyan, G.K., Waters, D.L.E., Katiyar, S.K., Sadananda, A.R., Vaddadi, S. and Henry, R.J. (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnol. J. 10, 623–634.
40. Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599.
41. Tao, C.H.E.N., Zhang, Y.D., Zhen, Z.H.U., Ling, Z.H.A.O., Zhaq, Q.Y., Zhou, L.H., Shu, Y.A.O. et al. (2014) Development of new indel marker to detect genotypes of Rf-1a conferring fertility restoration of BT-type cytoplasmic male sterility in rice. Rice Sci. 21, 13–19.
42. Thudi, M., Li, Y., Jackson, S.A., May, G.D. and Varshney, R.K. (2012) Current state-of-art of sequencing technologies for plant genomics research. Brief. Funct. Genomics, 11, 3–11.
43. Unterseer, S., Bauer, E., Haberer, G., Seidel, M., Knaak, C., Ouzunova, M., Meitinger, T. et al. (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600k SNP genotyping array. BMC Genom. 15, 823.
44. Vales, M.I., Srivastava, R.K., Sultana, R., Singh, S., Singh, I., Singh, G., Patil, S.B. et al. (2012) Breeding for earliness in pigeonpea: development of new determinate and nondeterminate lines. Crop Sci. 52, 2507–2516.
45. Varshney, R.K., Nayak, S.N., May, G.D. and Jackson, S.A. (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27, 522–530.
46. Varshney, R.K., Penmetsa, R.V., Dutta, S., Kulwal, P.L., Saxena, R.K., Datta, S., Sharma, T.R. et al. (2010) Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol. Breed. 26, 393–408.
47. Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J.A., Donoghue, M.T. et al. (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83–89.
48. Varshney, R.K., Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S. et al. (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31, 240–246.
49. Xu, X., Liu, X., Ge, S., Jensen, J.D., Hu, F.Y., Li, X., Dong, Y. et al. (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 3, 105–157.
50. Zheng, L.-Y., Guo, X.-S., He, B., Sun, L.-J., Peng, Y., Dong, S.-S., Liu, T.-F. et al. (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol. 12, R114.
51. Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., Yu, Y. et al. (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408–414.