Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.)

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Kale, Sandip M ^a   Jaganathan, Deepa ^a,b   Ruperao, Pradeep ^c,d   Chen, Charles ^e   Punna, Ramu ^f   Kudapa, Himabindu ^a   Thudi, Mahendar ^a   Roorkiwal, Manish ^a   Katta, Mohan Avsk ^a   Doddamani, Dadakhalandar ^a   Garg, Vanika ^a   Kishor, P B Kavi ^b   Gaur, Pooran M ^a   Nguyen, Henry T ^g   Batley, Jacqueline ^c   Edwards, David ^c   Sutton, Tim ^h,i   Varshney, Rajeev K ^a,c  

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

^b OSMANIA UNIVERSITY   (India)

^c UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^d UNIVERSITY OF QUEENSLAND   (Australia)

^e OKLAHOMA STATE UNIVERSITY   (United States)

^f Department of Obstetrics Gynecology   (United States)

^g UNIVERSITY OF MISSOURI   (United States)

^h SOUTH AUSTRALIAN RESEARCH AND DEVELOPMENT INSTITUTE   (Australia)

ⁱ UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CHICKPEA; DROUGHT TOLERANCE; GENE MUTATION; GENETIC MARKER; GENETIC POLYMORPHISM; PHENOTYPE; REAL TIME POLYMERASE CHAIN REACTION; RECOMBINANT INBRED STRAIN; SEASON; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; ADAPTATION; CHROMOSOMAL MAPPING; CHROMOSOME BREAKAGE; CICER; DROUGHT; GENE EXPRESSION REGULATION; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; INBREEDING; METABOLISM; PHYSIOLOGICAL STRESS; PLANT GENE; PLANT GENOME; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY;

ADAPTATION, BIOLOGICAL; CHROMOSOME BREAKPOINTS; CHROMOSOME MAPPING; CICER; DROUGHTS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENETIC LINKAGE; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INBREEDING; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; RECOMBINATION, GENETIC; REPRODUCIBILITY OF RESULTS; STRESS, PHYSIOLOGICAL;

EID: 84945176810     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep15296     Document Type: Article

References (55)

1. Jukanti, A. K., Gaur, P. M., Gowda, C. L. L., Chibbar, R. N. Nutritional quality and health benefits of chickpea (Cicer arietinum L.): a review. Brit. J. Nutr. 108, S11-S26 (2012).
2. Ahmad, F., Gaur, P. M., Croser, J. Chickpea (Cicer arietinum L.). In: Genetic Resources, Chromosome Engineering, and Crop Improvement-Grain Legumes (eds Singh, R. J., Jauhar, P. P.). CRC Press (2005).
3. Hamwieh, A., Imtiaz, M., Malhotra, R. S. Multi-environment QTL analyses for drought-related traits in a recombinant inbred population of chickpea (Cicer arientinum L.). Theor. Appl. Genet. 126, 1025-1038 (2013).
4. Rehman, A. U. et al. Mapping QTL associated with traits affecting grain yield in chickpea (Cicer arietinum L.) under terminal drought stress. Crop Sci. 51, 450-463 (2011).
5. Varshney, R. K. et al. Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 127, 445-462 (2014).
6. Roorkiwal, M. et al. Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers. Front. Plant Sci. 5, doi: 10.3389/fpls.2014.00248 (2014).
7. Thudi, M. et al. Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches. PLoS One 9, e96758, (2014).
8. Varshney, R. K. et al. Fast-track introgression of "QTL-hotspot" for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. Plant Genome 6, doi: 10.3835/plantgenome2013.07.0022 (2013).
9. Varshney, R. K. et al. Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Funct. Integr. Genomic 14, 59-73 (2014).
10. Jaganathan, D. et al. Genotyping-by-sequencing based intra-specific genetic map refines a "QTL-hotspot" region for drought tolerance in chickpea. Mol. Genet. Genomics 290, 559-571 (2015).
11. Craig, D. W. et al. Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 5, 887-893 (2008).
12. Cronn, R. et al. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36, e122 (2008).
13. Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6, e19379, (2011).
14. Deschamps, S., Nannapaneni, K., Zhang, Y., Hayes, K. Local assemblies of paired end reduced representation libraries sequenced with the illumina genome analyser in maize. Int. J. Plant Genomics 2012, 8 doi: 10.1155/2012/360598 (2012).
15. Poland, J. A., Rife, T. W. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5, 92-102 (2012).
16. Chen, Z. L. et al. An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F-2 maize population. BMC Genomics 15, doi: 10.1186/1471-2164-15-433 (2014).
17. Golicz, A. A., Bayer, P. E., Edwards, D. Skim-based genotyping by sequencing. Methods Mol. Biol. 1245, 257-270 (2015).
18. Huang, X. H. et al. High-throughput genotyping by whole-genome resequencing. Genome Res. 19, 1068-1076 (2009).
19. Sasaki, A. et al. Green revolution: A mutant gibberellin-synthesis gene in rice-New insight into the rice variant that helped to avert famine over thirty years ago. Nature 416, 701-702 (2002).
20. Xu, X. Y. et al. Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing. P. Natl. Acad. Sci. USA 110, 13469-13474 (2013).
21. Qi, X. P. et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat. Commun. 5, 1-11 (2014).
22. Xie, W. B. et al. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. P. Natl. Acad. Sci. USA 107, 10578-10583 (2010).
23. Varshney, R. K. et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31, 240-246 (2013).
24. Lai, J. S. et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat. Genet. 42, 1027-U1158 (2010).
25. Kujur, A. et al. Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea. Sci. Rep. 5, 9468, doi: 10.1038/srep09468 (2015).
26. Bayer, P. E. et al. High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theor. Appl. Genet. 128, 1039-1047 (2015).
27. Ruperao, P. et al. A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnol. J. 12, 778-786 (2014).
28. Li, J. M., Thomson, M., McCouch, S. R. Fine mapping of a grain-weight quantitative trait locus in the pericentromeric region of rice chromosome 3. Genetics 168, 2187-2195 (2004).
29. Osakabe, Y., Yamaguchi-Shinozaki, K., Shinozaki, K., Tran, L. S. P. Sensing the environment: key roles of membrane-localized kinases in plant perception and response to abiotic stress. J. Exp. Bot. 64, 445-458 (2013).
30. Ruiz, J. M., Blumwald, E. Salinity-induced glutathione synthesis in Brassica napus. Planta 214, 965-969 (2002).
31. Song, X. J., Huang, W., Shi, M., Zhu, M. Z., Lin, H. X. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39, 623-630 (2007).
32. Wang, X. S. et al. Transcriptional responses to drought stress in root and leaf of chickpea seedling. Mol. Biol. Rep. 39, 8147-8158 (2012).
33. Hashimoto, M., Komatsu, S. Proteomic analysis of rice seedlings during cold stress. Proteomics 7, 1293-1302 (2007).
34. Pokhilko, A. et al. Ubiquitin ligase switch in plant photomorphogenesis: A hypothesis. J. Theor. Biol. 270, 31-41 (2011).
35. Sonoda, Y. et al. Regulation of leaf organ size by the Arabidopsis RPT2a 19S proteasome subunit. Plant J. 60, 68-78 (2009).
36. Thomann, A. et al. Arabidopsis CUL3A and CUL3B genes are essential for normal embryogenesis. Plant J. 43, 437-448 (2005).
37. Lee, J. H., Kim, W. T. Regulation of abiotic stress signal transduction by E3 ubiquitin ligases in Arabidopsis. Mol. Cells 31, 201-208 (2011).
38. Lyzenga, W. J., Stone, S. L. Abiotic stress tolerance mediated by protein ubiquitination. J. Exp. Bot. 63, 599-616 (2012).
39. Ju, H. W., Min, J. H., Chung, M. S., Kim, C. S. The atrzf1 mutation of the novel RING-type E3 ubiquitin ligase increases proline contents and enhances drought tolerance in Arabidopsis. Plant Sci. 203, 1-7 (2013).
40. Kim, S. J., Kim, W. T. Suppression of Arabidopsis RING E3 ubiquitin ligase AtATL78 increases tolerance to cold stress and decreases tolerance to drought stress. Febs Lett. 587, 2584-2590 (2013).
41. Li, J. H. et al. The E3 ligase AtRDUF1 positively regulates salt stress responses in Arabidopsis thaliana. PLoS One 8, e71078, (2013).
42. Kim, J. H., Kim, W. T. The Arabidopsis RING E3 ubiquitin ligase AtAIRP3/LOG2 participates in positive regulation of high-salt and drought stress responses. Plant Physiol. 162, 1733-1749 (2013).
43. Dubreucq, B. et al. The Arabidopsis AtEPR1 extensin-like gene is specifically expressed in endosperm during seed germination. Plant J. 23, 643-652 (2000).
44. Cuc, L. M. et al. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol. 8, doi: 10.1186/1471-2229-8-55 (2008).
45. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
46. Lorenc, M. T. et al. Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1, 370-382 (2012).
47. Meng, L., Li, H., Zhang, L., Wang, J. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J. 3, 269-283 (2015).
48. Bayer, I. et al. Comparative visualization of genetic and physical maps with Strudel. Bioinformatics 27, 1307-1308 (2011).
49. Chen, C. et al. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PLoS One 7, e4659, (2012).
50. Lewontin, R. C. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 49-67 (1964).
51. Tian, F. et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43, 159-U113 (2011).
52. Ray, J. D., Sinclair, T. R. The effect of pot size on growth and transpiration of maize and soybean during water deficit stress. J. Exp. Bot. 49, 1381-1386 (1998).
53. Rozen, S., Skaletsky, H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132, 365-386 (2000).
54. Mir, R. R. et al. Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.). Theor. Appl. Genet. 127, 2663-2678 (2014).
55. Livak, K. J., Schmittgen, T. D. Analysis of relative gene expression data using realtime quantitative PCR and the 2Ct method. Methods 25, 402-408 (2001).