Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Kujur, Alice ^a   Upadhyaya, Hari D ^b   Bajaj, Deepak ^a   Gowda, C L L ^b   Sharma, Shivali ^b   Tyagi, Akhilesh K ^a   Parida, Swarup K ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

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

Author keywords

[No Author keywords available]

Indexed keywords

BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; IRON SULFUR PROTEIN; MALATE DEHYDROGENASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE;

ALLELE; CHROMOSOMAL MAPPING; CICER; GENE EXPRESSION PROFILING; GENETIC LINKAGE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; MERISTEM; PHYSIOLOGY; PLANT GENOME; PLANT LEAF; QUANTITATIVE TRAIT LOCUS; SHOOT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTORS; CHROMOSOME MAPPING; CICER; GENE EXPRESSION PROFILING; GENETIC LINKAGE; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; IRON-SULFUR PROTEINS; MALATE DEHYDROGENASE; MERISTEM; NADH DEHYDROGENASE; PLANT LEAVES; PLANT SHOOTS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84975456904     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep27968     Document Type: Article

References (74)

1. Griffiths, S. et al. Meta-QTL analysis of the genetic control of ear emergence in elite European winter wheat germplasm. Theor. Appl. Genet. 119, 383-395 (2009).
2. Podolska, G. Plant lodging, effects, and control. In Encyclopedia of Agrophysics, Part of the series Encyclopedia of Earth Sciences Series (ed. Gli?ski, J., Horabik, J., Lipiec, J.), 609-610 (Springer, Netherlands, 2014).
3. Peng, J. et al. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400, 256-261 (1999).
4. Spielmeyer, W., Ellis, M. H., Chandler, P. M. Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc. Natl. Acad. Sci. USA 99, 9043-9048 (2002).
5. Kumar, J., Choudhary, A. K., Solanki, R. K., Pratap, A. Towards marker-assisted selection in pulses: a review. Plant Breed. 130, 297-313 (2011).
6. Varshney, R. K. et al. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol. Adv. 31, 1120-1134 (2013).
7. Jain, M. et al. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. 74, 715-729 (2013).
8. Varshney, R. K. et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31, 240-246 (2013).
9. Parween, S. et al. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Sci. Rep. 5, 12806 (2015).
10. Garg, R., Patel, R. K., Tyagi, A. K., Jain, M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18, 53-63 (2011).
11. Garg, R., Bhattacharjee, A., Jain, M. Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Mol. Biol. Rep. 33, 388-400 (2014).
12. 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 Biotechnol. J. 10, 716-732 (2012).
13. Jhanwar, S. et al. Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. J. 10, 690-702 (2012).
14. Agarwal, G. et al. Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 7, e52443 (2012).
15. Singh, V. K., Garg, R., Jain, M. A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol. J. 11, 691-701(2013).
16. Kudapa, H. et al. Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using Sanger and next generation sequencing platforms: development and applications. PLoS One 9, e86039 (2014).
17. Pradhan, S. et al. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. Front. Plant Sci. 5, 698 (2014).
18. Parida, S. K. et al. Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Front. Plant Sci. 6, 645 (2015).
19. 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).
20. Gujaria, N. et al. Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor. Appl. Genet. 122, 1577-1589 (2011).
21. Thudi, M. et al. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One 6, e27275 (2011).
22. 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).
23. Kujur, A. et al. Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Res. 20, 355-374 (2013).
24. Kujur, A. et al. An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea. Mol. Breed. 34, 241-265 (2014).
25. Kujur, A. et al. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Front. Plant Sci. 6, 162 (2015).
26. 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 (2015).
27. Sabbavarapu, M. M. et al. Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.). Euphytica 193, 121-133 (2013).
28. 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, 1-9 (2013).
29. Varshney, R. K. et al. Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 127, 445-462 (2014).
30. Varshney, R. K. et al. Marker-assisted backcrossing to introgress resistance to Fusarium wilt race 1 and Ascochyta blight in C 214, an elite cultivar of chickpea. Plant Genome 7, 1-11 (2014).
31. Saxena, M. S. et al. An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea. DNA Res. 21, 695-710 (2014).
32. Bajaj, D. et al. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. J. Exp. Bot. 66, 1271-1290 (2015).
33. Bajaj, D. et al. A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Sci. Rep. 5, 9264 (2015).
34. 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).
35. Das, S. et al. Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea. DNA Res. 22, 193-203 (2015).
36. 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).
37. 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).
38. Kujur, A. et al. A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea. Sci. Rep. 5, 11166 (2015).
39. Tar'an, B. et al. Quantitative trait loci for lodging resistance, plant height and partial resistance to Mycosphaerella blight in field pea (Pisum sativum L.). Theor. Appl. Genet. 107, 1482-1491 (2003).
40. Blair, M. W., Iriarte, G., Beebe, S. QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean ? wild common bean (Phaseolus vulgaris L.) cross. Theor. Appl. Genet. 112, 1149-1163 (2006).
41. Josie, J., Alcivar, A., Rainho, J., Kassem, M. A. Genomic regions containing QTL for plant height, internodes length, and flower color in soybean [Glycine max (L.) Merr.]. Bios 78, 119-126 (2007).
42. Robins, J. G., Bauchan, G. R., Brummer, E. C. Genetic mapping forage yield, plant height, and regrowth at multiple harvests in tetraploid alfalfa (Medicago sativa L.). Crop Sci. 47, 11-18 (2007).
43. Checa, O. E., Blair, M. W. Mapping QTL for climbing ability and component traits in common bean (Phaseolus vulgaris L.). Mol. Breed. 22, 201-215 (2008).
44. Tullu, A., Tar'an, B., Warkentin, T., Vandenberg, A. Construction of an intraspecific linkage map and QTL analysis for earliness and plant height in lentil. Crop Sci. 48, 2254-2264 (2008).
45. Palomeque, L. et al. QTL in mega-environments: II. Agronomic trait QTL co-localized with seed yield QTL detected in a population derived from a cross of high-yielding adapted ? high-yielding exotic soybean lines. Theor. Appl. Genet. 119, 429-436 (2009).
46. Kumawat, G. et al. Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.). BMC Genet. 13, 84 (2012).
47. Rossi, M. E., Orf, J. H., Liu, L. J., Dong, Z., Rajcan, I. Genetic basis of soybean adaptation to North American vs. Asian megaenvironments in two independent populations from Canadian ? Chinese crosses. Theor. Appl. Genet. 126, 1809-1823 (2013).
48. Sun, Y. et al. Mapping and meta-analysis of height QTLs in soybean. Legume Genomics Genet. 3, 1-7 (2012).
49. Gao, L.-F., Guo, Y., Hao, Z.-B., Qiu, L. J. Integration and "overview" analysis of QTLs related to plant height in soybean. Yi Chuan 35, 215-224 (2013).
50. Liu, Y.-L. et al. Identification of quantitative trait loci underlying plant height and seed weight in soybean. Plant Genome 6, 1-11 (2013).
51. Stanton-Geddes, J. et al. 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 (2013).
52. Kumar, B. et al. Population structure and association mapping studies for important agronomic traits in soybean. J. Genet. 93, 775-784 (2014).
53. Mir, R. R. et al. Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.). Theor. Appl. Genet. 127, 2663-2678 (2014).
54. Li, F. et al. A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus). Plant Sci. 242, 169-177 (2015).
55. Gowda, S. J. M. et al. Mapping of QTLs governing agronomic and field traits in chickpea. J. Appl. Genet. 52, 9-21 (2011).
56. Hamwieh, A., Imtiaz, M., Malhotra, R. S. Multi-environment QTL analyses for drought-related traits in a recombinant inbred population of chickpea (Cicer arietinum L.). Theor. Appl. Genet. 12, 1025-1038 (2013).
57. Jamalabadi, J. G., Saidi, A., Karami, E., Kharkesh, M., Talebi, R. Molecular mapping and characterization of genes governing time to flowering, seed weight, and plant height in an intraspecific genetic linkage map of chickpea (Cicer arietinum). Biochem. Genet. 51, 387-397 (2013).
58. Karami, E., Talebi, R., Kharkesh, M., Saidi, A. A linkage map of chickpea (Cicer arietinum L.) based on population from ILC3279 ? ILC588 crosses: location of genes for time to flowering, seed size and plant height. Genetika 47, 253-263 (2015).
59. Stephens, A. et al. Genetic marker discovery, intraspecific linkage map construction and quantitative trait locus analysis of Ascochyta blight resistance in chickpea (Cicer arietinum L.). Mol. Breed. 33, 297-313 (2014).
60. Gaur, R. et al. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci. Rep. 5, 13387 (2015).
61. 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, e0125583 (2015).
62. Marienfeld, J. R., Newton, K. J. The maize NCS2 abnormal growth mutant has a chimeric nad4-nad7 mitochondrial gene and is associated with reduced complex I function. Genetics 138, 855-863 (1994).
63. Jenner, H. L. et al. NAD malic enzyme and the control of carbohydrate metabolism in potato tubers. Plant Physiol. 126, 1139-1149 (2001).
64. Welchen, E., Gonzalez, D. H. Differential expression of the Arabidopsis cytochrome c genes Cytc-1 and Cytc-2, Evidence for the involvement of TCP-domain protein-binding elements in anther-and meristem-specific expression of the Cytc-1 gene. Plant Physiol. 139, 88-100 (2005).
65. Tronconi, M. A. et al. Arabidopsis NAD-malic enzyme functions as a homodimer and heterodimer and has a major impact on nocturnal metabolism. Plant Physiol. 146, 1540-1552 (2008).
66. Welchen, E., Hildebrandt, T. M., Lewejohann, D., Gonzalez, D. H., Braun, H. P. Lack of cytochrome c in Arabidopsis decreases stability of Complex IV and modifies redox metabolism without affecting Complexes I and III. Biochem. Biophys. Acta 1817, 990-1001 (2012).
67. Wydro, M. M. et al. The evolutionarily conserved iron-sulfur protein INDH1 is required for complex I assembly and mitochondrial translation in Arabidopsis. Plant Cell 25, 4014-4027 (2013).
68. Palmer, J. M. The organization and regulation of electron transport in plant mitochondria. Ann. Rev. Plant Physiol. 27, 133-157 (1976).
69. Millar, A. H., Whelan, J., Soole, K. L., Day, D. A. Organization and regulation of mitochondrial respiration in plants. Annu. Rev. Plant Biol. 62, 79-104 (2011).
70. Fukazawa, J. et al. Repression of shoot growth, a bZIP transcriptional activator, regulates cell elongation by controlling the level of gibberellins. Plant Cell 12, 901-915 (2000).
71. Ishida, S., Fukazawa, J., Yuasa, T., Takahashi, Y. Involvement of 14-3-3 signaling protein binding in the functional regulation of the transcriptional activator REPRESSION OF SHOOT GROWTH by gibberellins. Plant Cell 16, 2641-2651 (2004).
72. Bai, S., Chaney, W. Gibberellin synthesis inhibitors affect electron transport in plant mitochondria. Plant Growth Regul. 35, 257-262 (2001).
73. Welchen, E. et al. A segment containing a G-box and an ACGT motif confers differential expression characteristics and responses to the Arabidopsis Cytc-2 gene, encoding an isoform of cytochrome c. J. Exp. Bot. 60, 829-845 (2009).
74. Elshire, R. J. et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6, e19379 (2011).