Abstract
We genotyped Setaria italica Dehydration-responsive element-binding 2 (SiDREB2) gene, which had been reported to be associated with dehydration stress tolerance, in 588 accessions of foxtail millet from various parts of Eurasia and other regions by a dCAPS marker. Of these, 480 accessions were genotyped in ribosomal DNA (rDNA), polyphenol oxidase (PPO) gene and Heading date 1 (HD1) gene in our previous studies, and 108 accessions from India were newly used in this study and genotyped in these genes in addition to the SiDREB2 gene. We compared the geographical distribution of the SiDREB2 genotypes with that of these three genes. Accessions from countries in South Asia including India and Sri Lanka were the most variable in the SiDREB2 gene followed by Korean accessions and Japanese accessions, suggesting that Indian accessions and East Asian accessions are useful as genetic resources for dehydration stress tolerance. This study also showed that although Indian accessions are not so diverse in rDNA and in transposon display markers previously studied, they are diverse in adaptive genes such as SiDREB2, PPO and HD1 genes.
References
Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25:1263–1274
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30:555–561
Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiol 149:137–141
Eda M, Izumitani A, Ichitani K, Kawase M, Fukunaga K (2013) Geographical variation of foxtail millet, Setaria italica (L.)P.Beauv. based on rDNA PCR–RFLP. Genet Resour Crop Evol 60:265–274
Fukunaga K (2016) Genetic differentiation and crop evolution of foxtail millet. In: Doust A, Diao X (eds) Genetics and genomics of Setaria. Springer, Berlin, pp 115–131
Fukunaga K, Wang ZM, Kato K, Kawase M (2002) Geographical variation of nuclear genome RFLPs and genetic differentiation in foxtail millet, Setaria italica (L.) P. Beauv. Genet Resour Crop Evol 49:95–101
Fukunaga K, Izuka N, Hachiken T, Mizuguchi S, Ito H, Ichitani K (2015) A nucleotide substitution at the 5′ splice site of intron 1 of rice HEADING DATE 1 (HD1) gene homolog in foxtail millet broadly found in landraces from Europe and Asia. Crop J 3:481–488
Hirano R, Naito K, Fukunaga K, Watanabe JN, Ohsawa R, Kawase M (2011) Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome 54:498–506
Inoue T, Yuo T, Ohta T, Hitomi E, Ichitani K, Kawase M, Taketa S, Fukunaga K (2015) Multiple origins of the phenol reaction negative phenotype in foxtail millet, Setaria italica (L.) P. Beauv., were caused by independent loss-of-function mutations of the polyphenol oxidase (Si7PPO) gene during domestication. Mol Genet Genomics 290:1563–1574
Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, Chai Y, Yang L, Liu K, Lu H, Zhu C, Lu Y, Zhou C, Fan D, Weng Q, Guo Y, Huang T, Zhang L, Lu T, Feng Q, Hao H, Liu H, Lu P, Zhang N, Li Y, Guo E, Wang S, Wang S, Liu J, Zhang W, Chen G, Zhang B, Li W, Wang Y, Li H, Zhao B, Li J, Diao X, Han B (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961
Lata C, Prasad M (2012) Validation of allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accession. Plant Breed 132:496–499
Lata C, Prasad M (2014) Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL. J Plant Biochem Biotech 23:119–122
Lata C, Sahu PP, Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem Biophys Res Commun 393:720–727
Lata C, Bhutty S, Bhadur RP, Majee M, Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet Setaria italica L.. J Exp Bot 62:3387–3401
Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res 8:4321–4325
Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387–392
Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, Li H, Li H, Li N, Wang J, Wang C, Wang R, Guo T, Cai Y, Liu C, Xiang H, Shi Q, Huang P, Chen Q, Li Y, Wang J, Zhao Z, Wang J (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30:549–554
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Suehiro, S., Ichitani, K., Domon, E. et al. Genotyping of the SiDREB2 gene in worldwide foxtail millet (Setaria italica (L.) P. Beauv.) genetic resources with special attention to Indian landraces. Genet Resour Crop Evol 65, 1559–1564 (2018). https://doi.org/10.1007/s10722-018-0645-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10722-018-0645-2