Cloning and sequence variation analysis of candidate genes involved in nitrogen metabolism in potato (Solanum tuberosum)

JAGESH KUMAR TIWARI; SAPNA DEVI; NILOFER ALI; VIJAY K DUA; RAJESH K SINGH; SWARUP K CHAKRABARTI

doi:10.56093/ijas.v88i5.80072

Authors

JAGESH KUMAR TIWARI Scientist (Senior Scale), ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh
SAPNA DEVI JRF, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh
NILOFER ALI JRF, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh
VIJAY K DUA Head and Principal Scientist, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh
RAJESH K SINGH Head and Principal Scientist, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh
SWARUP K CHAKRABARTI Director, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh

DOI:

https://doi.org/10.56093/ijas.v88i5.80072

Keywords:

Cloning, Nitrogen metabolism genes, Nitrogen use efficiency, Potato, Sequencing

Abstract

Objective of this study was to isolate, sequence and analyze variations in candidate genes involved in nitrogen (N) metabolism in potato (Solanum tuberosum L.) for future breeding application. Two contrasting potato varieties, viz. Kufri Gaurav (N efficient) and Kufri Jyoti (N inefficient) were used. Of the total 17 PCR primers tested for N metabolism genes in the both varieties and only 12 distinct bands were cloned and sequenced, which were amplified by six primers of five genes (nitrate transporter-NRT, ammonium transporter-AMT, nitrate reductase-NR, nitrite reductase-NIR and asparagines synthetase-AS). Following sequence analysis, non-redundant sequences with uninterrupted open reading frames of 12 ‘N-homologous genes’ were identified to the known N metabolic pathway genes. Thus, the identified 12 N-homologous genes may serve as an important genomic resource for novel gene/marker discovery and would be useful for marker-assisted selection (MAS) in potato with better nitrogen use efficiency (NUE).

Downloads

Download data is not yet available.

References

Li X-Q, Sveshnikov D, Zebarth B J, Tai H, Koeyer D D, Millard P, Haroon M and Singh M. 2010. Detection of nitrogen sufficiency in potato plants using gene expression markers. American Journal of Potato Research 87: 50–59. DOI: https://doi.org/10.1007/s12230-009-9116-9

Ospina C A, van Bueren E T L, Allefs J J H M, Engel B, van der Putten P E L, van der Linden C G and Struik P C. 2014. Diversity of crop development traits and nitrogen use efficiency among potato cultivars grown under contrasting nitrogen regimes. Euphytica 199: 13–29. DOI: https://doi.org/10.1007/s10681-014-1203-4

Tamura K, Stecher G, Peterson D, Filipski A and Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725–9. DOI: https://doi.org/10.1093/molbev/mst197

Tiwari J K, Devi S, Ali N, Buckseth T, Moudgil V, Singh R K, Chakrabarti S K, Dua V K, Kumar D and Kumar M. 2017. Genomics approaches for improving nitrogen use efficiency in potato. (In) The Potato Genome. Compendium of Plant Genomes. Chakrabarti S K, Conghua X and Tiwari J K (Eds) Springer, Cham. DOI: https://doi.org/10.1007/978-3-319-66135-3_11

Tiwari J K, Devi S, Sharma S, Chandel P, Rawat S and Singh B P. 2015. Allele mining in Solanum germplasm: cloning and characterization of RB-homologous gene fragments from late blight resistant wild potato species. Plant Molecular Biology and Reporter 33: 1584–98. DOI: https://doi.org/10.1007/s11105-015-0859-9

Tiwari J K, Plett D, Garnett T, Chakrabarti S K and Singh R K. 2018. Integrated genomics, physiology and breeding approaches for improving nitrogen use efficiency in potato: translating knowledge from other crops. Functional Plant Biology, https://doi.org/10.1071/FP17303. DOI: https://doi.org/10.1071/FP17303

Tiwari J K, Trehan S P, Sundaresha S, Poonam, Singh B P, Dua V K and Bhardwaj V. 2014. Gene expression analysis: indicators of nitrogen use efficiency in potato cultivars. Potato Journal 41: 175–9.

Trehan S P and Singh B P. 2013. Nutrient efficiency of different crop species and potato varieties – in retrospect and prospect. Potato Journal 40: 1–21.

Trehan S P. 2009. Improving nutrient use efficiency by exploiting genetic diversity of potato. Potato Journal 36: 121–35.

Zebarth B J, Tai G, Tarn R, de Jong H and Milburn P H. 2004. Nitrogen use efficiency characteristics of commercial potato cultivars. Canadian Journal of Soil Science 84: 589–98. DOI: https://doi.org/10.4141/P03-050

Zebarth B J, Tai H, Luo S, Millard P, De Koeyer D, Li X-Q and Xiong X. 2011. Differential gene expression as an indicator of nitrogen sufficiency in field-grown potato plants. Plant and Soil 345: 387–400. DOI: https://doi.org/10.1007/s11104-011-0793-z

Zebarth B J, Tai H, Luo S, Millard P, De Koeyer D, Li X-Q and Xiong X. 2012. Effect of nitrogen form on gene expression in leaf tissue of greenhouse grown potatoes during three stages of growth. American Journal of Potato Research 89: 315–27. DOI: https://doi.org/10.1007/s12230-012-9255-2

Zebarth B J, Tarn T R, de Jong H and Murphy A. 2008. Nitrogen use efficiency characteristics of andigena and diploid potato selections. American Journal of Potato Research 85: 210–18. DOI: https://doi.org/10.1007/s12230-008-9014-6