Research articles
ScienceAsia 47 (2021): 425-433 |doi:
10.2306/scienceasia1513-1874.2021.054
Genome-wide probing of NBS-LRR encoding genes in
red clover (Trifolium pratense L) for the identification
of resistance gene analogs in Trifolium alexandrinum L
Bukhtawer Nasira, Siddra Ijaza,*, Faisal Saeed Awana, Imran Ul Haqb
ABSTRACT: The nucleotide-binding sites (NBS) domain is the highly conserved domain of nucleotide-binding sitesleucine rich repeats (NBS-LRR) class encoded by resistance genes (R genes), and it is used to identify disease resistancerelated genes. This study was based on the genome-wide identification of NBS-LRR encoding genes in Trifolium pratense
to recover resistance gene analogs (RGAs) in Trifolium alexandrinum. In T. pratense, 251 protein sequences were
identified to have the NBS domain. Of these, 16 NBS proteins were predicted to be localized to the mitochondria, 9 to
the chloroplasts, 44 to the secretory pathways, and 182 to subcellular locations other than chloroplasts or mitochondria.
The structure pattern of predicted NBS genes of the NBS-LRR group was displayed as single gene architecture having an
untranslated region (UTRs) with four CD regions. The conserved sequences of the NBS-LRR group were used for primer
designing to recover RGAs from T. alexandrinum. A maximum likelihood method based phylogram was constructed for
exploring the phylogenetic relationship amongst NBS genes encoding protein sequences of T. pratense and R genes of
Medicago truncatula and Medicago sativa encoding protein sequences having NBS-LRR domain that showed the highly
close phylogenetic relationship among them, which supported the highly conserved nature of NBS-LRR class. Hence,
we used the conserved NBS-LRR genetic regions to recover the RGAs from the T. alexandrinum genome. Therefore,
the DNA of a cultivar of T. alexandrinum was subjected to polymerase chain reaction (PCR) analysis using the primer
designed from these regions; and all primers, except RNL3-F/R, RNL5-F/R, and RNL7-F/R, gave the amplification.
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| a |
Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture,
University Road, Faisalabad, Pakistan |
| b |
Department of Plant Pathology, University of Agriculture, University Road, Faisalabad, Pakistan |
* Corresponding author, E-mail: siddraijazkhan@yahoo.com
Received 5 Sep 2020, Accepted 16 Apr 2021
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