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Population structure, genetic diversity and bakanae disease resistance among rice varieties

Published online by Cambridge University Press:  30 March 2023

S. Raghu*
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
M. S. Baite
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
M. K. Yadav
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
S. R. Prabhukarthikeyan
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
U. Keerthana
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
C. Anil Kumar
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
B. Jeevan
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
S. Lenka
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
H. N. Subudhi
Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
P. C. Rath
Crop Protection Division, ICAR-National Rice Research Institute (NRRI), Cuttack, 753006 Odisha, India
Author for correspondence: S. Raghu, E-mail:


Availability of resistance sources among cultivated varieties helps in easy utilization as donor owing to no deleterious linkage drag. In the present investigation, 121 rice varieties were screened for their resistance against a virulent isolate of Fusarium fujikuroi (Ff-10) and genotyped using reported microsatellite markers. Among 121 varieties, only eight varieties, namely Luna Sankhi, Improved Tapaswini, Sarasa, Sadabahar, CR-311, Kshira, Wifa-10 and Binadhan-8, were found to be highly resistant (HR), seven varieties were resistant (R), 31 were moderately resistant (MR), 10 were moderately susceptible (MS), 11 were susceptible (S) and the rest 54 were highly susceptible (HS). The allele diversity of molecular markers classified the population into three clusters. The highly resistant varieties were grouped in major clusters II and III, whereas the remaining genotypes were distributed in all three clusters. Analysis of molecular variance (AMOVA) resulted in 95% of the maximum diversity within the test population and 5% diversity between populations. Population structure analysis grouped the genotypes into two sub-populations based on relatedness, where most of the resistant genotypes were grouped into one sub-population and other genotypes were distributed among sub-populations. Re-examination of reported markers' trait associations with bakanae resistance in the experimental population identified marker RM-3698 as associated with resistance accounting 8.4% explained phenotypic variation. This study shows that simple sequence repeat markers can be used to assess allelic diversity and population structure of bakanae resistance in rice varieties. The highly resistant genotypes, along with resistance markers, could be used as donors in marker-assisted bakanae improvement breeding programmes.

Research Article
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of NIAB

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