Novel major QTLs associated with low soil phosphorus tolerance identified from the Indian rice landrace, Wazuhophek

by Ravindra Ramrao Kale, Ch. V. Durga Rani, M. Anila, H. K. Mahadeva Swamy, V. P. Bhadana, P. Senguttuvel, D. Subrahmanyam, M. Ayyappa Dass, K. Swapnil, M. S. Anantha, E. Punniakotti, B. Laxmi Prasanna, G. Rekha, P. Sinha, M. B. V. N. Kousik, T. Dilip, S. K. Hajira, P. Brajendra, S. K. Mangrauthia, C. Gireesh, Mangaldeep Tuti, R. Mahendrakumar, Jitendra Giri, Pawandeep Singh, R. M. Sundaram

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.