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Identification of low phosphorus tolerant parental lines of hybrid rice based on stress indices and haplotype analysis using Pup1 linked markers

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A Correction to this article was published on 29 May 2024

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Phosphorus (P) stands as a crucial macronutrient, indispensable for a multitude of plant functions and a requisite for all crops, including rice. In Indian soil, the P content typically ranges from low to medium, dictating the application of P for targeted crop returns. The development of rice varieties resilient to low soil P has gained significance in ensuring future food security. To address this, 55 parental lines of rice hybrids were evaluated under both low and normal levels of soil P. The evaluation included identifying the presence or absence of the tolerant allele related to the major low soil P tolerance QTL, Pup1, using specific PCR-based markers-namely, K46-1, K46-2, K48 and K59. Stress indices were computed by comparing yields under low soil P (Ys) and normal soil P (Yp) conditions, revealing seven out of 55 parental lines to be categorized as low soil P tolerant. These lines demonstrated minimal yield reduction compared to the checks, with a majority carrying either the complete or partial Pup1 locus. Notably, the genotypes PSV-41 and Rasi, lacking the Pup1 locus, exhibited superior tolerance under low soil P conditions. Through biplot analysis utilizing Yp and Ys stress indices, promising genotypes such as AYT21, ATR-305, Rasi, RP bio 4919–50–13 and AR 19–42R were identified under low soil P conditions. These low soil P tolerant parental lines hold potential as donors and for generating low soil P tolerant rice hybrids in future breeding endeavors.

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Data availability

The data that support this study will be shared upon reasonable request to the corresponding author.

Change history


Low soil P:

Applied P @ 20 kg ha1

Normal soil P:

Applied P @ 60 kg ha1


Grain yield under low P Stress


Grain yield under normal P


Stress susceptibility index


Yield stability index


Tolerance index


Yield index


Stress tolerance index


Percent yield reduction


Yield reduction ratio


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Authors are grateful to the Indian Council of Agriculture Research (ICAR), ICAR-Indian Institute of Rice Research (ICAR-IIRR) and Govt. of India for their financial support and facilities for research.


Indian Council of Agricultural Research, ICAR-Indian Institute of Rice Research, Core budget and Indian Council of Agricultural Research, ICAR-SRF (PGS), F.No. EDN/1/27/2015/SRF-Exam cell dated 22/07/2015.

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Communicated by Hakan Özkan.

The original version of this article has been revised: Figure 3 has been corrected.

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Madhusudan, N., Sundaram, R.M., Beulah, P. et al. Identification of low phosphorus tolerant parental lines of hybrid rice based on stress indices and haplotype analysis using Pup1 linked markers. CEREAL RESEARCH COMMUNICATIONS (2024).

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