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ORIGINAL RESEARCH article

Front. Sustain. Food Syst.
Sec. Crop Biology and Sustainability
Volume 8 - 2024 | doi: 10.3389/fsufs.2024.1470871

Uncovering QTLs for Uppermost Internode Length and Panicle Exsertion in Rice (Oryza sativa L.)

Provisionally accepted
Harshitha Bheemapura Shivakumar Harshitha Bheemapura Shivakumar 1Vikram Jeet Singh Vikram Jeet Singh 2Shekharappa Nandakumar Shekharappa Nandakumar 1Brijesh Kumar Dixit Brijesh Kumar Dixit 1Sonu Shekhawat Sonu Shekhawat 1Shridhar Ragi Shridhar Ragi 1Deepak Saran Deepak Saran 1K K Vinod K K Vinod 1Gopala Krishnan S Gopala Krishnan S 1Ranjith Kumar Ellur Ranjith Kumar Ellur 1Nagarajan Mariappan Nagarajan Mariappan 3Haritha Bollinedi Haritha Bollinedi 1Tapan Kumar Mondal Tapan Kumar Mondal 4Ashok Kumar Singh Ashok Kumar Singh 1PROLAY KUMAR BHOWMICK PROLAY KUMAR BHOWMICK 5*
  • 1 Division of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, India
  • 2 Department of Seed Science and Technology, Acharya Narendra Deva University of Agriculture & Technology, Ayodhya, Uttar Pradesh, India
  • 3 Rice Breeding and Genetics Research Centre, Indian Agricultural Research Institute, Aduthurai, Tamil Nadu, India
  • 4 National Institute for Plant Biotechnology, Indian Council of Agricultural Research, New Delhi, Delhi, India
  • 5 Indian Agricultural Research Institute (ICAR), New Delhi, India

The final, formatted version of the article will be published soon.

    Uppermost internode length and panicle exsertion are the two important traits that contribute significantly to increased yield in rice. The present study was conducted using recombinant inbred lines (RILs) comprising of 201 lines derived from RTN10B and IRG213. These RILs were evaluated at three different locations namely, Delhi, Karnal, and Aduthurai, and we report mapping of quantitative trait loci (QTLs) for uppermost internode length and panicle exsertion ratio, together with QTLs for plant height, tiller number, length of second internode, length of third internode, length from flag leaf to panicle tip, panicle length. Mapping was done using a custom microsatellite linkage map constructed for the population, having a total span of 2077.1 cM with 104 markers. A total of 22 QTLs were identified for different traits, among which 19 were found distributed in four hotspots. A total of 11 major effect QTLs and 11 minor effect QTLs were identified for various internode length related traits. Among the four QTLs identified for PFL, three QTLs, qPFL1.1, qPFL1.2, and qPFL2.1, co-localised with the previous reported QTL while qPFL8.1 is a novel QTL. A major QTL hotspot was identified on chromosome 1, lying at the marker interval of RM12055-RM320. The size of the major QTL hotspot on chromosome 1 is 1.4 Mb and possess total seven HEs for PER, PFL, PH, PL, UIL, SIL, and TIL. Based on the in-silico analysis of the major QTL hotspot on chromosome 1, we were able to identify 15 putative candidate genes associated with internode length and panicle-related traits. Further, narrowing the genomic region through fine mapping of marker intervals facilitates the identification of candidate genes to enable more precise marker-assisted selection for uppermost internode length and panicle exsertion.

    Keywords: rice, QTL mapping, RIL, Uppermost internode length, panicle exsertion

    Received: 26 Jul 2024; Accepted: 07 Nov 2024.

    Copyright: © 2024 Shivakumar, Singh, Nandakumar, Dixit, Shekhawat, Ragi, Saran, Vinod, S, Ellur, Mariappan, Bollinedi, Mondal, Singh and BHOWMICK. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: PROLAY KUMAR BHOWMICK, Indian Agricultural Research Institute (ICAR), New Delhi, India

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