Superior haplotypes for early root vigor traits under dry direct seeded low nitrogen condition through Genome Wide Association Mapping

Annamalai Anandan* (Corresponding Author), Siddharth Panda, S. Sabarinathan, Anthony Travis, Gareth Norton, Adam Price

*Corresponding author for this work

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5 Citations (Scopus)
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Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.
Original languageEnglish
Article number911775
Number of pages21
JournalFrontiers in plant science
Publication statusPublished - 8 Jul 2022

Bibliographical note

This work was supported by the Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI) and the GCRF South Asia Nitrogen Hub (SANH). The BAAP was developed under funding from BBSRC (United Kingdom) BB/J003336/1, while the work by AT was also supported by project BB/N013492/1 (NEWS-India-United Kingdom) and SANH.

We gratefully acknowledge the support extended by the Director, NRRI, to conduct this experiment and special thanks go to the administrative staff of our institute who supported the conduct of this experiment in official terms.

Data Availability Statement

The original contributions presented in this study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.


  • rice
  • root
  • vigor
  • aus
  • nitrogen
  • haplotype
  • association mapping


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