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Genetic potential of grain-related traits in rice landraces: phenomics and multi-locus association analyses

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Abstract

Background

Grain length, width, weight, and the number of grains per panicle are crucial determinants contributing to yield in cereal crops. Understanding the genetic basis of grain-related traits has been the main research object in crop science.

Methods and results

Kerala has a collection of different rice landraces. Characterization of these valuable genetic resources for 39 distinct agro-morphological traits was carried out in two seasons from 2017 to 2019 directly in farmers field. Most characteristics were polymorphic except ligule shape, leaf angle, and panicle axis. The results of principal component analysis implied that leaf length, plant height, culm length, flag leaf length, and grain-related traits were the principal discriminatory characteristics of rice landraces. For identifying the genetic basis of key grain traits of rice, three multi locus GWAS models were performed based on 1,47,994 SNPs in 73 rice accessions. As a result, 48 quantitative trait nucleotides (QTNs) were identified to be associated with these traits. After characterization of their function and expression, 15 significant candidate genes involved in regulating grain width, number of grains per panicle, and yield were identified.

Conclusions

The detected QTNs and candidate genes in this study could be further used for marker-assisted high-quality breeding of rice.

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Data Availability

All data generated or analyzed during this study are included in this published article and its supplementary information files.

Code Availability

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Funding

This research was supported by grants from the Department of Science and Technology-Science and Engineering Research Board (DST-SERB), Government of India (Grant No. ECR/2016/001934).

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Authors and Affiliations

  1. Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod, 671316, Kerala, India

    Maya Peringottillam, Krishna T Sundaram & Alagu Manickavelu

  2. International Rice Research Institute (IRRI), South Asia hub, Patancheru, India

    Krishna T Sundaram

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  1. Maya Peringottillam
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  2. Krishna T Sundaram
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  3. Alagu Manickavelu
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Contributions

AM conceived and supervised the research work; MP prepared genetic materials; AM acquired research grant for the research; KTS, MP performed data analyses; MP wrote the manuscript; All authors read and approved the final manuscript.

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Correspondence to Alagu Manickavelu.

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Peringottillam, M., Sundaram, K.T. & Manickavelu, A. Genetic potential of grain-related traits in rice landraces: phenomics and multi-locus association analyses. Mol Biol Rep 50, 9323–9334 (2023). https://doi.org/10.1007/s11033-023-08807-5

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