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Molecular dissection of QTL governing grain size traits employing association and linkage mapping in Basmati rice

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Abstract

Grain size is one of the key traits that determines the quality of Basmati rice from the consumers’ as well as the traders’ point of view. Though many genes governing grain size have been identified in indica and japonica, little work has been done in Basmati rice. The present study aims at dissection of a QTL region governing grain size traits in Basmati employing association and linkage mapping approaches. Association mapping revealed that three markers, i.e., RM 6024 (grain breadth), RM1237 and RM18582 (grain length-breadth ratio), which cover 889 kb in the targeted QTL region have been significantly associated with grain size traits. Using linkage mapping, the targeted QTL region has been further delimited to a physical distance of 268 kb that comprises 24 annotated genes. The gene expression analysis of parents, revealed 19 genes differentially expressing within the QTL. Of them, 15 genes showed high expression in Basmati370, while four were expressed in Jaya, and whereas five genes did not show any differential expression between parents. Among differentially expressed genes, a highly expressed gene in Basmati370, Os05g0374200 (Cytokinin dehydrogenase 1 precursor) seems to be involved in accumulation of cytokinins, thus affecting the grain size. Therefore, our findings demonstrated that by complimenting association and linkage mapping, it is likely to dissect a QTL governing grain size traits in Basmati rice and also the QTL could be a potential target for marker-assisted breeding and map-based cloning studies.

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Acknowledgements

The authors wish to thank Acharya N G Ranga Agricultural University and CDFD for providing lab, field and financial support to carry out this work and also special thanks to the Department of Science and Technology for providing the INSPIRE fellowship to DAD.

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Author notes

  1. Dondapati Annekitty Deborah and Lakshminarayana R. Vemireddy have equally contributed.

Authors and Affiliations

  1. Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, AP, 500 030, India

    Dondapati Annekitty Deborah, Lakshminarayana R. Vemireddy, Veeraghattapu Roja, Santhosh Patil, Ganga Prasad Choudhary, Akkareddy Srividhya, Ghanta Anuradha, Kommineni Radhika, Kalinati N. Yamini, Gopalakrishna M. Kadambari, Ranjith Kumar Nagireddy & Ebrahimali A. Siddiq

  2. Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500 001, India

    Lakshminarayana R. Vemireddy, Sabahat Noor, Akkareddy Srividhya, Andi Kaliappan, B Sandhya Rani, Valluri V. Satyavathi, Ebrahimali A. Siddiq & Javaregowda Nagaraju

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  1. Dondapati Annekitty Deborah
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Contributions

LRV designed the experiment. LRV and DAD collected the germplasm and developed the mapping population. DAD performed all the experiments. VR, SP, GPC, GMK and RKC performed part of phenotypic data collection. AK, SR, and SN performed part of SSR genotyping. DAD constructed the association map, genetic linkage map; performed QTL analysis and wrote the manuscript. LRV and AS performed part of the genotypic analysis. LRV supported the bioinformatics analysis. LRV, AS, VVS and EAS revised the manuscript. All of the authors read and approved the final manuscript.

Corresponding author

Correspondence to Lakshminarayana R. Vemireddy.

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The authors declared that they have no conflicts of interest.

Electronic supplementary material

Supplementary Fig. 1

Frequency distribution of grain size related traits in association mapping panel (A) and in F2 populations derived from the cross of Basmati370 and Jaya (B). (JPEG 418 kb)

Supplementary Fig. 2

Genotypic variability of grain size in the representative association mapping panel of rice germplasm. The grain size of Pusa1121 is 8.2 mm. (JPEG 444 kb)

Supplementary Fig. 3

Genetic relationship of 96 rice genotypes estimated using Unbiased Neighbor-Joining method of DARwin 5.0 software. Aromatic (1–27)- Red colored, Indica (28–72) - Green colored; Japonica and Javanica (73–91) - Blue colored;; Aus (92–96)- Pink colored. For complete list of the rice genotypes (1–96) refer Supl Table 1. (JPEG 1645 kb)

Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Table 4

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Supplementary Table 5

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Supplementary Table 6

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Supplementary Table 7

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Supplementary Table 8

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Supplementary Table 9

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Deborah, D.A., Vemireddy, L.R., Roja, V. et al. Molecular dissection of QTL governing grain size traits employing association and linkage mapping in Basmati rice. Mol Breeding 37, 77 (2017). https://doi.org/10.1007/s11032-017-0678-9

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