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Identification of stable QTLs causing chalk in rice grains in nine environments

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A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk.

Abstract

Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10 % of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13 % of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.

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Acknowledgments

The authors thank Dr. Zhikang Li for kindly providing the T/L and L/T populations and linkage map. We also thank Ms. Lucena Samadio, Mr. Fernando Salisi and Mr. Teodoro Atienza for field management and quality evaluation. We appreciate Ms. Supanee Jongdee, Ms. Kuri Victoria Eugenia, Dr. Asfaliza Ramli, Dr. Lihong Xie, Dr. Hosien Rahim Souroush, Dr. Huu-Sheng Lur and Dr. Pedro Blanco kindly planted mapping populations. This research was supported by Australian Centre for International Agricultural Research (ACIAR) and the International Rice Research Institute.

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Author notes

  1. Venea D. Daygon & Melissa A. Fitzgerald

    Present address: School of Agriculture and Food Science, University of Queensland, St Lucia, QLD, 4072, Australia

Authors and Affiliations

  1. Grain Quality and Nutrition Centre, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines

    Xiangqian Zhao, Venea D. Daygon & Melissa A. Fitzgerald

  2. TT Chang Genetic Resources Centre, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines

    Kenneth L. McNally & Ruaraidh Sackville Hamilton

  3. Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines

    Xiangqian Zhao, Fangming Xie & Russell F. Reinke

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  1. Xiangqian Zhao
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Correspondence to Xiangqian Zhao or Melissa A. Fitzgerald.

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Communicated by L. Xiong.

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Zhao, X., Daygon, V.D., McNally, K.L. et al. Identification of stable QTLs causing chalk in rice grains in nine environments. Theor Appl Genet 129, 141–153 (2016). https://doi.org/10.1007/s00122-015-2616-8

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  • DOI: https://doi.org/10.1007/s00122-015-2616-8

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