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, 20 (1), 355

Identification of Stable QTLs and Candidate Genes Involved in Anaerobic Germination Tolerance in Rice via High-Density Genetic Mapping and RNA-Seq

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Identification of Stable QTLs and Candidate Genes Involved in Anaerobic Germination Tolerance in Rice via High-Density Genetic Mapping and RNA-Seq

Jing Yang et al. BMC Genomics.

Abstract

Background: Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties.

Results: In this study, a recombinant inbred line (RIL) population derived from a cross between YZX and 02428 exhibited obvious coleoptile phenotypic differences. Mapping analysis using a high-density bin map indicated that a total of 25 loci were detected across two cropping seasons, including 10 previously detected loci and a total of 13 stable loci. Analysis of the 13 stable loci demonstrated that the more elite alleles that were pyramided in an individual, the higher the values of these traits were in the two cropping seasons. Furthermore, some anaerobic germination-tolerant recombinant inbred lines, namely G9, G10, G16, and G151, were identified. A total of 84 differentially expressed genes were obtained from the 13 stable loci via genome-wide expression analysis of the two parents at three key periods. Among them, Os06g0110200, Os07g0638300, Os07g0638400, Os09g0532900, Os09g0531701 and Os12g0539751 constitute the best candidates associated with anaerobic germination.

Conclusions: Both the anaerobic germination-tolerant recombinant inbred lines and the loci identified in this study will provide new genetic resources for improving the anaerobic germination tolerance of rice using molecular breeding strategies, as well as will broaden our understanding of the genetic control of germination tolerance under anaerobic conditions.

Keywords: Anaerobic germination tolerance; Candidate genes; Direct-seeded rice; QTL mapping; RNA-Seq.

Conflict of interest statement

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Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Dynamic phenotypic changes in the coleoptiles of YZX and 02428 under anaerobic conditions. a, Phenotype of two parents for 1–6 d under anaerobic conditions; b, c, d, and e represent the changes in the length, surface area, diameter, and volume of the coleoptiles in 1–6 d under anaerobic conditions; f, The percentage daily increase in the length, surface area, diameter, and volume of the coleoptiles of YZX and 02428 under anaerobic conditions
Fig. 2
Fig. 2
The QTL position on the high-density bin map of the YZX × 02428 RIL population. Square brackets indicate that different QTLs are located at the same physical location on the chromosome. The red text indicates the QTLs that are mapped in the two cropping seasons
Fig. 3
Fig. 3
Pyramiding of favorable alleles. ad represent CL, CSA, CV, and CD, respectively. Letters from a to f indicate significantly different values according to statistical analysis using Duncan’s Multiple Range Test (alpha = 0.05)
Fig. 4
Fig. 4
DEGs between the parents on different days of germination. a Up and down regulated genes detected between the two parents on different days of germination. b Venn diagram of DEGs between the parents on different days of germination
Fig. 5
Fig. 5
Visualization analysis based on Pearson correlations between genes and the phenotype of CL, CSA, CV and CD. Nodes are genes and traits (CL, CSA, CV and CD); edges are their correlation coefficient values, red and green indicate positive and negative, respectively. The yellow node indicates a strong correlation between the gene and the trait
Fig. 6
Fig. 6
Expression levels of 12 highly promising candidate genes detected by qRT-PCR

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