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Euphytica

, 215:140 | Cite as

Identification of favorable alleles for rice seedling anoxic tolerance using natural and bi-parental populations

  • Xiaojing Dang
  • Yanhui Li
  • Yuanqing Zhang
  • Jie Ji
  • Dalu Li
  • Xiaoxiao Hu
  • Shangshang Zhu
  • Zhiyao Dong
  • Erbao Liu
  • Hui Wang
  • Bingjie Fang
  • Delin HongEmail author
Article

Abstract

The acreage of submerged direct-sown cultivation of Oryza sativa is gradually increasing in China because of the constantly decreasing number of laborers in rural areas. Identifying favorable alleles for seedling anoxic tolerance (SAT) is necessary for improving cultivars suitable for submerged direct-sown rice cultivation. In this study, we used two populations to detect quantitative trait loci (QTLs) for SAT. In the natural population consisting of 542 accessions, seven simple sequence repeat marker loci associated with SAT were detected in both 2016 and 2017, with 22 favorable alleles. RM5340 on chromosome 2 and RM6811 on chromosome 6 were newly identified. Allele RM6811-160 bp had the largest phenotypic effect (1.09 cm/cm). Seventy-one accessions carried this allele. In the backcross inbred line population (115 lines) derived from Wuyunjing 7 hao/Ludao//Wuyunjing 7 hao, 8 QTLs for SAT were detected, with the phenotypic variance explained (PVE) ranging from 2.51 to 12.11%. The qCELpc2, qCELpc3, qCELpc5 and qCELpc11 loci were newly detected. The favorable alleles of loci qCELpc3, qCELpc5 and qCELpc11 were from Ludao. The locus qCELpc11 had the largest PVE of 10.39%, with a substitutive effect of 0.82 cm averaged over 2 years. By sequencing the gene locus OsBIERF, which was within a 15.50–16.08 Mb chromosome region harboring SAT-associated RM3600 on chromosome 9 and was detected in both populations, a single nucleotide polymorphism locus at the first exon was found between Wuyunjing 7 hao (T) and Ludao (C). The favorable alleles detected in this study could be used to improve SAT of rice cultivars.

Keywords

Association mapping Direct-sown rice Favorable allele Linkage analysis Seedling anoxic tolerance 

Notes

Acknowledgements

This work was supported by a grant from the National Natural Science Foundation of China (31571743 and 31671658).

Author contributions

DH planned and designed the research; XD, YL and YZ performed the field experiment and germination experiment; XD, JJ, DL, XH, SZ, ZD, EL, HW and BF conducted the molecular experiment; XD, YL and YZ analysed the data and XD wrote the manuscript; and DH revised the manuscript. All authors read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

None declared.

Supplementary material

10681_2019_2463_MOESM1_ESM.tif (131 kb)
Figure S1 Changes in the mean LnP (K) (A) and (ΔK) (B) for the number of subpopulations and the structure analysis of 542 rice accessions using STRUCTURE software; a) A graph with the mean LnP (K) on the Y axis and the number of subpopulations on the X axis; (B) A graph showing ΔK and the number of subpopulations to determine the optimal number of subpopulations; (C) The structure analysis of 542 rice accessions (TIFF 131 kb)
10681_2019_2463_MOESM2_ESM.tif (484 kb)
Figure S2 Relationship between Dʹ and the genetic distance of syntenic marker pairs in subpopulations (TIFF 483 kb)
10681_2019_2463_MOESM3_ESM.tif (578 kb)
Figure S3 Frequency distribution of CLn, CLa and CELpc in the natural population in 2016 and 2017 (TIFF 578 kb)
10681_2019_2463_MOESM4_ESM.tif (1.6 mb)
Figure S4 Graphical genotypes showing the 262 markers in chromosome positions (cM) and the significant marker-traits associations detected for CLn, CLa and CELpc in the natural population (TIFF 1608 kb)
10681_2019_2463_MOESM5_ESM.tif (670 kb)
Figure S5 Frequency distribution of CLn, CLa and CELpc in the WL-BIL population in 2016 and 2017 (TIFF 670 kb)
10681_2019_2463_MOESM6_ESM.docx (89 kb)
Supplementary material 6 (DOCX 88 kb)
10681_2019_2463_MOESM7_ESM.xlsx (1.7 mb)
Supplementary material 7 (XLSX 1742 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina

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