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.
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Acknowledgements
This work was supported by a grant from the National Natural Science Foundation of China (31571743 and 31671658).
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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.
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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)
Figure S2
Relationship between Dʹ and the genetic distance of syntenic marker pairs in subpopulations (TIFF 483 kb)
Figure S3
Frequency distribution of CLn, CLa and CELpc in the natural population in 2016 and 2017 (TIFF 578 kb)
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)
Figure S5
Frequency distribution of CLn, CLa and CELpc in the WL-BIL population in 2016 and 2017 (TIFF 670 kb)
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Dang, X., Li, Y., Zhang, Y. et al. Identification of favorable alleles for rice seedling anoxic tolerance using natural and bi-parental populations. Euphytica 215, 140 (2019). https://doi.org/10.1007/s10681-019-2463-9
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DOI: https://doi.org/10.1007/s10681-019-2463-9