Identification of favorable alleles for rice seedling anoxic tolerance using natural and bi-parental populations
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.
KeywordsAssociation mapping Direct-sown rice Favorable allele Linkage analysis Seedling anoxic tolerance
This work was supported by a grant from the National Natural Science Foundation of China (31571743 and 31671658).
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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Conflict of interest
- Cao Y, Song F, Goodman M, Zheng Z (2006) Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. J Plant Physiol 163:1167–1178. https://doi.org/10.1016/j.jplph.2005.11.004 CrossRefPubMedGoogle Scholar
- Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374. https://doi.org/10.1146/annurev.arplant.54.031902.134907 CrossRefPubMedPubMedCentralGoogle Scholar
- Jiang H, Wu JL, Wang GL (1985) Studies on Ludao of Lianyungang. Crop Genet Resource 2:4–7Google Scholar
- Jiang L, Hou MY, Wang CM, Wan JM (2004) Quantitative trait loci and epistatic analysis of seed anoxia germinability in rice Oryza sativa L. Rice Sci 11:238–244Google Scholar
- Takahashi H, Greenway H, Matsumura H et al (2014) Rice alcohol dehydrogenase 1 promotes survival and has a major impact on carbohydrate metabolism in the embryo and endosperm when seeds are germinated in partially oxygenated water. Ann Bot 113:851–859. https://doi.org/10.1093/aob/mct305 CrossRefPubMedPubMedCentralGoogle Scholar
- Wang Y, Guo Y, Hong DL (2010) QTL analysis of the anoxic tolerance at the seedling stage in rice. Chin J Rice Sci 24:18–24. https://doi.org/10.3969/j.issn.1001-7216.2010.01.04 (in Chinese with English abstract) CrossRefGoogle Scholar
- Wang SC, Basten CJ, Zeng ZB (2012) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm. Accessed 16 Dec 2017
- Wei XH, Yang ZR, Dong L et al (2004) SSR evidence for taxonomic position of weedy rice ‘Ludao’. Sci Agric Sin 7:937–942 (in Chinese with English abstract) Google Scholar