Abstract
BackgroundSeed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. The genetic and molecular mechanisms underlying seed dormancy in rice remain largely unknown.ResultsQuantitative trait loci (QTLs) for seed dormancy were identified in two different mapping populations, a chromosome segment substitution line (CSSL) and backcross inbred line (BIL) population, both derived from the same parents Nipponbare, a japonica cultivar with seed dormancy, and 9311, an indica cultivar lacking seed dormancy. A total of 12 and 27 QTL regions for seed dormancy were detected in the CSSLs and BILs, respectively. Among these regions, four major loci (qSD3.1, qSD3.2, qSD5.2 and qSD11.2) were commonly identified for multiple germination parameters associated with seed dormancy in both populations, with Nipponbare alleles delaying the seed germination percentage and decreasing germination uniformity. Two loci (qSD3.1 and qSD3.2) were individually validated in the near-isogenic lines containing the QTL of interest. The effect of qSD3.2 was further confirmed in a CSSL-derived F2 population. Furthermore, both qSD3.1 and qSD3.2 were sensitive to abscisic acid and exhibited a significant epistatic interaction to increase seed dormancy.ConclusionsOur results indicate that the integration of the developed CSSLs and BILs with high-density markers can provide a powerful tool for dissecting the genetic basis of seed dormancy in rice. Our findings regarding the major loci and their interactions with several promising candidate genes that are induced by abscisic acid and specifically expressed in the seeds will facilitate further gene discovery and a better understanding of the genetic and molecular mechanisms of seed dormancy for improving seed quality in rice breeding programs.
Highlights
Seed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors
We identified a large number of Quantitative trait loci (QTLs) for seed dormancy in Chromosome segment substitution lines (CSSLs) and Backcross inbred lines (BILs) populations that were derived from common parental lines (NIP and 9311) and genotyped by using highdensity singlenucleotide polymorphism (SNP) markers (Fig. 2)
The present study identified 31 QTLs for seed dormancy using CSSL and BIL populations with high-density SNP maps that were developed from common parents
Summary
A quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. Seed dormancy 4 (Sdr4) on chromosome 7 (23.79 Mb), which encodes a protein of unknown function, was reported as the first cloned QTL in rice and is positively regulated by the seed maturation-related gene OsVP1 (Sugimoto et al 2010). More than 120 QTLs affecting seed dormancy have been detected in other model plants and crops (https://archive.gramene.org/qtl/), such as Arabidopsis (Bentsink et al 2006), wheat (Triticum aestivum L.) (Anderson et al 1993), oilseed rape (Brassica napus L.) (Schatzki et al 2013), barley (Hordeum vulgare L.) (Nagel et al 2019) and sorghum (Sorghum bicolor L.) (Cantoro et al 2016). DOG1 encodes a protein of unknown function and is regulated at the transcriptional and posttranscriptional levels in Arabidopsis (Bentsink et al 2006; Müller et al 2012; Chen and Penfield 2018) Overall, these data indicate that the genetic and molecular mechanisms underlying seed dormancy are very complex in Arabidopsis and other plant species. It is critical to identify the QTLs related to seed dormancy to dissect the molecular basis of this complex trait
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