Abstract
BackgroundAnaerobic 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.ResultsIn 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.ConclusionsBoth 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.
Highlights
Anaerobic germination tolerance is an important trait for direct-seeded rice varieties
Phenotypic performance of the parents and recombinant inbred line (RIL) population for Anaerobic germination (AG) tolerance The faster the rice coleoptile elongates, the sooner the seedling is able to escape the anoxic environment, which improves the chances of survival
We discovered that up to 10 of the 25 loci have been reported previously (Table 2). qCD-1, qCD-3-2, qCL-10, and qCSA-12–2 overlapped with four loci associated with the anaerobic response index [26]. qCD-2-2 and qCD-4-1 were located within the genomic region of qSHL2.2 and qSHL4.1, respectively [21]. qCD-3-1 was mapped to the genomic region of qSAT-3-B [19]
Summary
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. Direct-seeded rice (DSR), classified as wet DSR, dry DSR, or water DSR, is becoming increasingly popular across the world due to its cost efficiency and convenience [1]. When using the water DSR method, the rice seeds are completely submerged and suffer hypoxia or Insufficient energy supply under oxygen-deficient conditions caused by submergence is a major bottleneck for seed germination and seedling survival [5]. Yang et al BMC Genomics (2019) 20:355 elongation and seedling survival, in tolerant genotypes [3, 6], indicating that RAmy3D may be active during the anaerobic mobilization of rice. High expression of CIPK15, which encodes protein kinases, activates energy and the stressor receptor SnRK1A, resulting in a series of downstream cascade reactions, such as the induced expression of the transcription factor MYBS1, thereby enhancing the expression of α-amylases genes [9]
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