Tolerance Data 2012 En Francais Torrent
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3-D graphs showing relationship between Structure sub-population, SNP haplotype and percent survival of rice cultivars based on submergence tolerance data from IRRI in 2012. Reference alleles of Sub1A, Sub1B and Sub1C genes from tolerant variety FR13A are represented by haplotypes H8, H9 and H1, respectively.
Analysis of sequence polymorphism in the functional genes for agronomic traits is necessary for identification of superior alleles in the germplasm. Map-based cloning of Sub1A gene and its functional validation by genetic transformation has proven its role in submergence tolerance of rice19. But after the original work, which also included sequencing of Sub1A, Sub1B and Sub1C genes from 21 rice cultivars, no further studies have been undertaken on allelic sequence variation in the Sub1 genes, although marker based allele surveys have been done for Sub1A and Sub1C genes in larger sets of cultivars21,22,50. Here, we generated high-quality sequence information by targeted re-sequencing of pooled PCR products from 96 cultivars for Sub1A, 110 cultivars for Sub1B and 174 cultivars for Sbu1C gene, resulting in comprehensive allelic sequence information. We also analysed the publicly available whole genome sequence data on 66 rice genomes for this purpose. These together identified 9 SNPs in Sub1A, 37 SNPs in Sub1B and 56 SNPs plus four InDels in Sub1C gene. Of these, one, four and 10 SNPs were unique to the 179 cultivars set, whereas two, 29 and 22 SNPs were unique to the 66 genomes set, respectively. Most of the unique SNPs in the 66 genomes set were due to 14 wild rice accessions (Supplementary Table S5), suggesting that our res-sequencing work has provided a comprehensive coverage of the Sub1 gene sequence variation in rice cultivars.
No consistent association was found between SNPs in the Sub1 genes and percent survival after submergence of 179 cultivars by TASSEL analysis. Only significant association was obtained with SNPs in the Sub1C gene and submergence tolerance data from BHU 2012 and NDUAT 2013, where stress intensity was the highest with average survival rates of 11.6% and 31.3%, respectively (Supplementary Fig. S4). Whether or not this association is real need further validation using precise phenotyping repeated in different locations/seasons. Surprisingly, the known association of the Sub1A-1 allele with submergence tolerance was not validated in the present study due to presence of several exceptions in the present cultivar set. This was also reflected in a direct visualization of data in 3D plots (Fig. 8), where nine cultivars with the tolerant Sub1A-1 allele (haplotype H8) showed poor survival after submergence. On the other hand several cultivars with the sensitive Sub1A-2 allele (haplotype H2) showed high level of tolerance across locations (Fig. 8, Table 6). There are at least six published reports of Sub1A-1-independent mechanisms of submergence tolerance in rice5,9,14,21,50,55. Supporting our TASSEL results of significant associations with Sub1C SNPs at two locations, the 3D plot also showed only one exception to the association between submergence tolerance and tolerant Sub1C allele (haplotype H1). However, these exceptions need further analysis in bi-parental segregating populations. Importance of Sub1-independent mechanism of submergence tolerance has been highlighted decades ago56 and major non-Sub1 QTLs have been identified using Madabaru/IR72 and Chehrang-Sub1/IR10F365 populations, suggesting Sub1-independent mechanism of vegetative stage submergence tolerance14,21.
Research into the kinds of tolerances needed for critical systems involves a large amount of interdisciplinary work. The more complex the system, the more carefully all possible interactions have to be considered and prepared for. Considering the importance of high-value systems in transport, public utilities and the military, the field of topics that touch on research is very wide: it can include such obvious subjects as software modeling and reliability, or hardware design, to arcane elements such as stochastic models, graph theory, formal or exclusionary logic, parallel processing, remote data transmission, and more.[19]
Recent advances in statistical and dynamical modelling of wave effects at the coast, storm surges and inundation risk have reduced the uncertainties around the inundation risks at the coast (Vousdoukas et al., 2016316; Vitousek et al., 2017317; Melet et al., 2018318; Vousdoukas et al., 2018c319) and assessments of the resulting highly resolved coastal sea levels are now emerging (Cid et al., 2017320; Muis et al., 2017321; Wahl et al., 2017322). This progress was facilitated due to the availability of, for example, the Global Extreme Sea Level Analysis (GESLA-2; Woodworth et al., 2016323) high-frequency (hourly) datasets, advances in the Coordinated Ocean Wave Climate Project (COWCLIP; Hemer et al., 2013324), coastal altimetry datasets (Cipollini et al., 2017325), and the Global Tide and Surge Reanalysis (GTSR; Muis et al., 2016326), while new analyses of datasets that have been available since before the publication of AR5 have continued (e.g., PSML; Holgate et al., 2012327).
Although ESL is experienced episodically by definition, Marcos et al. (2015)328 examined the long-term behaviour of storm surge models and detected decadal and multidecadal variations in storm surge that are not related to changes in RSL. They found that, although 82% of their observed time series showed synchronous patterns at regional scales, the pattern tended to be non-linear, implying that it would be difficult to infer future behaviour unless the physical basis for the responses was understood. An analysis of the relative contributions of SLR and ESL due to storminess showed that in the US Pacific northwest since the early 1980s, increases in wave height and period have had a larger effect on coastal flooding and erosion than RSL (Ruggiero, 2012329) since the early 1980s. This is also true in other regions distributed over the entire globe (Melet et al., 2016330; Melet et al., 2018331). Changes since 1990 in the sea level harmonics and seasonal phases and amplitudes of the wave period and significant wave height were found for the Gulf of Mexico coast and along the US east coast (Wahl et al., 2014332; Wahl and Plant, 2015333). These authors found that high waters have increased twice as much as one would expect from long-term SLR alone, because of additional changes in the seasonal cycle, yielding a 30% increase in risk of flooding. Such effects are likely to be highly dependent on the local conditions. For example, using WAVEWATCH III, TOPEX/Poseidon altimetry tide model data and atmospheric forcing physically downscaled using Delft3D-WAVE and Delft3D-FLOW in what they call the Coastal Storm Modeling System (CoSMoS), Vitousek et al. (2017) were able to detect local inundation hazards (at a scale of hundreds of metres) across regions along the Californian coast. Similarly, Castrucci and Tahvildari (2018)334 simulated the impact of SLR along the Mid-Atlantic region in the USA. A study for the Maldives shows that the contribution of wave setup is essential to estimate flood risks (Wadey et al., 2017335).
While there is no literature on projected accommodation, current trends suggest further uptake of accommodation approaches in coming decades, especially where protection approaches are not economically viable. Flood proofing of houses and establishment of new building codes to accommodate coastal hazards is also expected to become more common in coming decades. Similarly, accommodation measures for salinity are under further development, such as rice breeding programs to improve salt tolerance (Linh et al., 2012; Quan et al., 2018b). However, the achievements to improve salinity tolerance in rice are rather modest so far (Hoang et al., 2016) although efforts are expected to continue or even intensify. Given that index based insurance products have been included in NDCs and NAPs in a number of countries (Kreft et al., 2017), uptake is expected to grow. Ports can continue elevating hazard-prone facilities and the critical parts of port infrastructure can be protected by flood walls. Alternatively, ports can use advance measures to develop port facilities seaward (Aerts, 2018). 2b1af7f3a8