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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]
tolerance data 2012 torrent
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.
To construct a genetic linkage map efficiently, we need a genome-wide marker set and an efficient genotyping system. The Ion AmpliSeq Targeted Sequencing technology (Thermo Fisher Scientific, Waltham, MA, USA) can quickly detect polymorphisms by amplicon-based multiplex targeted NGS [15, 16]. Here, we developed genetic maps with AmpliSeq and sought QTLs for PHS tolerance in buckwheat by NGS-BSA. We developed genome-wide markers for QTL analysis and detected several QTLs related to PHS tolerance. In addition, we developed linked markers and investigated the effect of selection with the markers. Furthermore, we demonstrated the effectiveness of NGS-BSA by developing linkage maps from AmpliSeq data of markers linked to the SC allele. Our findings and marker development system will be useful for advancing genetic research for buckwheat breeding.
The enhanced respiratory capacity in the gastrocnemius muscle of highland torrent ducks (Fig. 1A) could be important at high altitudes for increasing the thermogenic capacity for heat production in the cold, and/or increasing hypoxia tolerance. Birds meet the bulk of the demand for thermogenesis by shivering (West, 1965; Bicudo, 1996). Non-shivering thermogenesis may play a role in thermoregulation in ducklings (Teulier et al., 2010), but the relative importance of non-shivering thermogenesis in most species of birds is unclear (Barré et al., 1989; Connolly et al., 1989). Regardless of whether shivering or non-shivering thermogenesis predominates, the flight muscles (particularly the pectoralis and the supracoracoideus) are believed to be a major site of thermogenesis in adult birds (Petit and Vézina, 2014; Block, 1994; Bicudo et al., 2002). The thigh muscles are very important for thermogenesis in early development, but their relative importance decreases as the flight muscles grow and eventually reach a much larger mass (Marjoniemi and Hohtola, 2000; Sirsat et al., 2016). Therefore, although the increase in aerobic capacity in the gastrocnemius could be important for facilitating thermogenesis, it is curious that similar increases do not also occur in the pectoralis. Increases in oxidative capacity might have instead arisen to promote hypoxia resistance at high altitudes, a theory that has been suggested in other high-altitude taxa (Hochachka, 1985; Scott et al., 2009a,b; Lui et al., 2015). This theory suggests that, when the maximum attainable respiration of an individual muscle fiber is impaired from declines in intracellular O2 tension, a higher oxidative capacity should increase the total mitochondrial O2 flux of the entire muscle and thus help offset the inhibitory effects of hypoxia. This mechanism might be acting in torrent ducks to overcome intracellular hypoxia in the gastrocnemius muscle during swimming or diving at high altitude.
Major regulatory enzymes of glycolysis, PK and PFK, also had higher activity in the gastrocnemius of the high-altitude population compared with those from low altitudes (Table 1; Fig. 2). PK and PFK have been suggested to exert significant metabolic control over glycolytic pathway flux when assessed using metabolic control analysis (Vogt et al., 2002a,b), and they both catalyze irreversible reactions in the glycolytic pathway and have long been discussed as sites of allosteric regulation (Scrutton and Utter, 1968). This is in line with the enhanced glycolytic enzyme activities in the locomotory muscle of many high-altitude mammals, and likely serves to increase the capacity for producing ATP from carbohydrate oxidation (Semenza et al., 1994; Firth et al., 1994; McClelland et al., 1998; Schippers et al., 2012). This could be especially beneficial in high-altitude hypoxia because of the inherent O2 savings associated with oxidizing carbohydrates instead of other metabolic fuels (McClelland et al., 1998). This advantage seems to have been favored by natural selection in highland mice from the Andes, which have a greater preference for carbohydrate oxidation than lowland mice during exercise, even when compared at similar altitudes and exercise intensities (Schippers et al., 2012). The increased glycolytic activities in torrent ducks may also be reflective of an increased capacity for using anaerobic metabolism during short diving bouts, which may supply lactate for oxidation in the heart (see below). Many diving animals show increased glycolytic capacity in the muscles to support underwater locomotion (George and Ronald, 1973; Simon et al., 1974; Castellini et al., 1981), and it is predictable that the demands for anaerobic metabolism could be higher while diving in high-altitude hypoxia.
The numerous differences in enzyme activities between torrent duck populations suggest that life at high altitudes leads to metabolic restructuring of the left ventricle. The high-altitude population had a high activity of LDH in the heart (Table 1; Fig. 3), similar to what has been observed in various tissues of species that experience cold and hypoxic/anoxic environments (Rosser and Hochachka, 1993; Dawson et al., 2013; Shahriari et al., 2013; Katzenback et al., 2014). However, LDH in the heart likely facilitates lactate oxidation rather than production, a process that our data suggests might be enhanced in highland torrent ducks (Brooks, 1998; Gladden, 2004; Brooks, 2009). There is increasing evidence for a role of mitochondrial LDH that helps support lactate oxidation in an intracellular lactate shuttle, likely in an effort to balance glycolytic production of lactate with mitochondrial oxidation (Jouaville et al., 1999; Brooks et al., 1999; Van Hall, 2000; Passarella et al., 2008; Lottes et al., 2015), and it is possible that the capacity of this shuttle is enhanced in highland torrent ducks. An increased capacity for lactate oxidation in the left ventricle may also help minimize the inhibitory effects of lactate on fatty acid oxidation (Bielefeld et al., 1985; Wolfe, 1998; Liu et al., 2009). This could act in concert with the greater HOAD activity of highland torrent ducks (Fig. 3), an observation that is consistent with findings in several other high-altitude taxa (Bigard et al., 1991; Léon-Velarde, 1993; Sheafor, 2003; Scott et al., 2009a,b), in order to increase the sustainable yield of ATP from β-oxidation.
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