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Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.

Dissolved inorganic carbon (DIC) in headwater streams significantly contributes to the riverine CO2 emission to the atmosphere and oceans. However, understanding of the sources and mechanisms of DIC generation and mass balances of DIC flux in headwater streams at the scale of catchments remain poor and add to uncertainty in regional carbon estimates. In this study, the input and output of water fluxes and their chemical and isotopic compositions in a headwater stream were investigated from 2016 to 2019 in a subtropical plantation catchment. Our results showed that the headwater stream catchment experienced a net carbon loss of 262–4352 kg C km−2 yr−1 based on the water balance of annual precipitation, evapotranspiration, headwater stream and groundwater discharge, and change in soil water storage. The headwater stream exhibited comparable DIC flux (3561 ± 933 kg C km−2 yr−1) and higher DIC concentration (7.91 ± 3.13 mg L−1) than precipitation (3662 ± 682 kg C km−2 yr−1 and 2.63 ± 1.22 mg L−1, respectively). Differences in DIC concentration between precipitation and headwater stream were mainly controlled by soil CO2 dissolution, carbonate weathering, and their synergistic effects. Relative contributions to DIC fluxes in this headwater stream were 25.3 ± 5.2% by precipitation, 47.3 ± 6.2% by soil biological CO2, and 27.4 ± 7.3% by carbonate weathering. Our results indicated that the DIC-generating processes may result in an underestimation of soil biological CO2 efflux to the atmosphere. Further, soil carbonate weathering, and a net carbon loss at the scale of catchments may be overlooked in acid soils.