Exploration of quality variation and stability of hybrid rice under multi-environments.

Improving quality is an essential goal of rice breeding and production. However, rice quality is not solely determined by genotype, but is also influenced by the environment. Phenotype plasticity refers to the ability of a given genotype to produce different phenotypes under different environmental conditions, which can be a representation of the stability of traits. Seven quality traits of 141 hybrid combinations, deriving from the test-crossing of 7 thermosensitive genic male sterile (TGMS) and 25 restorer lines, were evaluated at 5 trial sites with intermittent sowing of three to five in Southern China. In the Yangtze River Basin, it was observed that delaying the sowing time of hybrid rice combinations leads to an improvement in their overall quality. Twelve parents were identified to have lower plasticity general combing ability (GCA) values with increased ability to produce hybrids with a more stable quality. The parents with superior quality tend to exhibit lower GCA values for plasticity. The genome-wide association study (GWAS) identified 13 and 15 quantitative trait loci (QTLs) associated with phenotype plasticity and BLUP measurement, respectively. Notably, seven QTLs simultaneously affected both phenotype plasticity and BLUP measurement. Two cloned rice quality genes, ALK and GL7, may be involved in controlling the plasticity of quality traits in hybrid rice. The direction of the genetic effect of the QTL6 (ALK) on alkali spreading value (ASV) plasticity varies in different cropping environments. This study provides novel insights into the dynamic genetic basis of quality traits in response to different cropping regions, cultivation practices, and changing climates. These findings establish a foundation for precise breeding and production of stable and high-quality rice. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01442-3.

Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice.

The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F1 hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, including indica, aus, and japonica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, including Ghd8/DTH8, Gn1a, and IPA1 existed in wild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.

Climate signals in tree-ring δ18 O and δ13 C from southeastern Tibet: insights from observations and forward modelling of intra- to interdecadal variability.

Stable isotopes in tree rings are increasingly used as proxies for climatic and ecophysiological changes. However, uncertainties remain about the strength and consistency of their response to environmental variation at different temporal (i.e. seasonal to inter-decadal) scales. We developed 5 yr of intra-seasonal and 62 yr of early- and late-wood δ13 C and δ18 O series of Smith fir (Abies georgei var. smithii) on the southeastern Tibetan Plateau, and used a process-based forward model to examine the relative importance of environmental and physiological controls on the isotopic data. In this temperate high-altitude region, the response, both δ18 O and δ13 C, is primarily to variations in relative humidity, but by different processes. In δ18 O, the response is via source water δ18 O but also arises from leaf water 18 O enrichment. In δ13 C, the response is via changes in stomatal conductance but is modified by carry-over effects from prior periods. We conclude that tree-ring δ18 O may be a more robust climate proxy than δ13 C, and δ13 C may be more suited to studies of site-related physiological responses to the local environment.

Fine mapping of BH1, a gene controlling lemma and palea development in rice.

KEY MESSAGE: A new rice floral organ mutant bh1 , had a negative effect on grain yield. BH1 was fine mapped to 87.5 kb on chr2. A 55 kb chromosome segment was deleted in bh1. The cereal spikelet is enclosed by the lemma and palea. The lemma and palea of the floral mutant designated bh1, a selection from a T-DNA library generated from the rice cultivar Asominori, takes on an abnormal curve-shaped appearance only late in floral development, finally forming a beak-shaped hull. The mutation had a negative effect on thousand grain weight, seed set rate and germination rate. Genetic analysis indicated that the mutant phenotype was determined by a single recessive gene. Through map-based approach, BH1 gene was finally located to a ~87.5-kbp region on the long arm of chromosome 2. An analysis of the gene content of this region indicated that the mutation involves the loss of a 55-kbp stretch, harboring four open reading frames. Transcription profiling based on qRT-PCR revealed that the genes OsMADS1, OsMADS14, OsMADS15, OsMADS18, REP1, CFO1, and DL, all of which are also involved in lemma and palea development and identity specification, were down-regulated in the bh1 mutant. BH1 is therefore an important floral organ development gene.

Effects of biochar on the growth of Vallisneria natans in surface flow constructed wetland.

To improve the nitrogen and phosphorus removal efficiency of surface flow constructed wetlands (SFCWs), biochar was added to an SFCW matrix. The effects of adding different amounts of biochar on water purification, the growth of Vallisneria natans (V. natans), and microbial mechanisms were explored through SFCW simulation experiments. The results showed that through the joint action of biochar and V. natans, the concentrations of total nitrogen, total phosphorus, and ammonia nitrogen in the effluent significantly decreased. The total biomass, relative growth rate, and chlorophyll content of V. natans were significantly reduced by adding biochar (≥20%, v/v), as the root activity and the root to leaf biomass ratio slightly increased at first and then decreased. The carbon and nitrogen contents of V. natans slightly increased with the addition of biochar (≥10%, v/v), but the phosphorus content slightly decreased. Moreover, the nitrogen content of the matrices decreased significantly over time (P<0.05), and the phosphorus content in the matrix showed an increasing trend in the same period. In addition, the microbial 16S rDNA sequencing results indicated that the diversity and abundance of the microbial community in the matrix of the biochar-added SFCW tended to decrease. Nevertheless, the abundance of functional bacteria related to nitrogen and phosphorus removal (i.e., Pseudomonas and Dechloromonas) slightly increased, which would benefit denitrification and dephosphorization in the SFCW. Hence, the addition of biochar to the SFCW matrix facilitated the improvement of effluent water quality, while excessive biochar addition (≥10%, v/v) restrained the growth of V. natans but did not cause death. This conclusion provides valid data support regarding the ability of biochar-added SFCW to purify lightly contaminated water.

Warming and CO2 enrichment modified the ecophysiological responses of Dahurian larch and Mongolia pine during the past century in the permafrost of northeastern China.

Tree-ring δ13C and δ18O of dominant Dahurian larch and Mongolia pine in the permafrost region of the northern Great Higgnan Mountains, China were used to elucidate species-specific ecophysiological responses to warming temperatures and increasing CO2 over the past century. Larch and pine stable carbon discrimination (Δ13C) 13C and δ18O in tree rings both showed synchronous changes during the investigated period (1901-2010), but with species-specific isotopic responses to atmospheric enriched CO2 and warming. Tree-ring Δ13C and δ18O were controlled by both maximum temperature and moisture conditions (precipitation, relative humidity and vapor pressure deficit), but with different growth periods (Δ13C in June-July and δ18O in July-August, respectively). In addition, stable isotopes of larch showed relatively greater sensitivity to moisture deficits than pine. Climatic conditions from 1920 to 1960 strongly and coherently regulated tree-ring Δ13C and δ18O through stomatal conductance. However, climatic-sensitivities of tree-ring Δ13C and δ18O recently diverged, implying substantial adjustments of stomatal conductance, photosynthetic rate and altered water sources over recent decades, which reveal the varied impacts of each factor on tree-ring Δ13C and δ18O over time. Based on expected changes in leaf gas-exchange, we isolated the impacts of atmospheric CO2 and climate change on intrinsic water-use efficiency (iWUE) over the past century. Higher intracellular CO2 in pine than larch from 1960 onwards suggests this species may be more resilient to severe droughts in the future. Our data also illustrated no weakening of the iWUE response to increasing CO2 in trees from this permafrost region. The overall pattern of CO2 enrichment and climate impacts on iWUE of pine and larch were similar, but warming increased iWUE of larch to a greater extent than that of pine over recent two decades. Taken together, our findings highlight the importance of considering how leaf gas-exchange responses to atmospheric CO2 concentration influence species-specific responses to climate and the alteration of the hydrological environment in forests growing in regions historically dominated by permafrost that will be changing rapidly in response to future warming and increased CO2.

Elevation-dependent variations of tree growth and intrinsic water-use efficiency in Schrenk spruce (Picea schrenkiana) in the western Tianshan Mountains, China.

Rising atmospheric CO2 concentration (C a) is expected to accelerate tree growth by enhancing photosynthesis and increasing intrinsic water-use efficiency (iWUE). However, the extent of this effect on long-term iWUE and its interactions with climate remains unclear in trees along an elevation gradient. Therefore, we investigated the variation in the radial growth and iWUE of mature Picea schrenkiana trees located in the upper tree-line (A1: 2700 m a.s.l.), middle elevation (A2: 2400 m a.s.l.), and lower forest limit (A3: 2200 m a.s.l.), in relation to the rising C a and changing climate in the Wusun Mountains of northwestern China, based on the basal area increment (BAI) and tree-ring δ(13)C chronologies from 1960 to 2010. We used the CRU TS3.22 dataset to analyze the general response of tree growth to interannual variability of regional climate, and found that BAI and δ(13)C are less sensitive to climate at A1 than at A2 and A3. The temporal trends of iWUE were calculated under three theoretical scenarios, as a baseline for interpreting the observed gas exchange at increasing C a. We found that iWUE increased by 12-32% from A1 to A3 over the last 50 years, and showed an elevation-dependent variation in physiological response. The significant negative relationship between BAI and iWUE at A2 and A3 showed that tree growth has been decreasing despite long-term increases in iWUE. However, BAI remained largely stable throughout the study period despite the strongest iWUE increase [at constant intercellular CO2 concentration (C i) before 1980] at A1. Our results indicate a drought-induced limitation of tree growth response to rising CO2 at lower elevations, and no apparent change in tree growth and diminished iWUE improvement since 1980 in the upper tree-line. This study may contradict the expectation that combined effects of elevated C a and rising temperatures have increased forest productivity, especially in high-elevation forests.

Pooled versus separate tree-ring δD measurements, and implications for reconstruction of the Arctic Oscillation in northwestern China.

Stable hydrogen isotope ratios (δD) in tree rings are an attractive but still rarely explored terrestrial archive of past climatic information. Because the preparation of the cellulose nitrate for δD measurements requires more wood and a longer preparation time than preparation techniques for other isotopes in cellulose (δ18O or δ13C), it is challenging to obtain high-resolution records, especially for slow-growing trees at high elevations and in boreal regions. Here, we tested whether annually pooled samples of Qinghai spruce (Picea crassifolia Kom.) trees from northwestern China provided results similar to those derived as the mean of individual measurements of the same trees and whether the resulting chronologies recorded useful climate information. Inter-tree variability of δD was higher than that of measured ring width for the same trees. We found higher and significant coherence between pooled and mean isotope chronologies than that among the individual series. It showed a logarithmic relationship between ring mass and δD; however, accounting for the influence of ring mass on δD values only slightly improved the strength of climatic signals in the pooled records. Tree-ring δD was significantly positively correlated with the mean, maximum, and minimum temperatures during the previous winter and with maximum temperature during the current August, and significantly negatively correlated with precipitation in the previous November to January and the current July. The winter climate signal seems to dominate tree-ring δD through the influence of large-scale atmospheric circulation patterns, i.e. the Arctic Oscillation. These results will facilitate reconstruction of winter atmospheric circulation patterns over northwestern China based on a regional tree-ring δD networks.

Tree growth and intrinsic water-use efficiency of inland riparian forests in northwestern China: evaluation via δ13C and δ18O analysis of tree rings.

The rising atmospheric CO2 concentration (Ca) has increased tree growth and intrinsic water-use efficiency (iWUE). However, the magnitude of this effect on long-term iWUE and whether this increase could stimulate the growth of riparian forests in extremely arid regions remain poorly understood. We investigated the relationship between growth [ring width; basal area increment (BAI)] and iWUE in a riparian Populus euphratica Oliv. forest to test whether growth was enhanced by increasing CO2 and whether this compensated for environmental stresses in the lower reaches of the inland Heihe River, northwestern China. We accomplished this using dendrochronological methods and carbon (δ(13)C) and oxygen (δ(18)O) isotopic analysis. We found an increase in BAI before 1958, followed by a decrease from 1958 to 1977 and an increase to a peak around 2000. Tree-ring carbon discrimination (Δ) and δ(18)O indicated significant negative overall trends from 1920 to 2012. However, the relationship shifted in strength and direction around 1977 from significantly negative to a weak connection. The seasonal minimum temperature in April to July showed strong influence on Δ, and δ(18)O was controlled by relative humidity (negatively correlated) and temperature (positively correlated) in June and July. The patterns of internal to atmospheric CO2 (Ci/Ca) suggest a specific adaptation of tree physiology to increasing CO2. Intrinsic water-use efficiency increased significantly (by 36.4%) during the study period. The increased iWUE explained 19.8 and 39.1% of the observed yearly and high-frequency (first-order difference) variations in BAI, respectively, after 1977. Our results suggest significant CO2 stimulation of riparian tree growth, which compensated for the negative influences of reductions in river streamflow and a drying climate during the study period.