Metabolomic analysis reveals metabolites and pathways involved in grain quality traits of high-quality rice cultivars under a dry cultivation system
Introduction
Rice (Oryza sativa L.), the most important staple food worldwide, provides approximately 20% of the daily calorie intake for nearly half of the world’s population (Zheng et al., 2018). However, labour shortages, low water availability and poor land-use practices are challenging rice cultivation systems, especially in the middle and lower reaches of the Yangtze River, China (Ye et al., 2013). To counteract these challenges, rice dry cultivation (which relies on direct mechanical or manual seeding with −10 ± 5 kPa of soil water potential and then depends on rainfall) was introduced for greater water productivity, lower input costs and minimal environmental impacts without dramatically sacrificing yields (Raj et al., 2017). Currently, scientists and breeders are also increasingly concerned with the quality improvement of rice for different purposes and markets (Chen, Wang, & Ouwerkerk, 2012). However, there are still major conflicts between grain quality (processing, appearance and nutritional quality) and resource (including water resource) utilization efficiency in rice dry cultivation systems, posing great challenges to the improvement of grain quality under this cultivation mode.
It is generally considered difficult to improve rice quality, including processing, appearance, nutritional, and cooking qualities (Zhang et al., 2008; Chen et al., 2012; Zheng et al., 2018). Rice quality traits are not only determined by genetic factors but are also affected by changes in starch, proteins, lipids and interactions among them under environmental stresses (Chang et al., 2010, Chen et al., 2012). In addition, the biological activities of the chemical components of the rice grains, including low molecular weight primary and secondary metabolites, also have obvious impacts on rice quality (nutritional and appearance qualities) (Hu et al., 2014, Lin et al., 2017). Thus, to improve the grain quality achieved with dry cultivation, studies should focus not only on the composition of starch, proteins and lipids but also on the metabolomics of rice grains. Metabolomic approaches have yielded new insights into the components of grain metabolism in different rice cultivars (Chen et al., 2013), such as the correlations between the metabolic phenotypes and geographic origins of japonica and indica rice (Hu et al., 2014), to explain the yield formation of transgenic rice cultivars under drought stress (Nam et al., 2016), to distinguish the grain filling-related metabolic differences of different cultivars under high temperature (Yamakawa & Hakata, 2010) and to increase the bioactive compounds in cooked rice (Heuberger et al., 2010, Lin et al., 2017). In addition, metabolomics was also used to examine traits related to rice quality. For example, phenolic and shikimic acids content were used to predict food quality and identify the links among metabolites in complex biological systems (Kim, Park, Lim, Yeo, & Cho, 2013), and metabolomic analysis was performed to explain the mechanism of rice whiteness index formation, showing that chalky endosperm was related to a reduction in the metabolites related to carbon and nitrogen metabolism involved in the synthesis of storage starch and proteins (Lin et al., 2017). Metabolomic analysis of cooked rice showed that the total phenol and tocopherol concentrations influence the nutritional components in rice (Heuberger et al., 2010), and gamma-amino butyric acid, choline, glucosamine, azelaic acid, and lysine also contribute greatly to nutritional quality, while ketones, 2 acetyl-1-pyrroline, and cysteine largely determine taste quality (Calingacion, Boualaphanh, Daygon, Anacleto, & Hamilton, 2012). Thus, metabolomics may provide a meaningful method to explore the formation of rice quality under dry cultivation.
Recently, to optimize grain yield, high-yield rice cultivars and drought-resistant rice cultivars were used in dry cultivation (Zhang et al., 2009; Jérôme, Garyn, Rachid, Arvind, & Dean, 2010). Some high-yield rice cultivars (such as Huanghuazhan) and drought-resistant rice cultivars (such as Hanyou73) have higher grain quality (processing and appearance quality) under drought stress than other cultivars (Yang et al., 2009; C. Chen, Huang, & Zhu, 2013, Chen et al., 2012). We hypothesized that the metabolites and metabolic pathways involved in rice grains could play biological and chemical roles to contribute to the head rice yield, whiteness index, protein content, amylose content and pasting traits in high-yield or drought-resistant rice cultivars under dry cultivation. Thus, in this study, a metabolomic analysis of rice grains was performed to reveal the relationship of metabolic pathways or metabolites with the head rice yield, whiteness index, protein content, amylose content, breakdown value, setback value and gelatinization temperature in high-yield or drought-resistant rice cultivars under dry cultivation systems.
Section snippets
Study site
The experiments were conducted in 2017 at the research farm of Huazhong Agricultural University at Xiaowan Village (31°58′ N, 112°45′ E), Wudian Township, Zaoyang County, Hubei Province, China. The 0–40 cm soil layer was characterised by a clay loam texture, pH = 6.03, 39.84 g kg−1 of organic matter, 1.32 mg kg−1 of total N, 8.25 mg kg−1 of available phosphorus and 90 mg kg−1 of available potassium. The soil had a bulk density of 1.15 g cm−3, and the water table depth was 120 cm below the soil
Effects of water treatments and varieties on rice grain quality traits
Rice dry cultivation significantly (P < 0.05) increased the whiteness index and amylose content (Table 1) but decreased (P < 0.05) the setback value, gelatinization temperature and protein content compared with the flooding irrigation treatment. This result indicated that dry rice cultivation reduced the appearance (including whiteness index), processing (including head rice yield), nutritional (including protein content and amylose content) and cooking qualities of rice (including breakdown
Conclusions
The use of high-yield and high-quality rice cultivars under dry cultivation (DHH) could result in better processing, appearance, cooking, and nutritional qualities of rice. These traits are associated with certain metabolites and metabolic pathways. DHH decreased the stress-responsive, antioxidant, and anti-adversity capabilities (m72, m98, m127, m165, m167, m213, m297, m298) but maintained certain levels of stress resistance (m29, m30, m39, m48, and m58) to aid in cell regeneration and
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgements
This study was funded by the State Key Special Program (2017YFD0301400) and National Natural Science Foundation of China (31801291).
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These authors equally contributed to this work.