2024 Vol. 23 No. 02 Previous Issue   
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Special Focus: Transforming agri-food systems for multiple wins in nutrition, inclusion and environ
Transforming agri-food systems for multiple wins in nutrition, inclusion and environment
Shenggen Fan, Qiran Zhao, Jingjing Wang
2024, 23(02): 355-358.  DOI: 10.1016/j.jia.2024.01.017
Abstract ( )   PDF in ScienceDirect  

The call for agri-food system transformation is urgent in many global development agendas (UN 2023).  Food systems have contributed to economic prosperity and feeding the world, but they are also associated with numerous challenges, including climate change, continued hunger, poor diets and malnutrition, and increasing disparities (Webb et al. 2020; Fanzo et al. 2021).  The vulnerabilities of food systems have been further aggravated by the COVID-19 pandemic, geopolitical disruptions, extreme weather events, and economic uncertainties (IPCC 2023; FAO 2023).  The rapid population growth, urbanization and industrialization have also resulted in significant land and water resource pressures, as well as food safety and security in many developing countries.

Thus, the agri-food systems transformation should shift from addressing singular dimension (e.g., grain supply or grain self-sufficiency) to achieving multiple goals simultaneously, including nutrition, health, inclusion, environmental sustainability and climate change (Fan et al. 2021). 

There are several strategies that can be used for achieving these multiple goals including access to modern technologies such as internet, changing production structure, promoting more stable and resilient income for farmers, implementing social programs to protect vulnerable population, and of course continued technological and productivity improvement .

Under this context, this special focus of the Journal of Integrative Agriculture is to provide empirical evidence on multiple win strategies to achieve agri-food systems transformation.  The issue comprises nine papers covering a wide array of topics aimed at improved nutrition, sustainability inclusion and continued efficiency or productivity improvement within the food systemWe trust that these papers will enhance readers’ comprehension of how food system transformation can contribute to multiple dimensions of the food system’s goals.

Section 1: Nutrition
Off-farm employment, agriculture production activities, and household dietary diversity in environmentally and economically vulnerable areas of Asia
Yunli Bai, Xuanye Zeng, Chao Fu, Linxiu Zhang
2024, 23(02): 359-373.  DOI: 10.1016/j.jia.2023.11.016
Abstract ( )   PDF in ScienceDirect  

Access to off-farm employment has been expected to be a critical approach to ending hunger and all forms of malnutrition, two important targets of achieving Zero Hunger.  This study aims to investigate the role of off-farm employment in improving dietary diversity through substitution effect and complementary effect with agricultural production activities and income effect.  This study adopts Poisson/Tobit/Probit/OLS regressions and the instrument variable method based on the primary survey data collected among 1,282 households at 12 sites in environmentally and economically vulnerable areas of China, Nepal, Cambodia, Thailand, and Myanmar in 2019.  The results show that off-farm employment is positively associated with household dietary diversity and the consumption of flesh meat, fish and other aquatic animals, fruits, and milk and dairy products, which are rich in protein and micronutrients.  The results of mechanism analysis show that off-farm employment contributes to household dietary diversity by improving crop diversity, especially for poor households, boosting the probability of livestock raising for households with the middle one-third disposal income, and increasing household income.  The positive association between off-farm employment and household dietary diversity is much higher for households with the bottom one-third disposal income, low illiteracy, and from upper-middle income countries.  These findings imply that off-farm employment does play a vital role in achieving multiple benefits of poverty alleviation, malnutrition reduction, and agrobiodiversity conservation in environmentally and economically vulnerable areas.  However, it may enlarge the gaps in dietary diversity between households with low human capital and from low and lower-middle income countries and those with high human captal and from middle-high countries.

The impact of Internet access on household dietary quality: Evidence from rural China
Yi Cui, Qiran Zhao, Thomas Glauben, Wei Si
2024, 23(02): 374-383.  DOI: 10.1016/j.jia.2023.11.014
Abstract ( )   PDF in ScienceDirect  

Over the past few decades, the Internet has rapidly diffused across China.  The spread of the Internet has had a profound economic and social impact on Chinese rural areas.  Existing research shows that Internet access significantly impacts agricultural production and improves smallholder farmers’ income.  Beyond these, the Internet can affect other dimensions of social welfare.  However, research about the impact of Internet access on dietary quality in rural China remains scarce.  This study utilizes multi-period panel data from Fixed Observation Point in rural China from 2009 to 2015 to estimate the impact of Internet access on dietary quality and food consumption of rural households and conducts a causal analysis.  Regression models with time and household fixed effects allow robust estimation while reducing potential issues of unobserved heterogeneity.  The estimates show that Internet access has significantly increased rural household dietary quality (measured by the Chinese Diet Balance Index).  Further research finds that Internet access has increased the consumption of animal products, such as aquatic and dairy products.  We also examine the underlying mechanisms.  Internet access improves dietary quality and food consumption mainly through increasing household income and food expenditure.  These results encourage the promotion of Internet access as a valuable tool for nutritional improvements, especially in rural areas. 

Resilience effects for household food expenditure and dietary diversity in rural western China

Xiao Han, Kaiyu Lyu, Fengying Nie, Yuquan Chen
2024, 23(02): 384-396.  DOI: 10.1016/j.jia.2023.12.010
Abstract ( )   PDF in ScienceDirect  

A more resilient livelihood is increasingly recognized as an efficient way to improve vulnerable households’ food security and optimize their dietary decisions.  This study quantifies rural household resilience in western China, identifies the three pillars (absorptive capacity, adaptive capacity, and transformative capacity) contribution to resilience, and then establishes the estimated Resilience Capacity Index (RCI) linked with food security and dietary diversity supported by the multiple indicator multiple cause (MIMIC) model.  Results show that, despite geographical heterogeneity, the RCI consistently increased from 2015 to 2021.  Households with a higher RCI inheriting better capacity to deal with risk and shocks are significantly and positively correlated with increasing food expenditure and diversifying food choices.  It can be because resilient households will allocate more money to food expenditure instead of saving for livelihood uncertainty.  Thus, policymakers can provide more incentives for rural households to adopt more dynamic and effective risk management strategies.  This, in turn, could yield positive spillover effects by preventing human capital loss associated with dietary-related chronic diseases and mortality.

Nutrition impacts of non-solid cooking fuel adoption on under-five children in developing countries

Yalin Tang, Yuhe Guo, Gang Xie, Chengfang Liu
2024, 23(02): 397-413.  DOI: 10.1016/j.jia.2023.11.032
Abstract ( )   PDF in ScienceDirect  

This paper examines the nutrition impacts of using non-solid cooking fuel on under-five children in developing countries.  We draw on data from more than 1.12 million children in 62 developing countries from the Demographic and Health Surveys (DHS).  Results from both fixed effects (FE) and instrumental variable (IV) estimates show that using non-solid cooking fuel significantly improves the nutrition outcomes of under-five children.  Compared with their peers from households mainly using solid fuel, children from households mainly using non-solid fuel exhibit a lower probability of experiencing stunting (by 5.9 percentage points) and being underweight (by 1.2 percentage points).  Our further investigation provides evidence for several underlying mechanisms, such as improved indoor air quality, induced reduction in children’s respiratory symptoms, benefits on maternal health, and reduction in maternal time spent on fuel collection or cooking.  Heterogenous analyses suggest that the nutrition benefits of using non-solid cooking fuel are more prominent among boys, children above three years old, and those from households of lower socioeconomic status, rural areas, and Southeast Asia.

Section 2: Sustainability

The impact of demographic dynamics on food consumption and its environmental outcomes: Evidence from China

Shaoting Li, Xuan Chen, Yanjun Ren, Thomas Glauben
2024, 23(02): 414-429.  DOI: 10.1016/j.jia.2023.11.017
Abstract ( )   PDF in ScienceDirect  


With increasing population and changing demographics, food consumption has experienced a significant transition in quantity and quality.  However, a dearth of knowledge remains regarding its environmental impacts and how it responds to demographic dynamics, particularly in emerging economies like China.  Using the two-stage Quadratic Almost Demand System (QUAIDS) model, this study empirically examines the impact of demographic dynamics on food consumption and its environmental outcomes based on the provincial data from 2000 to 2020 in China.  Under various scenarios, according to changes in demographics, we extend our analysis to project the long-term trend of food consumption and its environmental impacts, including greenhouse gas (GHG) emissions, water footprint (WF), and land appropriation (LA).  The results reveal that an increase in the proportion of senior people significantly decreases the consumption of grain and livestock meat and increases the consumption of poultry, egg, and aquatic products, particularly for urban residents.  Moreover, an increase in the proportion of males in the population leads to higher consumption of poultry and aquatic products.  Correspondingly, in the current scenario of an increased aging population and sex ratio, it is anticipated that GHG emissions, WF, and LA are likely to decrease by 1.37, 2.52, and 3.56%, respectively.  More importantly, in the scenario adhering to the standards of nutritional intake according to the Dietary Guidelines for Chinese Residents in 2022, GHG emissions, WF, and LA in urban areas would increase by 12.78, 20.94, and 18.32%, respectively.  Our findings suggest that changing demographics should be considered when designing policies to mitigate the diet-environment-health trilemma and achieve sustainable food consumption.


Repositioning fertilizer manufacturing subsidies for improving food security and reducing greenhouse gas emissions in China

Zongyi Wu, Xiaolong Feng, Yumei Zhang, Shenggen Fan
2024, 23(02): 430-443.  DOI: 10.1016/j.jia.2023.12.007
Abstract ( )   PDF in ScienceDirect  

China removed fertilizer manufacturing subsidies from 2015 to 2018 to bolster market-oriented reforms and foster environmentally sustainable practices.  However, the impact of this policy reform on food security and the environment remains inadequately evaluated.  Moreover, although green and low-carbon technologies offer environmental advantages, their widespread adoption is hindered by prohibitively high costs.  This study analyzes the impact of removing fertilizer manufacturing subsidies and explores the potential feasibility of redirecting fertilizer manufacturing subsidies to invest in the diffusion of these technologies.  Utilizing the China Agricultural University Agri-food Systems model, we analyzed the potential for achieving mutually beneficial outcomes regarding food security and environmental sustainability.  The findings indicate that removing fertilizer manufacturing subsidies has reduced greenhouse gas (GHG) emissions from agricultural activities by 3.88 million metric tons, with minimal impact on food production.  Redirecting fertilizer manufacturing subsidies to invest in green and low-carbon technologies, including slow and controlled-release fertilizer, organic–inorganic compound fertilizers, and machine deep placement of fertilizer, emerges as a strategy to concurrently curtail GHG emissions, ensure food security, and secure robust economic returns.  Finally, we propose a comprehensive set of government interventions, including subsidies, field guidance, and improved extension systems, to promote the widespread adoption of these technologies.

Section 3: Inclusion

The impact of the Rural Minimum Living Standard Guarantee (Rural Dibao) Program on child nutrition outcomes

Dian Chen, Xiangming Fang, Yu Chen, Xiaodong Zheng, Zhuo Chen, Rodney B.W. Smith
2024, 23(02): 444-456.  DOI: 10.1016/j.jia.2023.11.020
Abstract ( )   PDF in ScienceDirect  

The Rural Minimum Living Standard Guarantee (Rural Dibao) is an important unconditional cash transfer program to alleviate poverty in rural China.  Despite the importance of children’s nutrition in breaking poverty cycles, little is known about the impact of Rural Dibao on child nutrition outcomes.  Using China Family Panel Studies (CFPS), this paper examines the effects of Rural Dibao on child nutrition outcomes and investigates potential pathways and heterogeneous effects.  We exploit propensity score matching and difference-in-differences techniques to evaluate the effects of the Rural Dibao program on child nutrition outcomes.  Our results suggest that Rural Dibao significantly impacts the nutrition outcomes of children up to 15 years of age.  Specifically, our results suggest that Rural Dibao improves child height-to-age z-scores by 1.05 standard deviations and lowers the probability of stunting by 11.9 percentage points.  Additional analyses suggest that increased protein intake is the main pathway through which Rural Dibao participation contributes to better nutrition outcomes.  We also find that the effect of the program is more pronounced among girls, children who are non-left-behind or live with highly educated mothers, and those from low-income families and poor areas.  Our findings suggest that Rural Dibao participation helps improve child nutrition outcomes through improving diet quality.

Women’s empowerment and food consumption: Evidence from female-headed households in Tanzania

Mosses Lufuke, Xu Tian
2024, 23(02): 457-467.  DOI: 10.1016/j.jia.2023.12.005
Abstract ( )   PDF in ScienceDirect  

Despite the growing recognition of women’s increasing role in the household and corresponding empowerment programs in sub-Saharan Africa, intensive research on the relationship between women’s influence and household food consumption is minimal.  Using the most recent (2017–2018) national household survey data from Tanzania, this study examined the influence of women’s empowerment on household food consumption.  First, we compared the monthly consumption of eight food categories between female-headed households (FHHs) and male-headed households (MHHs) using both descriptive statistics and the propensity score matching (PSM) method.  Furthermore, we adopted the two-stage Linear Expenditure System and Almost Ideal Demand System model (LES-AIDS) to estimate income and price elasticities for the two household types.  The results show that FHHs consume bread and cereals, fish, oils and fats, vegetables, and confectionery (sugar, jam, honey, chocolate, etc.) more than MHHs.  Moreover, FHHs have a significantly higher income elasticity of demand for all food groups than MHHs.  They are also more price elastic than MHHs in meat, fish, oils, fats, sugar, jam, honey, chocolate, etc.

Section 4: Efffciency

Winter wheat yield improvement by genetic gain across different provinces in China

Wei Chen, Jingjuan Zhang, Xiping Deng
2024, 23(02): 468-483.  DOI: 10.1016/j.jia.2023.11.015
Abstract ( )   PDF in ScienceDirect  
The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide, with remarkable progress in China.  Drawing on two sets of data, production yield from the National Bureau of Statistics of China and experimental yield from literature, this study aims to (1) illustrate the increasing patterns of production yield among different provinces from 1978 to 2018 in China, (2) explore the genetic gain in yield and yield relevant traits through the variety replacement based on experimental yield from 1937 to 2016 in China, and (3) compare the yield gap between experimental yield and production yield.  The results show that both the production and experimental yields significantly increased along with the variety replacement.  The national annual yield increase ratio for the production yield was 1.67% from 1978 to 2018, varying from 0.96% in Sichuan Province to 2.78% in Hebei Province; such ratio for the experimental yield was 1.13% from 1937 to 2016.  The yield gap between experimental and production yields decreased from the 1970s to the 2010s.  This study reveals significant increases in some yield components consequent to variety replacement, including thousand-grain weight, kernel number per spike, and grain number per square meter; however, no change is shown in spike number per square meter.  The biomass and harvest index consistently and significantly increased, whereas the plant height decreased significantly.
Crop Science

Creating large EMS populations for functional genomics and breeding in wheat

Wenqiang Wang, Xizhen Guan, Yong Gan, Guojun Liu, Chunhao Zou, Weikang Wang, Jifa Zhang, Huifei Zhang, Qunqun Hao, Fei Ni, Jiajie Wu, Lynn Epstein, Daolin Fu
2024, 23(02): 484-493.  DOI: 10.1016/j.jia.2023.05.039
Abstract ( )   PDF in ScienceDirect  

Wheat germplasm is a fundamental resource for basic research, applied studies, and wheat breeding, which can be enriched normally by several paths, such as collecting natural lines, accumulating breeding lines, and introducing mutagenesis materials.  Ethyl methane sulfonate (EMS) is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.  In this study, we created a million-scale EMS population (MEP) that started with the Chinese wheat cultivars ‘Luyan 128’, ‘Jimai 38’, ‘Jimai 44’, and ‘Shannong 30’.  In the M1 generation, the MEP had numerous phenotypical variations, such as >3,000 chlorophyll-deficient mutants, 2,519 compact spikes, and 1,692 male sterile spikes.  There were also rare mutations, including 30 independent tillers each with double heads.  Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable, appearing in the M2 or M3 generations.  To advance the entire MEP to higher generations, we adopted a single-seed descendent (SSD) approach.  All other seed composites of M2 were used to screen other agronomically important traits, such as the tolerance to herbicide quizalofop-P-methyl.  The MEP is available for collaborative projects, and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

Metabolic profiles and morphological characteristics of leaf tips among different sweet potato (Ipomoea batatas Lam.) varieties

Wenqing Tan, Xinbo Guo, Zhangying Wang, Rong Zhang, Chaochen Tang, Bingzhi Jiang, Ruixue Jia, Yuanyuan Deng, Shaohai Yang, Jingyi Chen
2024, 23(02): 494-510.  DOI: 10.1016/j.jia.2023.04.029
Abstract ( )   PDF in ScienceDirect  

Sweet potato leaf tips have high nutritional value, and exploring the differences in the metabolic profiles of leaf tips among different sweet potato varieties can provide information to improve their qualities.  In this study, a UPLC-Q-Exactive Orbitrap/MS-based untargeted metabolomics method was used to evaluate the metabolites in leaf tips of 32 sweet potato varieties.  Three varieties with distinct overall metabolic profiles (A01, A02, and A03), two varieties with distinct profiles of phenolic acids (A20 and A18), and three varieties with distinct profiles of flavonoids (A05, A12, and A16) were identified.  In addition, a total of 163 and 29 differentially expressed metabolites correlated with the color and leaf shape of sweet potato leaf tips, respectively, were identified through morphological characterization.  Group comparison analysis of the phenotypic traits and a metabolite-phenotypic trait correlation analysis indicated that the color differences of sweet potato leaf tips were markedly associated with flavonoids.  Also, the level of polyphenols was correlated with the leaf shape of sweet potato leaf tips, with lobed leaf types having higher levels of polyphenols than the entire leaf types.  The findings on the metabolic profiles and differentially expressed metabolites associated with the morphology of sweet potato leaf tips can provide useful information for breeding sweet potato varieties with higher nutritional value.

Regulation of 2-acetyl-1-pyrroline and grain quality in early-season indica fragrant rice by nitrogen and silicon fertilization under different plantation methods

Yongjian Chen, Lan Dai, Siren Cheng, Yong Ren, Huizi Deng, Xinyi Wang, Yuzhan Li, Xiangru Tang, Zaiman Wang, Zhaowen Mo
2024, 23(02): 511-535.  DOI: 10.1016/j.jia.2023.05.009
Abstract ( )   PDF in ScienceDirect  
Fragrant rice has a high market value, and it is a popular rice type among consumers owing to its pleasant flavor.  Plantation methods, nitrogen (N) fertilizers, and silicon (Si) fertilizers can affect the grain yield and fragrance of fragrant rice.  However, the core commercial rice production attributes, namely the head rice yield (HRY) and 2-acetyl-1-pyrroline (2-AP) content of fragrant rice, under various nitrogen and silicon (N-Si) fertilization levels and different plantation methods remain unknown.  The field experiment in this study was performed in the early seasons of 2018 and 2019 with two popular indica fragrant rice cultivars (Yuxiangyouzhan and Xiangyaxiangzhan).  They were grown under six N-Si fertilization treatments (combinations of two levels of Si fertilizer, 0 kg Si ha−1 (Si0) and 150 kg Si ha−1 (Si1), and three levels of N fertilizer, 0 kg N ha−1 (N0), 150 kg N ha−1 (N1), and 220 kg N ha−1 (N2)) and three plantation methods (artificial transplanting (AT), mechanical transplanting (MT), and mechanical direct-seeding (MD)).  The results showed that the N-Si fertilization treatments and all the plantation methods significantly affected the HRY and 2-AP content and related parameters of the two different fragrant rice cultivars.  Compared with the Si0N0 treatment, the N-Si fertilization treatments resulted in higher HRY and 2-AP contents.  The rates of brown rice, milled rice, head rice, and chalky rice of the fragrant rice also improved with the N-Si fertilization treatments.  The N-Si fertilization treatments increased the activities of N metabolism enzymes and the accumulation of N and Si in various parts of the fragrant rice, and affected their antioxidant response parameters.  The key parameters for the HRY and 2-AP content were assessed by redundancy analysis.  Furthermore, the structural equation model revealed that the Si and N accumulation levels indirectly affected the HRY by affecting the N metabolism enzyme activity, N use efficiency, and grain quality of fragrant rice.  Moreover, high N and Si accumulation directly promoted the 2-AP content or affected the antioxidant response parameters and indirectly regulated 2-AP synthesis.  The interactions of the MT method with the N-Si fertilization treatments varied in the fragrant rice cultivars in terms of the HRY and 2-AP content, whereas the MD method was beneficial to the 2-AP content in both fragrant rice cultivars under the N-Si fertilization treatments.

Night warming increases wheat yield by improving pre-anthesis plant growth and post-anthesis grain starch biosynthesis

Yonghui Fan, Boya Qin, Jinhao Yang, Liangliang Ma, Guoji Cui, Wei He, Yu Tang, Wenjing Zhang, Shangyu Ma, Chuanxi Ma, Zhenglai Huang
2024, 23(02): 536-550.  DOI: 10.1016/j.jia.2023.06.024
Abstract ( )   PDF in ScienceDirect  

Global climate change is characterized by asymmetric warming, i.e., greater temperature increases in winter, spring, and nighttime than in summer, autumn, and daytime.  Field experiments were conducted using four wheat cultivars, namely ‘Yangmai 18’ (YM18), ‘Sumai 188’ (SM188), ‘Yannong 19’ (YN19), and ‘Annong 0711’ (AN0711), in the two growing seasons of 2019–2020 and 2020–2021, with passive night warming during different periods in the early growth stage.  The treatments were night warming during the tillering–jointing (NWT–J), jointing–booting (NWJ–B), and booting–anthesis (NWB–A) stages, with ambient temperature (NN) as the control.  The effects of night warming during different stages on wheat yield formation were investigated by determining the characteristics of dry matter accumulation and translocation, as well as sucrose and starch accumulation in wheat grains.  The wheat yields of all four cultivars were significantly higher in NWT–J than in NN in the 2-year experiment.  The yield increases of semi-winter cultivars YN19 and AN0711 were greater than those of spring cultivars YM18 and SM188.  Treatment NWT–J increased wheat yield mainly by increasing the 1,000-grain weight and the number of fertile spikelets, and it increased dry matter accumulation in various organs of wheat at the anthesis and maturity stages by increasing the growth rate at the vegetative growth stage.  The flag leaf and spike showed the largest increases in dry matter accumulation.  NWT–J also increased the grain sucrose and starch contents in the early and middle grain-filling stages, promoting yield formation.  Overall, night warming between the tillering and jointing stages increased the pre-anthesis growth rate, and thus, wheat dry matter production, which contributed to an increase in wheat yield.

Timing effect of high temperature exposure on the plasticity of internode and plant architecture in maize

Binbin Li, Xianmin Chen, Tao Deng, Xue Zhao, Fang Li, Bingchao Zhang, Xin Wang, Si Shen, Shunli Zhou
2024, 23(02): 551-565.  DOI: 10.1016/j.jia.2023.07.003
Abstract ( )   PDF in ScienceDirect  

The occurrence of high temperature (HT) in crop production is becoming more frequent and unpredictable with global warming, severely threatening food security.  The state of an organ’s growth and development is largely determined by the temperature conditions it is exposed to over time.  Maize is the main cereal crop, and its stem growth and plant architecture are closely related to lodging resistance, and especially sensitive to temperature.  However, systematic research on the timing effect of HT on the sequentially developing internode and stem is currently lacking.  To identify the timing effect of HT on the morphology and plasticity of the stem in maize, two hybrids (Zhengdan 958 (ZD958), Xianyu 335 (XY335)) characterized by distinct morphological traits in the stem were exposed to a 7-day HT treatment from the V6 to V17 stages (Vn presents the vegetative stage with n leaves fully expanded) in 2019–2020.  The results demonstrated that exposure to HT during V6–V12 accelerated the rapid elongation of stems.  For instance, HT occurring at V7 and V12 specifically promoted the lengths and weights of the 3rd–5th and 9th–11th internodes, respectively.  Meanwhile, HT slowed the growth of internodes adjacent to the promoted internodes.  Interestingly, compared with control, the plant height was significantly increased soon after HT treatment, but the promotion effect became narrower at the subsequent flowering stage, demonstrating a self-adjusting mechanism in the maize plant in response to HT.  Importantly, HT altered the plant architectures, including a rising of the ear position and increase in the ear position coefficient.  XY335 exhibited greater sensitivity in stem development than ZD958 under HT treatment.  These findings improve our systematic understanding of the plasticity of internode and plant architecture in response to the timing of HT exposure.

Plant Protection

Prevalence and ecological factors affecting the distribution of plant-parasitic nematodes in Prunus groves in Spain

Ilenia Clavero-Camacho, Antonio Archidona-Yuste, Carolina Cantalapiedra-Navarrete, Pablo Castillo, Juan Emilio Palomares-Rius
2024, 23(02): 566-589.  DOI: 10.1016/j.jia.2023.02.033
Abstract ( )   PDF in ScienceDirect  
A wide survey was conducted to study plant-parasitic nematodes (PPNs) associated with Prunus groves in Spain.  This research aimed to determine the prevalence and distribution of PPNs in Prunus groves, as well as the influence of explanatory variables describing soil, climate and agricultural management in structuring the variation of PPNs community composition.  A total of 218 sampling sites were surveyed and 84 PPN species belonging to 32 genera were identified based of an integrative taxonomic approach.  PPN species considered as potential limiting factors in Prunus production, such as Meloidogyne arenaria, Mincognita, Mjavanica, Pratylenchus penetrans and Pvulnus, were identified in this survey.  Seven soil physico-chemical (C, Mg, N, Na, OM, P, pH and clay, loamy sand and sandy loam texture classes), four climate (Bio04, Bio05, Bio13 and Bio14) and four agricultural management variables (grove-use history less than 10 years, irrigation, apricot seedling rootstock, and Montclar rootstock) were identified as the most influential variables driving spatial patterns of PPNs communities.  In particular, younger plantations showed higher values for species richness and diversity indices than groves cultivated for more than 20 years with Prunus spp.  Our study increases the knowledge of the distribution and prevalence of PPNs associated with Prunus rhizosphere, as well as on the influence of explanatory variables driving the spatial structure PPNs communities, which has important implications for the successful design of sustainable management strategies in the future in this agricultural system.

The evolution and diurnal expression patterns of photosynthetic pathway genes of the invasive alien weed, Mikania micrantha

WANG Kang-kang, JIN Meng-jiao, LI Jing-jing, REN Ye-song, LI Zai-yuan, REN Xing-hai, HUANG Cong, WAN Fang-hao, QIAN Wan-qiang, LIU Bo
2024, 23(02): 590-604.  DOI: 10.1016/j.jia.2023.04.011
Abstract ( )   PDF in ScienceDirect  

Mikania micrantha is a fast-growing global invasive weed species that causes severe damage to natural ecosystems and very large economic losses of forest and crop production.  It has advantages in photosynthesis, including a similar net photosynthetic rate as C4 plants and a higher carbon fixation capacity.  We used a combination of genomics and transcriptomics approaches to study the evolutionary mechanisms and circadian expression patterns of Mmicrantha.  In Mmicrantha, 16 positive selection genes focused on photoreaction and utilization of photoassimilates.  In different tissues, 98.1% of the genes associated with photoresponse had high expression in stems, and more than half of the genes of the C4 cycle had higher expression in stems than in leaves.  In stomatal opening and closing, 2 genes of carbonic anhydrase (CAs) had higher expression at 18:00 than at 8:00, and the slow anion channel 1 (SLAC1) and high-leaf-temperature 1 kinase (HT1) genes were expressed at low levels at 18:00.  In addition, genes associated with photosynthesis had higher expression levels at 7:00 and 17:00.  We hypothesized that Mmicrantha may undergo photosynthesis in the stem and flower organs and that some stomata of the leaves were opening at night by CO2 signals.  In addition, its evolution may attenuate photoinhibition at high light intensities, and enhance more efficient of photosynthesis during low light intensity.  And the tissue-specific photosynthetic types and different diurnal pattern of photosynthetic-related genes may contribute to its rapid colonization of new habitats of Mmicrantha.

The role of cAMP-dependent protein kinase A in the formation of long-term memory in Bactrocera dorsalis

Jinxin Yu, Yanmin Hui, Jiayi He, Yinghao Yu, Zhengbing Wang, Siquan Ling, Wei Wang, Xinnian Zeng, Jiali Liu
2024, 23(02): 605-620.  DOI: 10.1016/j.jia.2023.07.016
Abstract ( )   PDF in ScienceDirect  

The cAMP-dependent protein kinase A (PKA) signaling pathway has long been considered critical for long-term memory (LTM) formation.  Previous studies have mostly focused on the role of PKA signaling in LTM induction by multiple spaced conditioning with less attention to LTM induction by a single conditioning.  Here, we conducted behavioral-pharmacology, enzyme immunoassay and RNA interference experiments to study the role of the PKA signaling pathway in LTM formation in the agricultural pest Bactrocera dorsalis, which has a strong memory capacity allowing it to form a two-day memory even from a single conditioning trial.  We found that either blocking or activating PKA prior to conditioning pretreatment affected multiple spaced LTM, and conversely, they did not affect LTM formed by single conditioning.  This was further confirmed by enzyme-linked immunosorbent assay (ELISA) and silencing of the protein kinase regulatory subunit 2 and catalytic subunit 1.  Taken together, these results suggest that activating PKA during memory acquisition helps to induce the LTM formed by multiple spaced conditioning but not by a single conditioning.  Our findings challenge the conserved role of PKA signaling in LTM, which provides a basis for the greater diversity of molecular mechanisms underlying LTM formation across species, as well as possible functional and evolutionary implications.

Synergistic effects of the entomopathogenic fungus Isaria javanica and low doses of dinotefuran on the efficient control of the rice pest Sogatella furcifera
Tingting Zhou, Qian Zhao, Chengzhou Li, Lu Ye, Yanfang Li, Nemat O. Keyhani, Zhen Huang
2024, 23(02): 621-638.  DOI: 10.1016/j.jia.2023.06.007
Abstract ( )   PDF in ScienceDirect  
The rice planthopper, Sogatella furcifera, is a piercing-sucking insect pest of rice, Oryza sativa.  It is responsible for significant crop yield losses, and has developed moderate to high resistance to several commonly used chemical insecticides.  We investigated the effects of the insect fungal pathogen Isaria javanica, alone and in combination with the chemical insecticide dinotefuran, on Sfurcifera under both laboratory and field conditions.  Our results show that Ijavanica displays high infection efficiency and mortality for different stages of Sfurcifera, reducing adult survival, female oviposition and ovary development.  Laboratory bioassays showed that the combined use of Ijavanica with a low dose (4–16 mg L–1) of dinotefuran resulted in higher mortality in Sfurcifera than the use of Ijavanica or dinotefuran alone.  The combined treatment also had more significant effects on several host enzymes, including superoxide dismutase, catalase, peroxidase, and prophenol oxidase activities.  In field trials, Ijavanica effectively suppressed populations of rice planthoppers to low levels (22–64% of the level in untreated plots).  Additional field experiments showed synergistic effects, i.e., enhanced efficiency, for the control of Sfurcifera populations using the combination of a low dose of Ijavanica (1×104 conidia mL–1) and a low dose of dinotefuran (~4.8–19.2% of normal field use levels), with control effects of >90% and a population level under 50 insects per 100 hills at 3–14 days post-treatment.  Our findings indicate that the entomogenous fungus Ijavanica offers an attractive biological control addition as part of the integrated pest management (IPM) practices for the control of rice plant pests.
Animal Science · Veterinary Medicine

Evaluating the performance of genomic selection on purebred population by incorporating crossbred data in pigs

Jun Zhou, Qing Lin, Xueyan Feng, Duanyang Ren, Jinyan Teng, Xibo Wu, Dan Wu, Xiaoke Zhang, Xiaolong Yuan, Zanmou Chen, Jiaqi Li, Zhe Zhang, Hao Zhang
2024, 23(02): 639-648.  DOI: 10.1016/j.jia.2023.09.004
Abstract ( )   PDF in ScienceDirect  
Genomic selection (GS) has been widely used in livestock, which greatly accelerated the genetic progress of complex traits.  The population size was one of the significant factors affecting the prediction accuracy, while it was limited by the purebred population.  Compared to directly combining two uncorrelated purebred populations to extend the reference population size, it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.  In this study, we simulated purebred offspring (PAS and PBS) and crossbred offspring (CAB) base on real genotype data of two base purebred populations (PA and PB), to evaluate the performance of genomic selection on purebred while incorporating crossbred information.  The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship (REL) was better than the other methods (individuals closet or farthest to the purebred population, CP/FP) in term of the prediction accuracy.  Furthermore, the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA, which was similar to combine PA and PAS.  Moreover, the rank correlation between the multiple of the increased relationship (MIR) and reliability improvement was 0.60–0.70.  But for individuals with low correlation (Cor(Pi, PA or B), the reliability improvement was significantly lower than other individuals.  Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.  The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.

The virulence regulator AbsR in avian pathogenic Escherichia coli has pleiotropic effects on bacterial physiology

Dongfang Zhao, Haobo Zhang, Xinyang Zhang, Fengwei Jiang, Yijing Li, Wentong Cai, Ganwu Li
2024, 23(02): 649-668.  DOI: 10.1016/j.jia.2023.07.035
Abstract ( )   PDF in ScienceDirect  

Avian pathogenic Escherichia coli (APEC) belonging to extraintestinal pathogenic Ecoli (ExPEC) can cause severe infections in extraintestinal tissues in birds and humans, such as the lungs and blood.  MprA (microcin production regulation, locus A, herein renamed AbsR, a blood survival regulator), a member of the MarR (multiple antibiotic resistance regulator) transcriptional regulator family, governs the expression of capsule biosynthetic genes in human ExPEC and represents a promising druggable target for antimicrobials.  However, a deep understanding of the AbsR regulatory mechanism as well as its regulon is lacking.  In this study, we present a systems-level analysis of the APEC AbsR regulon using ChIP-Seq (chromatin immunoprecipitation sequencing) and RNA-Seq (RNA sequencing) methods.  We found that AbsR directly regulates 99 genes and indirectly regulates 667 genes.  Furthermore, we showed that: 1) AbsR contributes to antiphagocytotic effects by macrophages and virulence in a mouse model for systemic infection by directly activating the capsular gene cluster; 2) AbsR positively impacts biofilm formation via direct regulation of the T2SS (type II secretion system) but plays a marginal role in virulence; and 3) AbsR directly upregulates the acid tolerance signaling system EvgAS to withstand acid stress but is dispensable in ExPEC virulence.  Finally, our data indicate that the role of AbsR in virulence gene regulation is relatively conserved in ExPEC strains.  Altogether, this study provides a comprehensive analysis of the AbsR regulon and regulatory mechanism, and our data suggest that AbsR likely influences virulence primarily through the control of capsule production.  Interestingly, we found that AbsR severely represses the expression of the type I-F CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) systems, which could have implications in CRISPR biology and application.

Agro-ecosystem & Environment

Straw return increases crop production by improving soil organic carbon sequestration and soil aggregation in a long-term wheat–cotton cropping system

Changqin Yang, Xiaojing Wang, Jianan Li, Guowei Zhang, Hongmei Shu, Wei Hu, Huanyong Han, Ruixian Liu, Zichun Guo
2024, 23(02): 669-679.  DOI: 10.1016/j.jia.2023.06.009
Abstract ( )   PDF in ScienceDirect  

Straw return is a promising strategy for managing soil organic carbon (SOC) and improving yield stability.  However, the optimal straw return strategy for sustainable crop production in the wheat (Triticum aestivum L.)–cotton (Gossypium hirsutum L.) cropping system remains uncertain.  The objective of this study was to quantify the long-term (10 years) impact of carbon (C) input on SOC sequestration, soil aggregation and crop yields in a wheat–cotton cropping system in the Yangtze River Valley, China.  Five treatments were arranged with a single-factor randomized design as follows: no straw return (Control), return of wheat straw only (Wt), return of cotton straw only (Ct), return of 50% wheat and 50% cotton straw (Wh-Ch) and return of 100% wheat and 100% cotton straw (Wt-Ct).  In comparison to the Control, the SOC content increased by 8.4 to 20.2% under straw return.  A significant linear positive correlation between SOC sequestration and C input (1.42–7.19 Mg ha−1 yr−1) (P<0.05) was detected.  The percentages of aggregates of sizes >2 and 1–2 mm at the 0–20 cm soil depth were also significantly elevated under straw return, with the greatest increase of the aggregate stability in the Wt-Ct treatment (28.1%).  The average wheat yields increased by 12.4–36.0% and cotton yields increased by 29.4–73.7%, and significantly linear positive correlations were also detected between C input and the yields of wheat and cotton.  The average sustainable yield index (SYI) reached a maximum value of 0.69 when the C input was 7.08 Mg ha−1 yr−1, which was close to the maximum value (SYI of 0.69, C input of 7.19 Mg ha−1 yr–1) in the Wt-Ct treatment.  Overall, the return of both wheat and cotton straw was the best strategy for improving SOC sequestration, soil aggregation, yields and their sustainability in the wheat–cotton rotation system.

Dynamic regulation of the irrigation–nitrogen–biochar nexus for the synergy of yield, quality, carbon emission and resource use efficiency in tomato

Ping’an Zhang, Mo Li, Qiang Fu, Vijay P. Singh, Changzheng Du, Dong Liu, Tianxiao Li, Aizheng Yang
2024, 23(02): 680-697.  DOI: 10.1016/j.jia.2023.06.006
Abstract ( )   PDF in ScienceDirect  

Integrated water and fertilizer management is important for promoting sustainable development of facility agriculture, and biochar plays an important role in guaranteeing food production, as well as alleviating water shortages and the overuse of fertilizers.  The field experiment had twelve treatments and a control (CK) trial including two irrigation amounts (I1, 100% ETm; I2, 60% ETm; where ETm is the maximum evapotranspiration), two nitrogen applications (N1, 360 kg ha–1; N2, 120 kg ha–1) and three biochar application levels (B1, 60 t ha–1; B2, 30 t ha–1 and B3, 0 t ha–1).  A multi-objective synergistic irrigation–nitrogen–biochar application system for improving tomato yield, quality, water and nitrogen use efficiency, and greenhouse emissions was developed by integrating the techniques of experimentation and optimization.  First, a coupled irrigation–nitrogen–biochar plot experiment was arranged.  Then, tomato yield and fruit quality parameters were determined experimentally to establish the response relationships between irrigation–nitrogen–biochar dosage and yield, comprehensive quality of tomatoes (TCQ), irrigation water use efficiency (IWUE), partial factor productivity of nitrogen (PFPN), and net greenhouse gas emissions (NGE).  Finally, a multi-objective dynamic optimization regulation model of irrigation–nitrogen–biochar resource allocation at different growth stages of tomato was constructed which was solved by the fuzzy programming method.  The results showed that the application of irrigation and nitrogen to biochar promoted increase in yield, IWUE and PFPN, while it had an inhibitory effect on NGE.  In addition, the optimal allocation amounts of water and fertilizer were different under different scenarios.  The yield of the S1 scenario increased by 8.31% compared to the B1I1N2 treatment; TCQ of the S2 scenario increased by 5.14% compared to the B2I2N1 treatment; IWUE of the S3 scenario increased by 10.01% compared to the B1I2N2 treatment; PFPN of the S4 scenario increased by 9.35% compared to the B1I1N2 treatment; and NGE of the S5 scenario decreased by 11.23% compared to the B2I1N1 treatment.  The optimization model showed that the coordination of multiple objectives considering yield, TCQ, IWUE, PFPN, and NGE increased on average from 4.44 to 69.02% compared to each treatment when the irrigation–nitrogen–biochar dosage was 205.18 mm, 186 kg ha–1 and 43.31 t ha–1, respectively.  This study provides a guiding basis for the sustainable management of water and fertilizer in greenhouse tomato production under drip irrigation fertilization conditions.

Manure substitution improves maize yield by promoting soil fertility and mediating the microbial community in lime concretion black soil

Minghui Cao, Yan Duan, Minghao Li, Caiguo Tang, Wenjie Kan, Jiangye Li, Huilan Zhang, Wenling Zhong, Lifang Wu
2024, 23(02): 698-710.  DOI: 10.1016/j.jia.2023.05.040
Abstract ( )   PDF in ScienceDirect  

Synthetic nitrogen (N) fertilizer has made a great contribution to the improvement of soil fertility and productivity, but excessive application of synthetic N fertilizer may cause agroecosystem risks, such as soil acidification, groundwater contamination and biodiversity reduction.  Meanwhile, organic substitution has received increasing attention for its ecologically and environmentally friendly and productivity benefits.  However, the linkages between manure substitution, crop yield and the underlying microbial mechanisms remain uncertain.  To bridge this gap, a three-year field experiment was conducted with five fertilization regimes: i) Control, non-fertilization; CF, conventional synthetic fertilizer application; CF1/2M1/2, 1/2 N input via synthetic fertilizer and 1/2 N input via manure; CF1/4M3/4, 1/4 N input synthetic fertilizer and 3/4 N input via manure; M, manure application.  All fertilization treatments were designed to have equal N input.  Our results showed that all manure substituted treatments achieved high soil fertility indexes (SFI) and productivities by increasing the soil organic carbon (SOC), total N (TN) and available phosphorus (AP) concentrations, and by altering the bacterial community diversity and composition compared with CF.  SOC, AP, and the soil C:N ratio were mainly responsible for microbial community variations.  The co-occurrence network revealed that SOC and AP had strong positive associations with Rhodospirillales and Burkholderiales, while TN and C:N ratio had positive and negative associations with Micromonosporaceae, respectively.  These specific taxa are implicated in soil macroelement turnover.  Random Forest analysis predicted that both biotic (bacterial composition and Micromonosporaceae) and abiotic (AP, SOC, SFI, and TN) factors had significant effects on crop yield.  The present work strengthens our understanding of the effects of manure substitution on crop yield and provides theoretical support for optimizing fertilization strategies.

A hybrid CNN-LSTM model for diagnosing rice nutrient levels at the rice panicle initiation stage

Fubing Liao, Xiangqian Feng, Ziqiu Li, Danying Wang, Chunmei Xu, Guang Chu, Hengyu Ma, Qing Yao, Song Chen
2024, 23(02): 711-723.  DOI: 10.1016/j.jia.2023.05.032
Abstract ( )   PDF in ScienceDirect  

Nitrogen (N) and potassium (K) are two key mineral nutrient elements involved in rice growth.  Accurate diagnosis of N and K status is very important for the rational application of fertilizers at a specific rice growth stage.  Therefore, we propose a hybrid model for diagnosing rice nutrient levels at the early panicle initiation stage (EPIS), which combines a convolutional neural network (CNN) with an attention mechanism and a long short-term memory network (LSTM).  The model was validated on a large set of sequential images collected by an unmanned aerial vehicle (UAV) from rice canopies at different growth stages during a two-year experiment.  Compared with VGG16, AlexNet, GoogleNet, DenseNet, and inceptionV3, ResNet101 combined with LSTM obtained the highest average accuracy of 83.81% on the dataset of Huanghuazhan (HHZ, an indica cultivar).  When tested on the datasets of HHZ and Xiushui 134 (XS134, a japonica rice variety) in 2021, the ResNet101-LSTM model enhanced with the squeeze-and-excitation (SE) block achieved the highest accuracies of 85.38 and 88.38%, respectively.  Through the cross-dataset method, the average accuracies on the HHZ and XS134 datasets tested in 2022 were 81.25 and 82.50%, respectively, showing a good generalization.  Our proposed model works with the dynamic information of different rice growth stages and can efficiently diagnose different rice nutrient status levels at EPIS, which are helpful for making practical decisions regarding rational fertilization treatments at the panicle initiation stage.

Short Communication

Targeted mutations of BnPAP2 lead to a yellow seed coat in Brassica napus L.

Wei Huang, Ruyu Jiao, Hongtao Cheng, Shengli Cai, Jia Liu, Qiong Hu, Lili Liu, Bao Li, Tonghua Wang, Mei Li, Dawei Zhang, Mingli Yan
2024, 23(02): 724-730.  DOI: 10.1016/j.jia.2023.05.001
Abstract ( )   PDF in ScienceDirect  
The yellow seed trait is preferred by breeders for its potential to improve the seed quality and commercial value of Brassica napus.  In the present study, we produced yellow seed mutants using a CRISPR/Cas9 system when the two BnPAP2 homologs were knocked out.  Histochemical staining of the seed coat demonstrated that proanthocyanidin accumulation was significantly reduced in the pap2 double mutants and decreased specifically in the endothelial and palisade layer cells of the seed coat.  Transcriptomic and metabolite profiling analysis suggested that disruption of the BnPAP2 genes could reduce the expression of structural and regulated genes in the phenylpropanoid and flavonoid biosynthetic pathways.  The broad suppression of these genes might hinder proanthocyanidin accumulation during seed development, and thereby causing the yellow seed trait in Bnapus.  These results indicate that BnPAP2 might play a vital role in the regulatory network controlling proanthocyanidin accumulation.
Letter
First identification of the oxazolidinone/phenicol resistance gene optrA in Streptococcus pluranimalium worldwide
Kuan Zhao, Longyu Zhou, Shixia Zhang, Wanjiang Zhang, Yao Zhu
2024, 23(02): 731-734.  DOI: 10.1016/j.jia.2023.11.042
Abstract ( )   PDF in ScienceDirect  

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