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10 January 2024, Volume 38 Issue 1 Previous Issue    Next Issue
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Review and Special Topic

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Prospects for the Application of Gene Editing and Genomic Selection in Rice Breeding LIANG Chuyan, WU Mingming, HUANG Fengming, ZHAI Rongrong, YE Jing, ZHU Guofu, YU Faming, ZHANG Xiaoming, YE Shenghai 2024, 38(1): 1-12.  DOI: 10.16819/j.1001-7216.2024.230503 Abstract ( )   HTML ( )   PDF (324KB) ( )   Rice is the main grain crop in China. Due to large population and limited land resources in China, rice breeding goals have long been yield oriented. Chinese researchers have continuously achieved breakthroughs in rice breeding technology, and the adoption of dwarf breeding and hybrid rice breeding technology has resulted in two significant leaps in rice yield in China. However, with the improvement of living standards and the increasing frequency of extreme weather events, higher demands have been placed on rice in terms of yield, quality, and resistance. At present, biotechnology is undergoing constant innovation, particularly with the rapid development of gene editing and genomic selection breeding technology. This progress is expected to provide robust support for the development of new rice varieties with high yield, superior quality, and resistance to multiple factors. It helps promote the green and sustainable development of rice production. This paper reviews the recent advancements in gene editing technology and genomic selection technology in rice breeding for high yield, superior quality, disease and insect resistance, stress tolerance, and heterosis. The goal is to provide breeding strategies for the efficient development of new varieties to meet demands.

Research Papers

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Mapping of Grain Shape QTLs Using RIL Population from Longdao 5/Zhongyouzao 8 HOU Benfu, YANG Chuanming, ZHANG Xijuan, YANG Xianli, WANG Lizhi, WANG Jiayu, LI Hongyu, JIANG Shukun 2024, 38(1): 13-24.  DOI: 10.16819/j.1001-7216.2024.230602 Abstract ( )   HTML ( )   PDF (2738KB) ( )   【Objective】Grain shape significantly influences the yield, quality, and commercial value of rice. This study aimed to identify Quantitative Trait Loci (QTLs) controlling grain shape using a rice recombinant inbred line population, thereby facilitating the mining of rice grain shape genes and the breeding of long-grain japonica rice. 【Method】 A population of 176 recombinant inbred lines was developed by crossing the japonica super rice variety Longdao 5 (LD5) with short round grain and the early maturing indica rice variety Zhongyouzao 8(ZYZ8) with long slender grain. Grain shape traits, including grain length(GL), grain width(GW), grain length to width ratio(LWR), and grain thickness(GT), were measured for three years using Smart Grain software, and the interrelationship between these traits was analyzed. Complete Interval Mapping (CIM) and Multi-Environment Trials (MET) were employed for QTL mapping and comparative analysis. 【Result】 Eight QTLs, comprising three for grain length (qGL3, qGL7, and qGL11), two for grain width (qGW3 and qGW5), two for grain thickness (qGT3 and qGT6), and one for grain length to width ratio (qLWR3), were identified on chromosomes 3, 5, 6, 7, and 11 using the CIM method. These QTLs explained 4.69%−18.89% of the phenotypic variation, with an LOD range from 2.52 to 8.74. Additionally, qGL3, qGL7, qGW3, qGW5, and qLWR3 were consistently detected over three years. Fourteen QTLs, including four for grain length, two for grain width, three for grain thickness, and five for grain length to width ratio, were detected on chromosomes 2, 3, 5, 6, 7, and 11 using the MET method. These QTLs explained 2.28%−15.78% of the phenotypic variation, with an LOD range from 4.20 to 20.90. Comparison with cloned grain shape genes revealed the proximity of qGL3/qLWR3a to GL3.1, qGW5 to GW5, and qLWR3b/qGT3 to TGW3. 【Conclusion】 A total of 8 and 14 grain shape QTLs were identified using the CIM and MET methods, respectively, including three cloned grain shape genes (GL3.1, TGW3, and GW5).

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Genetic Effects of Antioxidant Components in Red Rice and Its Interactions with Environment CHENG Zuxin, XIAO Changchun, ZHANG Yuting, HUANG Xinying, SHI Xialei, LING Bo, WANG Hongchao, CHEN Xiaoling, LIN Lihui 2024, 38(1): 25-32.  DOI: 10.16819/j.1001-7216.2024.221206 Abstract ( )   HTML ( )   PDF (539KB) ( )   【Objective】 This study aims to dissect the genetic effects of total phenols, total flavonoids, procyanidins, and anthocyanins in red rice, to offer insights for cultivating high-nutrition red hybrid rice. 【Methods】 Forty-eight hybrid combinations were generated using eight red rice restorer lines as male parents and six sterile lines as female parents. Employing the additive-dominance genetic model (AD model) and statistical methods, the study analyzed the genetic effects, heterosis, genetic correlation of antioxidant components in red rice across diverse environmental conditions, and their interactions with the environment. 【Results】 Genetic main effects primarily control anthocyanins, procyanidins, total phenols, and total flavonoids. Procyanidins, total phenols, and total flavonoids exhibit high narrow-sense heritability, mainly governed by gene additive effects, enabling effective early-generation selection. Anthocyanins are predominantly influenced by dominant effects, suitable for medium and high generation selection. All four antioxidant components display positive correlations among phenotype, genetics, additive and dominance effects, as well as additive × environment and dominance × environment interactions, with high correlation coefficients. Procyanidins exhibit a small genotype × environment interaction effect, indicating good stability. Using procyanidins as a selection indicator effectively enhances the other three components, reduces workload, and improves breeding efficiency. Higher temperatures contribute to increased accumulation of antioxidant components in red rice hybrid offspring, enhancing population heterosis. Elevating the content of antioxidant components in sterile lines benefits the cultivation of offspring with higher antioxidant content. Restorer lines 18Rr174 and 18Rr175 effectively increase the contents of total phenols, total flavonoids, and procyanidins in offspring and are less influenced by the environment. 【Conclusion】 Utilizing the additive-dominance genetic model for quantitative traits could effectively predict parental genetic effects on antioxidant components. 18Rr174 and 18Rr175 can be used to breed red rice with high antioxidant activity components.

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Effect of Drought Stress on Root Morphology and Leaf Photosynthetic Characteristics of Good Taste japonica Rice from Late Stage of Panicle Differentiation to Early Stage of Grain Filling JING Xiu, ZHOU Miao, WANG Jing, WANG Yan, WANG Wang, WANG Kai, GUO Baowei, HU Yajie, XING Zhipeng, XU Ke, ZHANG Hongcheng 2024, 38(1): 33-47.  DOI: 10.16819/j.1001-7216.2024.230804 Abstract ( )   HTML ( )   PDF (2122KB) ( )   【Objective】 The study aims to investigate the impact of soil drought from the late stage of panicle differentiation to the early stage of grain filling, on root morphology, physiology, and leaf photosynthetic characteristics of high-quality japonica rice. This research provides a theoretical foundation for drought-resistant cultivation. 【Method】 Nanjing 9108 and Fengjing 1606 were chosen as test materials. Two soil drought treatments were implemented: light drought (LD, soil water potential at −20±5 kPa) and severe drought (SD, soil water potential at −40±5 kPa). These treatments were applied for 20 days, spanning from the late stage of panicle differentiation to the early stage of grain filling (BAH, 10 days before & 10 days after heading), 10 days during the late stage of panicle differentiation (BH, 10 days before heading), and 10 days during the early stage of grain filling (AH, 10 days after heading). A well-watered treatment was used as the control (CK). 【Result】 1) Root length, root surface area, root volume, root tip number, root dry weight, and root activity for treatments within BAH, BH, AH followed a trend of SD<LD<CK at the end of drought stresses, 10 days after the end of drought stresses, 30 days after heading, and maturity. However, the root-shoot ratio exhibited the opposite trend. At the end of drought stresses, root indicators for SD and LD treatments within BAH significantly differed from CK, while root indicators for SD within BH and AH significantly differed from CK, except for the root-shoot ratio. Root indicators for LD treatments within BH and AH were not significantly different from CK. At the three stages after the end of drought stresses, root indicators for SD within BAH significantly differed from CK, and LD treatments were not significantly different except for root tip number. Root surface area, root volume, root tip number, and root dry weight for SD treatments within BH significantly differed from CK, while no significant differences were observed among the three water treatments within AH. 2) Net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs), intercellular CO2 concentration (Ci), maximum photochemical efficiency (Fv/Fm), and photochemical quenching coefficient (qp) for the treatments within BAH, BH, AH showed SD<LD<CK at the end of drought stresses, 10 days after the end of drought stresses, 30 days after heading, and maturity. Conversely, non-photochemical quenching coefficient (NPQ) exhibited the opposite trend. At the end of drought stresses, indicators of photosynthetic parameters for SD and LD treatments within BAH significantly differed from CK, and there were significant differences between LD and SD, except for Ci. Indicators for SD treatments within BH and AH significantly differed from CK, while LD treatments were not significantly different from CK. At the three stages after the end of drought stresses, indicators for SD treatments within BAH significantly differed from CK, while LD treatments did not. Only Pn, Tr, and Fv/Fm for SD treatments within BH significantly differed from CK, with no significant differences observed among the three water treatments within AH. 3) Yield for drought treatments within all three periods showed SD<LD<CK. Significant differences were observed among the three drought treatments within BAH and BH, with no significant difference between LD and CK within AH, both of which significantly differed from SD. 【Conclusion】 SD and LD within BAH inhibited root growth and leaf photosynthesis, resulting in a significant reduction in yield, with a smaller impact under LD. Plants under SD within BH found it challenging to return to control levels after treatment, leading to yield reduction. In contrast, plants under SD and LD within AH could recover quickly after treatment. In conclusion, rice root and leaf growth are more sensitive to drought treatments during the BH period in the late stage of panicle differentiation and early stage of grain filling.

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Effect of Nitrogen Fertilizer Topdressing for Panicle Differentiation on Grain Filling of Hybrid indica Rice and Its Relationship with the Activities of Key Enzymes for Starch Synthesis WU Ziniu, HE Limei, XIONG Ying, CHEN Kairui, YANG Zhiyuan, SUN Yongjian, LÜ Xu, MA Jun 2024, 38(1): 48-56.  DOI: 10.16819/j.1001-7216.2024.230401 Abstract ( )   HTML ( )   PDF (1038KB) ( )   【Objective】 To elucidate the impact of nitrogen panicle fertilizer on the key enzymes involved in grain filling and starch synthesis in hybrid rice. 【Methods】 Two hybrid rice varieties, Jinyou 1319 (high amylose) and Rongyou 702 (low amylose), characterized by substantial differences in amylose content, were chosen for a study examining the effects of the levels of nitrogen fertilizer topdressing for panicle differentiation on the activities of key enzymes in grain filling and starch synthesis. Various nitrogen topdressing treatments were applied, representing four pure nitrogen levels (0, 60, 90, and 120 kg/hm2 denoted as CK, N1, N2, and N3, respectively). 【Results】 Grain filling characteristics of hybrid rice exhibited significant variations under different nitrogen fertilizer topdressing treatments, with diverse performances observed among different varieties. The application of nitrogen fertilizer topdressing notably decreased the amylose content of rice. Both Gmax and Gmean of Jinyou 1319 exhibited a trend of N2>CK>N1>N3 under different nitrogen fertilizer topdressing levels, while those of Rongyou 702 followed a tendency of N3>N2>CK>N1. The nitrogen fertilizer topdressing significantly increased the activities of ADPG and DBE in grains at 5－25 days after anthesis, reduced the activities of GBSS in grains at 5－15 days after anthesis, and decreased the activities of SSS and SBE in grains at 5－25 days after anthesis. 【Conclusion】 The optimal application rate of nitrogen fertilizer topdressing for panicle differentiation was lower for the high-amylose variety Jinyou 1319 compared to the low-amylose variety Rongyou 702: the optimal rate of nitrogen fertilizer topdressing for Jinyou 1319 was 90 kg/hm2, and for Rongyou 702, it was 120 kg/hm2. The nitrogen fertilizer topdressing significantly reduced the activities of GBSS and SSS, accompanied by a decrease in SBE activity and an increase in DBE activity, ultimately leading to a reduction in rice amylose content. Seed ADPG activity did not significantly affect rice amylose content in this study.

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Rice Starch Structure and Physicochemical Properties of Good Taste japonica Rice Varieties and Their Regulations by Nitrogen YONG Mingling, YE Miao, ZHANG Yu, TAO Yu, NI Chuan, KANG Yuying, ZHANG Zujian 2024, 38(1): 57-71.  DOI: 10.16819/j.1001-7216.2024.230209 Abstract ( )   HTML ( )   PDF (1269KB) ( )   【Objective】 Starch is the main component of rice grain, and its composition and physicochemical properties play a fundamental role in shaping the taste characteristics of rice. Investigating the starch composition characteristics of good taste rice varieties and analyzing the effect of nitrogen levels at grain filling stage are of great significance for the optimization and cultivation of good taste rice varieties. 【Method】 Taking rice varieties Jinxiangyu 1, Wuyujing 3, Wumijing and Huaidao 5, which have significant differences in taste, as experimental materials, the relationship between the physicochemical properties of rice starch and taste quality and its response to varing nitrogen levels at the grain filling stage were explored. 【Result】 The taste value ranking was as follows: Jinxiangyu 1>Wuyujing 3>Wumijing>Huaidao 5, which was consistent across different nitrogen levels. For good taste rice varieties, they exhibited low amylose and protein contents, high breakdown and low setback in the RVA spectrum, easy gelatinization, better solubility, swelling power and starch granule morphology, along with higher relative crystallinity of starch. Furthermore, they displayed a higher proportion of short branches in the distribution of amylopectin chain length. With the increase of nitrogen level at the filling stage, the taste value of rice decreased significantly, combined with decreased amylose content, increased protein content, shortened gel consistency, decreased peak viscosity and breakdown in RVA spectrum, and increased setback; The starch granule morphology of starch became worse; The gelatinization enthalpy, relative crystallinity of starch and the chain B2 and chain B3 contents in the branching of amylopectin increased, while the solubility, swelling power, chain A and chain B1 contents decreased. Varieties responded variously to nitrogen in terms of their physicochemical properties and taste value to nitrogen. Good taste rice varieties displayed relatively stable taste, being less sensitive to nitrogen. 【Conclusion】 The results showed that good taste rice varieties had low amylose and protein contents, better cooking properties and starch granule morphology, better starch crystallization features and a well-balanced amylopectin structure with higher short amylopectin content. Elevated nitrogen level at the grain filling stage increased the proportion of long branched amylopectin, and the energy required for starch gelatinization, reduced starch solubility and swelling power, and significantly degraded the cooking and eating quality.

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Effect of High Temperature Stress at Grain Filling Stage on Early indica Rice Quality Traits YI Xiaoxuan, LIU Weiqi, ZENG Gai, LUO Lihua, XIAO Yinghui 2024, 38(1): 72-80.  DOI: 10.16819/j.1001-7216.2024.221114 Abstract ( )   HTML ( )   PDF (581KB) ( )   【Objective】 This study aims to investigate the impact of high-temperature stress during the filling stage on the milling, appearance, cooking, and eating quality of early indica rice and to reveal the response patterns of quality traits in early indica rice to high temperatures during the filling stage. 【Method】 Experimental materials included R996, Xiangzaoxian 45, and six newly bred early indica rice varieties. Natural high-temperature stress treatment was applied through staged sowing. The milling, appearance, and cooking and eating qualities of the eight varieties were analyzed. Heat-insensitive and heat-sensitive rice varieties were identified, and the response of rice quality to high temperatures during the filling stage was explored. 【Result】 Temperature within 10 days after heading had the most significant impact on the milling quality and cooking and eating quality of rice, while temperature within 30 days after heading had the most significant effect on the appearance quality of rice. High-temperature stress significantly reduced the brown rice rate, milled rice rate, head rice rate, and grain length, increased chalky grain rate and chalkiness, and adversely affected milling quality and appearance quality of rice. The amylose content was significantly reduced, whereas rice comprehensive score, appearance, taste, and viscosities were significantly improved, enhancing rice palatability. Rice varieties exhibited varying responses to high-temperature stress based on specific quality traits. Q3, Q8, Q11, and Q13 were identified as high-temperature-insensitive varieties, according to the high-temperature stress index (HTSI) for milling quality. However, Q3, Q4, Q5, and Q11, which demonstrated excellent cooking and eating quality under high-temperature growth conditions, were classified as high-temperature-insensitive varieties based on the high-temperature stress index for appearance quality. 【Conclusion】 High-temperature stress during the grain-filling period reduced the milling quality and appearance quality of rice but improved rice palatability. Rice varieties Q3 and Q11, characterized by good milling quality, appearance quality insensitive to high temperatures, and good cooking and eating quality, hold promise as new germplasm for the high-quality breeding of early indica rice.

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Hyperspectral Properties of Rice Varieties with Varying Resistance Under Brown Planthopper (Nilaparvata lugens) Infestation YANG Qixin, LAI Fengxiang, HE Jiachun, WEI Qi, WANG Weixia, WAN Pinjun, FU Qiang 2024, 38(1): 81-90.  DOI: 10.16819/j.1001-7216.2024.230409 Abstract ( )   HTML ( )   PDF (1366KB) ( )   【Objective】 The objective of this study is to investigate changes in hyperspectral reflectance curves and sensitive spectral features in rice varieties displaying varying resistance levels to brown planthopper infestation. Additionally, the study aims to examine changes in hyperspectral values in different parts of the rice plant. The obtained results are utilized to develop a machine learning model for identifying brown planthopper resistance, providing essential fundamental data for the development of intelligent technologies in identifying brown planthopper resistance. 【Method】 Three rice varieties (TN1, Mudgo, and RHT), each with varying resistance levels to brown planthoppers, were selected. The differences in hyperspectral values and vegetation indices were analyzed, and a random forest model was established to predict their resistance level. 【Results】 The study revealed that the number of significant spectral bands and the number of significant differences in spectral bands, significantly correlated with the duration of brown planthopper infestations, decrease with increasing resistance levels of the rice plant. At around 680 nm, the correlation with the duration of brown planthopper infestations was strongest for all three varieties. The analysis of vegetation indices showed that SIPI, SR605/760, and PSNDb had higher absolute values of correlation coefficients with resistance levels than those beyond 680 nm. Differences in different plant parts appeared first in TN1, a variety sensitive to brown planthoppers, followed by Mudgo, a moderately resistant variety, and finally RHT, a highly resistant one. The differences first appeared in the sheath of the first leaf, followed by the sheath of the second leaf, and the sheath of the third leaf. The results of the prediction model showed that the model with all spectral bands as input performed better than the random forest model built with a single vegetation index, SIPI, and achieved an accuracy of 85.9%.【Conclusion】 The study highlights spectral changes associated with brown planthopper resistance among rice varieties and different plant parts. It confirms the suitability of machine learning technology for predicting the resistance level of rice.

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Study on the Species and Spatial Distribution Patterns of Overwintering Rice Stem Borers in Guangxi Zhuang Automomous Region, China HUANG Qian, LONG Liping, WU Feng, CHENG Xuejiang, WU Biqiu, LI Cheng, HUANG Suosheng, HUANG Fengkuan, LING Yan 2024, 38(1): 91-98.  DOI: 10.16819/j.1001-7216.2024.230608 Abstract ( )   HTML ( )   PDF (636KB) ( )   【Objective】 Rice borers are widely distributed in Guangxi and pose a serious threat to rice production. The aim of this study is to clarify the overwintering situation and spatial distribution pattern of rice stem borers in Guangxi, understand the distribution and species of rice stem borers, and provide a basis for prediction and scientific control. 【Method】 Rice stem borers were investigated in 27 cities (counties) in the northeast, northwest, southeast, southwest, and coastal areas of Guangxi, respectively. The checkerboard sampling method was employed to investigate the overwintering borers. Rice stubbles were collected and brought back to the laboratory for careful species identification and quantification of borers. The spatial distribution pattern of the borer population was analyzed. 【Result】 The results of the overwintering survey revealed that the overwintering borer species in our region included Sesamia inferens, Chilo suppressalis, Scirpophaga incertulas, and Chilotraea auricilia. Among them, the overwintering population was primarily composed of S. inferens and C. suppressalis, with S. incertulas occurring mainly in the latitude of 23°－25°. The overwintering population density of other borers did not exhibit an obvious regular distribution in our region. Spatial distribution parameters indicated that borers in other fields displayed an aggregation distribution, with the degree of aggregation increasing with density, except for S. inferens in fields 13, 20, and 22, where they were uniformly distributed. The aggregation of borers in paddy field was mostly attributed to environmental factors. 【Conclusion】 In Guangxi, overwintering borers are clustered, with dominant populations of S. inferens and C. suppressalis in the field, followed by C. auricilia, while S. incertulas occurred sporadically.

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Population Dynamics of Dryinidae, Natural Predators of Rice Planthoppers in Panjin Prefecture, Liaoning Province MA Xiaohui, XING Yanan, GUO Li, LIU Yu, CHE Xiqing, SANG Haixu 2024, 38(1): 99-105.  DOI: 10.16819/j.1001-7216.2024.230302 Abstract ( )   HTML ( )   PDF (776KB) ( )   【Objective】 Dryinidae is an important natural enemy of rice planthoppers, with both predatory and parasitic habits, plays an important role in regulating the paddy ecosystem. To understand the species composition and occurrence of Dryinidae, a four-year investigation was conducted in Panjin Prefecture, Liaoning Province, a siginicant japonica rice producing area in northern China. 【Method】 We used the rice planthopper with “back sac”(Hereafter referred to as“back sac” host), the cocoon and the female adult of Dryinidae as index, to research the species of Dryinidae, the population dynamics of different stages of Dryinidae in conventional paddies(CP) and crab-rice paddies(CR), and the correlation of population dynamics for Dryinidae and its host in conventional paddy fields. 【Result】 The results showed that there are two species of Dryinidae in Panjin Prefecture, which are Haplogonatopus oratorius (Westwood) and Haplogonatopus apicalis R. C. L. Perkins. Haplogonatopus oratorius(Westwood) is the dominant species. The peak population of Dryinidae for natural enemy of rice planthoppers appeared on August 15 in Panjin Prefecture(9.80±0.20). The number of “back sac” host, the cocoon and the female adult of Dryinidae peaked in crab-rice paddy field. The peak period is on August 15th, September 15th and July 30th in turn, and the peak value is 6.40±0.51, 3.20±1.24, and 4.40±0.60, respectively. 【Conclusion】 There was no significant correlation of population dynamics between rice planthoppers and Dryinidae in conventional paddy fields. We believe that the population quantity of Dryinidae for natural enemy of rice planthoppers in crab-rice paddy field is larger than that in conventional paddy field in Panjin Prefecture. We speculate that this was because almost no insecticides were applied in crab-rice paddy field, which increased the population density of Dryinidae. It is beneficial to its controlling function on pests in the paddy field ecosystem.

Experimental Technique

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Development of HRM-based Functional Marker for Gelatinization Temperature Gene ALK in Rice WANG Jun, ZHOU Jing, TAO Yajun, LI Wenqi, ZHU Jianping, FAN Fangjun, WANG Fangquan, XU Yang, CHEN Zhihui, JIANG Yanjie, LI Xia, YANG Jie 2024, 38(1): 106-110.  DOI: 10.16819/j.1001-7216.2024.221203 Abstract ( )   HTML ( )   PDF (756KB) ( )   【Objective】 Gelatinization temperature is an important parameter in rice eating quality which is mainly controlled by the ALK gene. Fast and high-throughput gene functional markers for ALK can improve selection efficiency in quality improvement. 【Method】 According to single nucleotide polymorphism in the functional region of ALK alleles, we developed the gene functional marker based on high resolution melting (HRM) technology. 【Result】 Through PCR amplification and sequencing test, we selected gene markers ALKH4 and ALKH5 in two functional regions of ALK. ALKH4 and ALKH5 were employed to genotype 81 indica varieties and 279 japonica varieties. The results showed that only 16 japonica varieties and 19 indica varieties carrying G-GC genotype were identified as well as 51 japonica varieties carrying A-GC genotype; while 212 japonica varieties and 62 indica varieties fell into G-TT genotype. 【Conclusion】 The HRM-based functional markers ALKH4 and ALKH5 could distinguish different genotypes of gelatinization temperature ALK locus in a fast and high-throughput manner, and have significance in breeding practice.