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Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

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Journal of Integrative Agriculture 2024年第3期23卷 769-780页

作者： Shuliang Jiao Qinyan Li Fan Zhang Yonghong Tao Yingzhen Yu Fan Yao Qingmao Li Fengyi Hu Liyu Huang Key Laboratory of Biology and Germplasm Innovation of Perennial rice Ministry of Agriculture and Rural Affairs/School of AgricultureYunnan UniversityKunming 650091China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Wenshan Academy of Agricultural Sciences Wenshan 663000China

Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant heigh

关键词： Green Revolution Semidwarf 1 high-yield breeding upland rice plant height

Natural alleles of a uridine 5'-diphospho-glucosyltransferase gene responsible for differential endosperm development between upland rice and paddy rice

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Journal of Integrative Plant Biology 2022年第1期64卷 135-148页

作者： Zihao Wu Xiao Zhang Guimei Chang Jun Yang Jinpeng Wan Feijun Wang Dayun Tao Jiawu Zhou Lianguang Shang Peng Xu Diqiu Yu School of Life Sciences University of Science and Technology of ChinaHefei 230027China CAS Key Laboratory of Tropical Plant Resources and Sustainable Use Xishuangbanna Tropical Botanical Gardenthe Chinese Academy of SciencesKunming 650223China Yunnan Key Laboratory for rice Genetic Improvement Food Crops Research InstituteYunnan Academy of Agricultural SciencesKunming 650200China The Innovative Academy of Seed Design Chinese Academy of SciencesMengla 666303China Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agricultural and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China Center of Economic Botany Core Botanical GardensChinese Academy of SciencesMergla 666303China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan UniversityKunming 650091China

Traditional upland rice generally exhibits insufficient grains resulting from abnormal endosperm development compared to paddy rice. However, the underlying molecular mechanism of this trait is poorly understood. Here,we cloned the uridine 5’-diphospho(UDP)-glucosyltransferase gene EDR1(Endosperm Development in rice) responsible for differential endosperm development between upland rice and paddy rice by performing quantitative trait loci analysis and map-based cloning. EDR1 was highly expressed in developing seeds duringgrain filling. Natural variations in EDR1 significantly reduced the UDP-glucosyltransferase activity of EDR1 YZNcompared to EDR1 YD1,resulting in abnormal endosperm development in the near-isogenic line, accompanied by insufficient grains and changes in grain quality.By analyzing the distribution of the two alleles EDR1 YD1 and EDR1 YZNamong diverse paddy rice and upland rice varieties, we discovered that EDR1 was conserved in upland rice, but segregated in paddy rice. Further analyses of grain chalkiness in the alleles of EDR1 YD1 and EDR1 YZNvarieties indicated that rice varieties harboring EDR1 YZNand EDR1 YD1 preferentially showed high chalkiness, and low chalkiness,respectively. Taken together, these results suggest that the UDP-glucosyltransferase gene EDR1 is an important determinant controlling differential endosperm development between upland rice and paddy rice.

关键词： EDR1 endosperm development grain quality UDP-glucosyltransferase upland rice

Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

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Journal of Genetics and Genomics 2011年第11期38卷 547-556页

作者： Junzhou Li Deping Wang Yan Xie Hongliang Zhang Guanglong Hu Jinjie Li Anyong Dai Lifeng Liu Zichao Li Key Laboratory of Crop Heterosis and Utilization （MOE） and Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100193 China College of Agriculture Henan Agricultural University Zhengzhou 450002China China National Centre for Biotechnology Development Beijing 100039 China

Introgression lines （ILs） are valuable materials for identifying quantitative trait loci （QTLs）, evaluating genetic interactions, and marker assisted breeding. A set of 430 ILs （BC5F3） containing segments from upland tropical japonica cultivar IRAT109 in a lowland temperate japonica cultivar Yuefu background were developed. One hundred and seventy-six polymorphic markers were used to identify introgressed segments. No segment from IRAT109 was found in 160 lines. Introgressed segments of the other 270 lines covered 99.1% of the donor genome. The mean number of introgressed donor segments per individual was 3.3 with an average length of 14.4 cM. QTL analysis was conducted on basal root thickness （BRT） of the 270 ILs grown under irrigated lowland, upland and hydroponic conditions. A total of 22 QTLs affecting BRT were identified, six QTLs （qBRT3.1, qBRT3.2, qBRT6.1, qBRTS.2, qBRT9.1, and qBRT9.2） were consistently expressed under at least two environments （location and water regime）, and qBRT7.2 was a new BRT QTL identified under lowland conditions. IL255 containing qBRT9.1 showed an increase of 10.09% and 7.07% BRT over cultivar Yuefu when grown under upland and lowland conditions, respectively. Using a population of 304 F2：3 lines derived from the cross IL255 Yuefu, qBRT9.1 was validated and mapped to a 1.2 cM interval between RM24271 and RM566. The presence of qBRT9.1 explained 12% of BRT variation. The results provide upland rice ILs and BRT QTLs for analyzing the genetic basis of drought resistance, detecting favorable genes from upland rice, and rice drought resistance breeding.

关键词： upland rice Quantitative trait loci Introgression lines Basal root thickness

Evaluation of stability and yield potential of upland rice genotypes in North and Northeast Thailand

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Journal of Integrative Agriculture 2018年第1期17卷 28-36页

作者： Wasan Jaruchai Tidarat Monkham Sompong Chankaew Bhalang Suriharn Jirawat Sanitchon Department of Plant Science and Agricultural Resources Faculty of AgricultureKhon Kaen University

The planting of upland rice is one cropping option in area with limited water availability and low soil fertility in North and Northeast Thailand. The varietal selection was determined by grain yield potential, wide adaptation, and good stability. This study was aimed at evaluation of indigenous upland rice germplasm for yield and yield stability in multi-locations. Thirty-six upland rice genotypes collected from six provinces of the North and Northeast Thailand and one check variety （Sewmaejan） were assessed under five locations in the rainy seasons of 2009 and 2010. The experiment was laid out in a randomized complete block design with three replications. The genotype grain yield was highly affected by location （59.90%）, followed by genotypes （G）xlocation （L） interaction （12.80%） and genotype （6.79%）. The most suitable location for the genotype eval- uation was L3 （Khon Kaen-KKU 10） which associated with stability of grain yield for all genotypes. Furthermore, biplot and regression analysis indicated that genotype numbers 6 （Jaowmong 1）, 10 （Neawmong 1）, 18 （Neawdum 1）, 19 （Leamna）, 20 （Prayaleamkang）, 32 （Kunwang 2）, and 33 （Kunwang 3） showed great yield stability over five locations. The genotypes will be applicant for upland rice production area and parental base in breeding program.

关键词： upland rice yield stability germplasm multi-location trails GxL interaction

Improvement of upland rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable rice Production

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rice science 2021年第5期28卷 493-500,I0033-I0036页

作者： Vishalakshi Balija Umakanth Bangale Senguttuvel Ponnuvel Kalyani Makarand Barbadikar Srinivas Prasad Madamshetty Sanjeeva Rao Durbha Hari Yadla Sheshu Madhav Maganti Biotechnology Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Hybrid rice Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Plant Pathology Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Plant Physiology Division ICAR-Indian Institute of Rice ResearchRajendra NagarHyderabad 500030India Regional Agricultural Research Station Professor Jayashankar Telangana State Agricultural UniversityWarangal 506006India Department of Biotechnology Acharya Nagajna UniversityGuntur 522510India

Varalu is an early maturing rice variety widely grown in the rainfed ecosystem preferred for its grain type and cooking quality.However,the yield of Varalu is substantially low since it is being affected by reproductive drought stress along with the blast disease.The genetic improvement of Varalu was done by introgressing a major yield QTL,qDTY_(12.1),along with two major blast resistance genes i.e.Pi54 and Pi1 through marker-assisted backcross breeding.Both traits were transferred till BC_(2) generation and intercrossing was followed to pyramid the two traits.Stringent foreground selection was carried out using linked markers as well as peak markers(RM28099,RM28130,RM511 and RM28163)for the targeted QTL(qDTY_(12.1)),RM206 for Pi54 and RM224 for Pi1.Extensive background selection was done using genome-wide SSR markers.Six best lines(MSM-36,MSM-49,MSM-53,MSM-57,MSM-60 and MSM-63)having qDTY_(12.1) and two blast resistance genes in homozygous condition with recurrent parent genome of 95.0%-96.5% having minimal linkage drag of about 0.1 to 0.7 Mb were identified.These lines showed yield advantage under drought stress as well as irrigated conditions.MSM-36 showed better performance in the national coordinated trials conducted across India,which indicated that improved lines of Varalu expected to replace Varalu and may have an important role in sustaining rice production.The present study demonstrated the successful marker-assisted pyramiding strategy for introgression of genes/QTLs conferring biotic stress resistance and yield under abiotic stress in rice.

关键词： blast resistance drought stress marker-assisted gene pyramiding rainfed ecosystem upland rice

Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in upland rice

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rice science 2021年第4期28卷 379-390,I0027-I0034页

作者： Tatiana Rakotoson Julie Dusserre Philippe Letourmy Julien Frouin Isabelle Ramonta Ratsimiala Noronirina Victorine Rakotoarisoa Tuong-Vi CAO Kirsten Vom Brocke Alain Ramanantsoanirina Nourollah Ahmadi Louis-Marie Raboin National Center for Applied Research on Rural Development Regional Research Station AntsirabeAntsirabe 110Madagascar Faculty of Sciences University of AntananarivoAntananarivo 101Madagascar Higher Education Institute of Antsirabe Vakinankaratra University of AntananarivoAntsirabe 110Madagascar Agroecology and Sustainable Intensification of Annual Crops Research Unit French Agricultural Research Centre for International Development(CIRAD)Avenue AgropolisMontpellier 34398France Genetic Improvement and Adaptation of Mediterranean and Tropical Plants Research Unit(UMR AGAP) CIRADAvenue AgropolisMontpellier 34398France UMR AGAP Highland Production Systems and Sustainability in Madagascar Platform in PartnershipCIRADAntsirabe 110Madagascar University of Montpellier/CIRAD Montpellier 34398France

Genome-wide association study(GWAS)was performed for 16 agronomic traits including nitrogen use efficiency(NUE)and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38390 single nucleotide polymorphism(SNP)markers.This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels.Using another set of five grain traits,we identified previously known genes(GW5,GS3,Awn1 and Glabrous1),thus validating the pertinence and accuracy of our datasets for GWAS.A total of 369 significant associations were detected between SNPs and agronomic traits,gathered into 46 distinct haplotype groups and 28 isolated markers.Few association signals were identified for the complex quantitative trait NUE,however,larger number of quantitative trait loci(QTLs)were detected for its component traits,with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency,respectively.Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb.The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits.However,because of the quantitative and complex nature of NUE-related traits,GWAS might have not captured a large number of QTLs with limited effects.

关键词： genome-wide association study nitrogen use efficiency agronomic trait upland rice

Analysis of Gene Expression Profile Induced by Water Stress in upland rice(Oryza sativa L.var.IRAT109)Seedlings using Subtractive Expressed Sequence Tags Library

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Journal of Integrative Plant Biology 2007年第10期49卷 1455-1463页

作者： Haiguang Wang Hongliang Zhang Zichao Li Key Laboratory of Crop Genomics and Genetic Improvement of Ministry of Agriculture Key Laboratory of Crop Heterosis and Utilizition of Ministry of Education and Beijing Key Lab of Crop Genetic Improvement China Agricultural University Beijing China100094

To identify the water stress induced genes of upland rice cultivar IRAT109, which is resistant to drought, a subtractive cDNA library was developed from polyethylene glycol- （PEG） treated and non-treated seedlings by suppression subtractive hybridization, from which 2112 recombinant colonies were obtained, Eight hundred clones were selected randomly for sequencing analysis, and 384 unique expressed sequence tags （ESTs） were obtained, They were found to be involved in diverse biological processes, such as metabolism, transcription, signal transduction, protein synthesis and others, Notably a number of known functional genes in drought tolerance, including genes related to biosynthesis of osmoprotectants, defense against active oxygen, removal of toxic compounds, recovery of proteins and reinforcement of cell wall were also found in the study, Several genes related to deleterious responses were upregulated by PEG stress, The differential expression patterns of 11 SSH-derived ESTs were confirmed by real-time polymerase chain reaction.

关键词： expressed sequence tag subtracted library suppression subtractive hybridization upland rice water stress.

Ammonium Effects on Nitrate Uptake by Roots of upland and Paddy rice Seedlings Related to Membrane Potential Differences

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Agricultural Sciences in China 2010年第6期9卷 799-805页

作者： WANG Xiao-li WANG Yu-qian TAO Yue-yue FENG Ke College of Environmental Science and Engineering Yangzhou University Yangzhou 225009 P.R. China

Nitrate uptake characteristics and ammonium effects on nitrate uptake were compared between upland rice （Brazilian upland rice） and paddy rice （Wuyujing 3 and Yangdao 6） through the glass microelectrode technique and the concentration gradient method of uptake kinetics.Results indicated that nitrate uptake by rice seedlings and ammonium effects were depending on membrane potential of root cells.And upland rice and paddy rice presented obviously different responses.For all cultivars,the nitrate treatments induced rapid depolarization and then slow repolarization of membrane potential in root epidermal cells,and even hyperpolarization was observed when nitrate concentration was low.The membrane potential of epidermal cells in Brazilian upland rice roots was larger and its response to NO3- was bigger than those of two paddy rice cultivars.Depolarization of membrane potential was amplified when ammonium was simultaneously added with nitrate into the measure medium,but repolarization was reduced,even disappeared.Brazilian upland rice seedlings had high Vmax of nitrate uptake and low Km,furthermore,Vmax and Km were little affected by ammonium,but Vmax of Wuyujing 3 was reduced significantly.Therefore,inhibition of NH4＋ differed obviously between upland rice and paddy rice.

关键词： nitrate uptake membrane potential ammonium upland rice paddy rice

Arbuscular Mycorrhizal Fungi Colonization in upland rice as Influenced by Agrochemical Application

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rice science 2009年第4期16卷 307-313页

作者： Velu RAJESHKANNAN Chettipalayam Samiappan SUMATHI Sellamuthu MANIAN Rhizosphere Biology Laboratory Department of MicrobiologyBharathidasan UniversityTiruchirappalli 620 024India Department of Botany Bharathiar UniversityCoimbatore 641 046India

Mycorrhizal status of rice under upland conditions was studied using potted seedlings, Percentage of arbuscular mycorrhizal fungi （AMF） root colonization varied between 17.35% and 37.18% over an age series of 7 to 70 days old rice plants, AMF root colonization was increased up to 35-42 days, beyond which the root colonization steadily declined, The vesicles appeared after two weeks and reached their maximum intensity on the 35th day. The arbuscules were formed late on the 42^rd day （2.93%） and slightly varied up to the 70^th day （3.03%）. Higher dosage of urea application suppressed plant growth whereas the superphosphate treatment had no marked impact on plant growth. Generally, application of these agrochemicals registered less influence on the hyphal colonization of AMF in rice plants, whereas arbuscular colonization was adversely affected by higher dosages of fertilizers. There were pronounced decreases in both the plant growth and their AMF colonization due to the application of systemic fungicides, carbendazim and thiophanate methyl. The application of single sprays of fungicides was less deleterious over multiple sprays.

关键词： Oryza sativa arbuscular mycorrhizal fungi agrochemical upland rice