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BreedingAIDB: A database integrating crop genome-to-phenotype paired data with machine learning tools applicable to breeding

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Plant Communications 2024年第7期5卷 12-15页

作者： Zijie Shen Enhui Shen Kun Yang Zuoqian Fan Qian-Hao Zhu Longjiang Fan Chu-Yu Ye Hainan institute Zhejiang UniversitySanya 572025China institute of crop Science&institute of Bioinformatics College of Agriculture&BiotechnologyZhejiang UniversityHangzhou 310058China CSIRO Agriculture and Food CanberraACT 2601Australia

Machine learning(ML)is one of the key technologies for next-generation breeding,and“big data”is the cornerstone for development of ML algorithms that are applicable to crop breeding ***,there is a shortage of databases containing phenotype data and corresponding genomic data,i.e.,genome-to-phenotype(G2P)paired data,that can be used in the development of ML algorithms for *** fill this gap,we constructed a user-friendly database named the BreedingAIDB(http://***/BreedingAIDB)to provide breeders and ML experts with easily accessible G2P paired data for crops,as well as ML tools.

关键词： database learning breeding

Revisiting the role of delta-1-pyrroline-5-carboxylate synthetase in drought-tolerant crop breeding

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The crop Journal 2022年第4期10卷 1213-1218页

作者： Xuanjun Feng Yue Hu Weixiao Zhang Rongqian Xie Huarui Guan Hao Xiong Li Jia Xuemei Zhang Hanmei Zhou Dan Zheng Ying Wen Qingjun Wang Fengkai Wu Jie Xu Yanli Lu State Key Laboratory of crop Gene Exploration and Utilization in Southwest China Wenjiang 611130SichuanChina Maize Research institute of Sichuan Agricultural University Wenjiang 611130SichuanChina

The delta-1-pyrroline-5-carboxylate synthetase(P5CS)gene exercises a protective function in stressed ***,the relationship between proline accumulation caused by P5CS and abiotic stress tolerance in plants is not always clear,as P5CS overexpression has been reported to repress plant growth under normal conditions in several *** re-evaluated the role of P5CS in drought-tolerant rice breeding by expressing the AtP5CS1 and feedback-inhibition-removed AtP5CS1(AtP5CS1^(F128A))genes under the regulation of an ABA-inducible promoter to avoid the potential side effects of P5CS overexpression under normal ***-inducible AtP5CS1 and AtP5CS1^(F128A) increased seedling growth in a nutrient solution(under osmotic stress)and grain yield in pot ***,the evidently deleterious effects of AtP5CS1 on grain quality,tiller number,and grain yield in the field indicated the unsuitability of P5CS for drought-tolerance breeding.

关键词： P5CS Proline Drought Tiller number Chalkiness

Biochar-mediated Cd accumulation in rice grains through altering chemical forms,subcellular distribution,and physiological characteristics

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Biochar 2023年第1期5卷 830-843页

作者： Le Chen Lin Guo Qiangqiang Xiong Ping Liao Xueyun Deng Xiaohua Pan Xueming Tan Xiaobing Xie Qigen Dai Hui Gao Haiyan Wei Yongjun Zeng Hongcheng Zhang Jiangsu Key Laboratory of crop Genetics and Physiology and Jiangsu Key Laboratory of crop Cultivation and Physiology and Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops and Research institute of Rice industrial Engineering Technology Yangzhou UniversityYangzhou 225009China Ministry of Education Key Laboratory of Crop PhysiologyEcology and Genetic BreedingJiangxi Agricultural UniversityNanchang 330045China

Biochar can change the availability and morphology of soil ***,the influence of biochar on Cd chemical form and subcellular fraction in rice is poorly understood,particularly under different irrigation methods.A pot experiment of biochar application combined with two irrigation methods(continuous flooding and intermittent irrigation,CF and Ⅱ)was *** Cd accumulation,chemical form and subcellular fraction in rice organs and the associated physiological responses were *** significantly reduced soil available Cd(30.85-47.26%and 32.35-52.35%)under CF and Ⅱ but increased the Cd content(30.4-63.88%and 13.03-18.59%)in brown ***,the Cd content in shoots/grains under Ⅱ was higher than that under *** elevated the Cd soluble fraction in roots while lowered the cell wall fraction under both irrigation methods,whereas the opposite result was observed in *** increased water-,ethanol-,and NaCl-extractable Cd in roots meanwhile increased ethanol-extractable Cd in leaves under both irrigation ***,the total amount of water-,ethanol-,and NaCl-extractable Cd in rice roots was higher under Ⅱ than under *** hormones and antioxidant enzymes may also be involved in biochar-mediated Cd accumulation in rice ***,changes in Cd chemical form and subcellular fraction in the root and leaf are the main mechanisms of biochar-induced rice grains Cd accumulation.

关键词： Biochar Rice Cd accumulation Chemical forms Subcellular distribution Endogenous hormone Antioxidant enzyme

Functional diversifications of Gh ERF1 duplicate genes after the formation of allotetraploid cotton

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Journal of Integrative Plant Biology 2019年第1期61卷 60-74页

作者： Chunxiao Liu Tian Zhen Zhang National Key Laboratory of crop Genetics & Germplasm Enhancement Cotton Research InstituteNanjing Agricultural University crop Science institute Agronomy DepartmentCollege of Agriculture and BiotechnologyZhejiang University

Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.

关键词： Functional diversifications of Gh ERF1 duplicate genes after the formation of allotetraploid cotton

Fine-tuning the spatial allocation of phytohormones for smart canopy, smart breeding, and smart agriculture

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Science China Life Sciences 2025年第1期 309-310页

作者： Tao Zhou Lin Li National Key Laboratory of crop Genetic Improvement Huazhong Agricultural University HuBei HongShan Laboratory

The dual challenges of global climate change and population growth have increased demand for higher crop yields per unit area. The innovative technology of smart agriculture aims to synergize breeding, cultivation, and production through the application of biological and informatics technologies. Historically, the “Green Revolution” introduced semidwarf varieties of certain key crops by utilizing mutations affecting gibberellin pathways, which significantly increased planting densities and yields.

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Comparative analysis of metabolite changes in two contrasting rice genotypes in response to low-nitrogen stress

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The crop Journal 2018年第5期6卷 464-474页

作者： Xiuqin Zhao Wensheng Wang Ziyan Xie Yongming Gao Chunchao Wang Muhammed Mahbubur Rashid Mohammad Rafiqul Islam Binying Fu Zhikang Li institute of crop Sciences National Key Facility for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences Shenzhen institute for Innovative Breeding Chinese Academy of Agricultural Sciences

Identification of metabolites responsible for tolerance to low nitrogen availability(low-N)will aid in the genetic improvement of rice yield under nitrogen *** this study,a backcross introgression line(G9)and its recurrent parent Shuhui 527(SH527),which show differential responses to low-N stress,were used to identify metabolites associated with lowN tolerance in *** in metabolite contents in the leaves of G9 and SH527 at three growth stages under low-N stress were assessed by gas chromatography–mass *** metabolites,including amino acids and derivatives,were highly enriched in G9 compared with SH527 under the control condition,suggesting that the two genotypes had basal metabolite ***-N stress induced genotype-specific as well as growth stagedependent metabolite *** induced specifically in G9 that were involved in glycolysis and tricarboxylic acid metabolism were enriched at the tillering and grain filling stages,and metabolites involved in nitrogen and proline metabolism were enriched at the booting *** of pyroglutamate,glutamate,2-oxoglutarate,sorbose,glycerate-2-P,and phosphoenolpyruvic acid in G9 suggests that these metabolites could be involved in low-N stress *** results presented here provide valuable information for further elucidation of the molecular mechanisms of low-N tolerance in crops.

关键词： Rice Low-nitrogen stress Metabolite Nitrogen metabolism

QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

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The crop Journal 2015年第3期3卷 269-283页

作者： Lei Meng Huihui Li Luyan Zhang Jiankang Wang The National Key Facility for crop Gene Resources and Genetic Improvement Institute of Crop Science and CIMMYT China OfficeChinese Academy of Agricultural Sciences

QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

关键词： Biparental populations Map construction QTL mapping Software

Gm NAC15 overexpression in hairy roots enhances salt tolerance in soybean

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Journal of Integrative Agriculture 2018年第3期17卷 530-538页

作者： LI Ming HU Zheng JIANG Qi-yan SUN Xian-jun GUO Yuan QI Jun-cang ZHANG Hui Agricultural College Shihezi University National Key Facilities for crop Genetic Resources and Improvement/institute of crop Sciences Chinese Academy of Agricultural Sciences

The NAC （NAM, ATAF1/2 and CUC2） transcription factor family plays a key role in plant development and responses to abiotic stress. GmNAC15 （Glyma 15g40510.1）, a member of the NAC transcription factor family in soybean, was functionally characterized, especially with regard to its role in salt tolerance. In the present study, qRT-PCR （quantitative reverse transcription PCR） analysis indicated that GmNAC15 was induced by salt, drought, low temperature stress, and ABA treatment in roots and leaves. GmNAC15 overexpression in soybean （Glycine max） hairy roots enhanced salt tolerance. Transgenic hairy roots improved the survival of wild leaves; however, overexpression of GmNAC15 in hairy root couldn＇t influnce the expression level of GmNAC15 in leaf. GmNAC15 regulates the expression levels of genes responsive to salt stress. Altogether, these results provide experimental evidence of the positive effect of GmNAC15 on salt tolerance in soybean and the potential application of genetic manipulation to enhance the salt tolerance of important crops.

关键词： NAC salt tolerance soybean hairy roots

Optimized tillage methods increase mechanically transplanted rice yield and reduce the greenhouse gas emissions

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Journal of Integrative Agriculture 2024年第4期23卷 1150-1163页

作者： Shuang Cheng Zhipeng Xing Chao Tian Mengzhu Liu Yuan Feng Hongcheng Zhang Jiangsu Key Laboratory of crop Cultivation and Physiology/Jiangsu Co-innovation Center for Modern Production Technology of Grain crops/Research institute of Rice industrial Engineering Technology Yangzhou UniversityYangzhou 225009China

Biaxia lrotary tillage in dryland(DBRT)can complete biaxial rotary tillage with straw incorporation,secondary suppression,and ditching,and it has been previously studied in direct-seeded rice and ***,the effects of DBRT on the mechanically transplanted rice yield and greenhouse gas emissions remain *** evaluate the effects of DBRT on improving the food security of mechanically transplanted rice and reducing the greenhouse gas emissions,we conducted an experiment for two years with wheat straw *** tillage methods were set up:DBRT,uniaxial rotary tillage in dryland and paddy(DPURT),and uniaxial rotary tillage in paddy(PURT).The results showed that compared with DPURT and PURT,DBRT increased the yield of machine-transplanted rice by 7.5-11.0%and 13.3-26.7%,respectively,while the seasonal cumulative CH_(4) emissions were reduced by 13.9-21.2%and 30.2-37.0%,respectively,and the seasonal cumulative N_(2)O emissions were increased by 13.5-28.6%and 50.0-73.1%,***,DBRT reduced the global warming potential by 10.7-15.5%and 23.7-28.6%,respectively,andtheyield-scaledglobalwarmingpotentialby18.2-21.8%and36.4-39.3%,respectively,compared to DPURT and *** results were mainly related to the fact that DBRT significantly reduced soil bulk density and increased soil redox potential(Eh).Therefore,implementing DBRT in machine-transplanted rice fields is feasible,which cannot only increase the rice yield,but also reduce the greenhouse gas emissions.

关键词： integrated tillage rice grain yield CH_(4) N_(2)O