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Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice

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The Crop Journal 2024年第2期12卷 549-557页

作者： Yan Zheng Ei Ei Khine Khin Mar Thi Ei Ei Nyein Likun Huang Lihui Lin Xiaofang Xie Min Htay Wai Lin Khin Than Oo Myat Myat Moe San San Aye Weiren Wu College of Life Sciences Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Fujian Provincial Key Laboratory of Crop Breeding by Design Fujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Key Laboratory of genetics Breeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina department of Botany Mawlamyine UniversityMon StateMawlamyineMyanmar department of Botany Dagon UniversityNorth DagonYangonMyanmar

Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.

关键词： BSA-seq QTL mapping Large F3 population Multi-environment experiment Cross-validation

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A perspective review on the biosynthesis of plant-based secondary metabolites and their application as potent drugs

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BIOCELL 2024年第4期48卷 541-557页

作者： JHILAM PRAMANIK AKASH KUMAR SARVESH RUSTAGI MEHAK KATYAL SHEETAL THAKUR JUTISHNA BORA SUMIRA MALIK ANCHAL TREHAN NAYAN TALUKDAR PETR SLAMA department of Food Technology ITM UniversityGwaliorIndia department of Food Technology SRM UniversitySonipatIndia department of Food Technology Uttaranchal UniversityDehradunIndia department of Nutrition and Dietetics Manav Rachna International Institute of Research&Studies(MRIIRS)FaridabadIndia University Centre for Research and Development UIBTChandigarh UniversityMohaliIndia Amity institute of Biotechnology Amity UniversityJharkhandRanchiIndia department of Biotechnology University Center for Research&Development(UCRD)Chandigarh UniversityMohaliPunjabIndia department of Science Guru Nanak College of Pharmaceutical SciencesDehradunIndia Program of Biotechnology Faculty of ScienceAssam down town UniversityGuwahatiIndia department of Animal Morphology Physiology and GeneticsMendel University in BrnoBrnoCzech Republic

Many phytochemicals and their derived metabolites produced by plants are extensively employed in commercial goods,pharmaceutical products as well as in the environmental and medicalﬁelds.However,these secondary metabolites obtained from plants are in low amounts,and it is difﬁcult to synthesize them at the industrial level.Despite these challenges,they may be utilized for a variety of medicinal products that are either available in the market or are being researched and tested.Secondary metabolites are complex compounds that exhibit chirality.Further,under controlled conditions with elicitors,desired secondary metabolites may be produced from plant cell cultures.This review emphasizes the various aspects of secondary metabolites including their types,synthesis,and applications as medicinal products.The article aims to promote the use of plant secondary metabolites in the management and treatment of various diseases.

关键词： Secondary metabolites Medicinal plant Synthesis Health benefits

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A phylogenetic approach identifies patterns of beta diversity and floristic subregions of the Qinghai-Tibet Plateau

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plant Diversity 2024年第1期46卷 59-69页

作者： Haibin Yu Man Yang Zixin Lu Weitao Wang Fangyuan Yu Yonghua Zhang Xue Yin Hongjun Yu Junjie Hu David C.Deane Key Laboratory of Conservation and Application in Biodiversity of South China School of Life SciencesGuangzhou UniversityGuangzhou 510006China School of Ecology Sun Yat-Sen UniversityShenzhen 510275China School of Geography and Remote Sensing Guangzhou UniversityGuangzhou 510006China College of Life and Environmental Science Wenzhou UniversityWenzhou 325035China Centre for Future Landscapes and department of Environment and genetics La Trobe UniversityBundooraVIC 3083Australia

Patterns of taxonomic and phylogenetic beta diversity and their relationships with environmental correlates can help reveal the origin and evolutionary history of regional biota.The Qinghai-Tibet Plateau(QTP)harbors an exceptionally diverse flora,however,a phylogenetic perspective has rarely been used to investigate its beta diversity and floristic regions.In this study,we used a phylogenetic approach to identify patterns of beta diversity and quantitatively delimit floristic regions on the Qinghai-Tibet Plateau.We also examined the relationships between multifaceted beta diversity,geographical distance,and climatic difference,and evaluated the relative importance of various factors(i.e.,climate,topography and history)in shaping patterns of beta diversity.Sørensen dissimilarity indices indicated that patterns of species turnover among sites dominated the QTP.We also found that patterns of both taxonomic and phylogenetic beta diversity were significantly related to geographical distance and climatic difference.The environmental factors that contributed most to these patterns of beta diversity include annual precipitation,mean annual temperature,climatic gradients and climatic instability.Hierarchical dendrograms of dissimilarity and non-metric multidimensional scaling ordination based on phylogenetic beta diversity data identified ten floristic subregions in the QTP.Our results suggest that the contemporary environment and historical climate changes have filtered species composition among sites and eventually determined beta diversity patterns of plants in the QTP.

关键词： Biogeographical regionalization Phylogenetic beta diversity Seed plants Sørensen dissimilarity Qinghai-Tibet Plateau

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Molecular docking insights into nuclear factor Y(NF-Y)transcription factor and pyrabactin resistance 1(PYL)receptor proteins reveal abiotic stress regulation in finger millet

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Crop Design 2024年第1期3卷 35-44页

作者： Varsha Rani Vinay Kumar Singh D.C.Joshi Rajesh Singh Dinesh Yadav department of Biotechnology Deen Dayal Upadhyaya Gorakhpur UniversityGorakhpur273009Uttar PradeshIndia Centre for Bioinformatics School of BiotechnologyBanaras Hindu UniversityVaranasi221005Uttar PradeshIndia ICAR-Vivekananda Institute of Hill Agriculture Almora263601UttarakhandIndia department of genetics and plant Breeding Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar Pradesh221005India

Finger Millet(Eleusine coracana-(L.)Gaertn),is an important nutraceutical crop with the potential for imparting food and nutritional security.These plants have a comparatively higher tolerance for several abiotic stresses like drought,salinity,and heat.Several players including Transcription Factor(TF)like Nuclear Factor Y(NF-Y)might be associated with this enhanced level of tolerance.Further,it is unclear how phytohormones like Abscisic acid(ABA)regulate the expression of NF-Y,whether in ABA-dependent or ABA-Independent pathway.The interaction of PYL(Pyrabactin resistance1-like)receptor proteins with Nuclear Factor Y(NF-Y)Transcription Factor in the presence of phytohormones like abscisic acid(ABA)provides one insight related to the enhanced tolerance towards abiotic stresses under ABA-dependent signaling in finger millet crop.A total of three PYL receptors of finger millet designated as EcPYL1,EcPYL5,and EcPYL9 were retrieved in the finger millet genome.These receptors were modeled through the SWISS-MODEL using templates 5gwo and 3wg8 and docked with ABA.The bestdocked protein-ligand complex PYL5-ABA(binding energyΔG=-8.8 kcal mol^(-1))was found to be most stable at the 50ns MD simulation study.Further protein-protein interaction between PYL5 and NF-YA2/B3/C1 subfamily members showed a good interaction.This clearly indicates the possibility of the NF-Y-PYL module in the ABA transduction pathway,which performs a crucial role in the expression of stress-responsive genes.These studies reveal the intricate relationship between the ABA,PYL receptors of finger millet,and NF-Y transcription factor in regulating the stress-responsive genes and provide an insight into the abiotic stress tolerance mechanisms,which can be targeted for crop improvement.

关键词： ABA receptors PYL NF-Y molecular docking Abiotic stress MD simulation Finger millet Hotspot

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Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

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The Crop Journal 2024年第2期12卷 558-568页

作者： Junqiao Song Angela Pacheco Amos Alakonya Andrea S.Cruz-Morales Carlos Muoz-Zavala Jingtao Qu Chunping Wang Xuecai Zhang Felix San Vicente Thanda Dhliwayo College of agronomy Henan University of Science and TechnologyLuoyang 471000HenanChina International Maize and Wheat Improvement Center(CIMMYT) El BatanMexico Anyang Academy of Agricultural Sciences Anyang 455000HenanChina CIMMYT-China Specialty Maize Research Center Crop Breedingand Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201403China

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

关键词： Maize stalk rot Genome-wide association mapping Haplotype analysis Genomic prediction G×E interaction

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High temperature treatment induced production of unreduced 2n pollen in Camellia oleifera

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Horticultural plant Journal 2024年第3期10卷 879-896页

作者： Hongda Deng Xiaoyu Zhang Song Sheng Yuxun Huang Ziqi Ye Tongyue Zhang Xing Liu Zhiqiang Han The Laboratory of Forestry genetics Central South University of Forestry and TechnologyChangshaHunan 410004China Yuelushan Laboratory ChangshaHunan 410128China Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education Central South University of Forestry and TechnologyChangshaHunan 410004China National Forest and Seedling Workstation of Hunan Province The Forestry Department of Hunan ProvinceChangshaHunan 410004China

Unreduced gametes through chromosome doubling play a major role in the process of plant polyploidization.Our previous work confirmed that Camellia oleifera can produce natural 2n pollen,and it is possible to induce the 2n pollen formation by high temperature treatment.This study focused on the optimization of the 2n pollen induction technique and the mechanisms of high temperature-induced2n pollen formation in C.oleifera.We found that the optimal protocol for inducing 2n pollen via high temperature was to perform 45℃with4 h at the prophaseⅠstage of the pollen mother cells(PMCs).Meanwhile,high temperature significantly decreased the yield and fertility of2n pollen.Through the observation of meiosis,abnormal chromosome and cytological behaviour was discovered under high-temperature treatment,and we confirmed that the formation of 2n pollen is caused by abnormal cell plate.Based on weighted gene co-expression network analysis,fifteen hub genes related to cell cycle control were identified.After male flower buds were exposed to heat shock,polygalacturonase gene(CoPGX3)was significantly upregulated.We inferred that high temperature causes the CoPGX3 gene to be overexpressed and that CoPGX3 is redistributed into the cytosol where it degrades cytoplasmic pectin,which leads to an abnormal cell plate.Furthermore,abnormal cytokinesis resulted in the formation of dyads and triads,and PMCs divided to produce 2n pollen.Our findings provide new insights into the mechanism of 2n pollen induced by high temperature in a woody plant and lay a foundation for further ploidy breeding of C.oleifera.

关键词： Camellia oleifera Pollen mother cells(PMCs) High temperature Meiosis 2n pollen CoPGX3

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High-Throughput Field plant Phenotyping:A Self-Supervised Sequential CNN Method to Segment Overlapping plants

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plant Phenomics 2023年第2期5卷 285-294页

作者： Xingche Guo Yumou Qiu Dan Nettleton Patrick S.Schnable department of Statistics Iowa State UniversityAmesIAUSA plant Sciences Institute Iowa State UniversityAmesIAUSA department of agronomy Iowa State UniversityAmesIAUSA

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely used.The first step in this process is typically plant segmentation,which requires a well-labeled training dataset to enable accurate segmentation of overlapping plants.However,preparing such training data is both time and labor intensive.To solve this problem,we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping systems.This first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth stages.The proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are needed.We then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and genotypes.We show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision techniques.This approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

关键词： computer preparing plant

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Sensory Phenotypic and Molecular Identification of Aromatic Rice Accessions Cultivated in Benin

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Advances in Bioscience and Biotechnology 2024年第3期15卷 195-206页

作者： Chimène Nadège Mahoussi Nanoukon Koffi David Montcho Hambada Deless Edmond Fulgence Thiémélé Bignon Meyrix Pamela Franzel Loumedjinon Babatoundé Franel Carel Wenceslas Affolabi Amed Sèmèvo Havivi Kéllya Laurinzo Déguénon Grâce Finagnon Vitoekpon Arielle Bankole Lambert Gustave Djedatin Laboratory of Molecular Biology and Bioinformatics Applied to Genomics National School of Applied Biosciences and Bio-technologies National University of Science Technology Engineering and Mathematics Dassa-Zoumè Benin Laboratory of Molecular Biology and Bioinformatics Applied to Genomics National School of Applied Biosciences and Biotechnologies National University of Science Technology Engineering and Mathematics Dassa-Zoumè Benin Laboratory of plant Horticultural and Forestry Sciences National University of Agriculture Kétou Benin genetics Teaching and Research Unit Department of Biochemistry-Genetics Peleforo GON COULIBALY University Korhogo C&#244te d’Ivoire

Rice is one of the most widely cultivated cereals in the world, and its aroma is increasingly in demand. With the advancement of research, a major rice flavor gene has been identified on rice chromosome 8. It encodes non-functional betaine aldehyde dehydrogenase leading to the accumulation of 2-acetyl-1-pyrroline which is the major olfactory compound that confers the fragrant character to rice. The aroma of rice is considered a special trait of enormous economic importance that determines the prime price in world trade. To satisfy the needs of the population and reduce rice imports into Benin, we conducted this study to identify aromatic rice accessions grown in Benin. Seventy-two rice accessions collected across Benin were PCR amplified with three SSR markers RM 7049, Aro 7, and RM 223, linked to the fgr (fragrance of rice) aroma gene. Molecular analysis revealed that 12 of the 72 accessions, namely Bagou 19, Bagou 22, Tchaka 34, Foun 15, Tchaka 41, Nana 32, Kan 61, Kung 69, Kung 67, Bagou 20, Agbab 101 and Koum 55 possess the fgr gene and can be considered as aromatic rice accessions. A sensory phenotypic test using KOH was carried out on rice accessions carrying fgr gene. Of the twelve positives, only one had the smell of aromatic rice, like the Azucena control. These results show that Benin also has aromatic rice varieties that can be sold on national and international markets.

关键词： Aromatic Rice 2-Acetyl-1-Pyrroline SSR Markers Benin

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Nutrient-hormone relations:Driving root plasticity in plants

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Molecular plant 2022年第1期15卷 86-103页

作者： Zhongtao Jia Ricardo F.H.Giehl Nicolaus von Wirén Molecular plant Nutrition Department of Physiology&Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research(IPK)Corrensstr.306466 Stadt SeelandOT GaterslebenGermany

Optimal plant development requires root uptake of 14 essential mineral elements from the soil.Since the bioavailability of these nutrients underlies large variation in space and time,plants must dynamically adjust their root architecture to optimize nutrient access and acquisition.The information on external nutrient availability and whole-plant demand is translated into cellular signals that often involve phytohormones as intermediates to trigger a systemic or locally restricted developmental response.Timing and extent of such local root responses depend on the overall nutritional status of the plant that is transmitted from shoots to roots in the form of phytohormones or other systemic long-distance signals.The integration of these systemic and local signals then determines cell division or elongation rates in primary and lateral roots,the initiation,emergence,or elongation of lateral roots,as well as the formation of root hairs.Here,we review the cascades of nutrient-related sensing and signaling events that involve hormones and highlight nutrient-hormone relations that coordinate root developmental plasticity in plants.

关键词： root development root plasticity nutrient sensing nutrient signaling plant hormones nutrient use efficiency

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Poplar wood-inside out:High-resolution spatial,cellular,and pseudotime projections from cambial transcriptomes

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Molecular plant 2023年第10期16卷 1490-1492页

作者： Shruti Choudhary Hannele Tuominen Umeåplant Science Centre Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural Sciences90183 UmeåSweden

The lifestyle of trees may seem sedentary,but behind the scenes,various meristems are busy stacking layers of cells in differentdirections,which allows trees to soar to great heights and girths.Procambial cells are formed continuously during"primarygrowth"very close to the shoot apex,guaranteeing the continuityof the vascular system throughout the stem and vertical growth.Primary growth turns,by definition,into"secondary growth"with the advent of the vascular cambium.

关键词： guarantee directions continuously

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