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Rice-wheat comparative genomics:Gains and gaps

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The Crop Journal 2024年第3期12卷 656-669页

作者： Akila Wijerathna-Yapa Ruchi Bishnoi Buddhini Ranawaka Manu Maya Magar Hafeez Ur Rehman Swati G.Bharad Michal T.Lorenc Vinita Ramtekey Sasha Gohar Charu Lata Md.Harun-Or-Rashid Maryam Razzaq Muhammad Sajjad Bhoja *** School of Agriculture and Food Sustainability The University of QueenslandSt LuciaQLD 4072Australia ARC Centre of Excellence for plant Success in Nature and Agriculture The University of QueenslandSt LuciaQLD 4072Australia department of Genetics and plant Breeding College of AgricultureUmmedganj-KotaAgriculture UniversityKotaRajasthan 324001India Centre for Agriculture and the Bioeconomy Queensland University of Technology(QUT)2 George StreetBrisbaneQLD 4000Australia UWA School of Agriculture and Environment The University of Western Australia35 Stirling HighwayCrawleyWA 6009Australia Nepal Agriculture research Council KhumaltarLalitpurNepal department of Agronomy University of AgricultureFaisalabad 38040Pakistan department of Agricultural Botany Dr Panjabrao Deshmukh Krishi VidyapeethAkola 444104MaharashtraIndia ICAR-Indian Institute of seed Science MauUttar Pradesh 275103India School of Natural Sciences Macquarie UniversityMacquarie ParkNSW 2109Australia ICAR-Indian Institute of Wheat and Barley research Flowrdale 54642ShimlaIndia International Maize and Wheat improvement Center(CIMMYT)Bangladesh Office Gulshan-2Dhaka 1212Bangladesh Center for seed Science University of AgricultureFaisalabad 38000Pakistan department of Biosciences COMSATS University IslamabadPark RoadTarlai KalanIslamabad 45550Pakistan CGIAR’s Excellence in Breeding(EiB)Platform/Accelerated Breeding Initiative International Maize and Wheat Improvement Center(CIMMYT)El Batán 56237Mexico

Rice and wheat provide nearly 40%of human calorie and protein *** share a common ancestor and belong to the Poaceae(grass)*** their genetic homology is crucial for developing new cultivars with enhanced *** wheat genes and gene families have been characterized based on their rice ***–wheat orthology can identify genetic regions that regulate similar traits in both ***–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping,deduce their putative functions and biochemical pathways,and develop molecular markers for marker-assisted breeding.A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering,gene editing,or wide crossing.

关键词： Comparative genomics Orthologs Genes Synteny Genetic engineering Molecular breeding

Creating large EMS populations for functional genomics and breeding in wheat

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Journal of Integrative Agriculture 2024年第2期23卷 484-493页

作者： 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 Spring Valley Agriscience Co. Ltd.Jinan 250300China College of Life Sciences Zaozhuang UniversityZaozhuang 277160China National Key Laboratory of Wheat improvement College of AgronomyShandong Agricultural UniversityTai’an 271018China department of plant Pathology University of CaliforniaDavisCA 95616USA

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 *** methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant *** 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 *** were also rare mutations,including 30 independent tillers each with double *** M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 *** advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)*** other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide *** MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

关键词： wheat germplasm ethyl methane sulfonate genetics and breeding

Genetic Diversity in Cowpea (Vigna unguiculata (L.) Walp) under Two Growing Conditions^*

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Advances in Bioscience and Biotechnology 2024年第5期15卷 310-324页

作者： Omotola Oluwakemi Dairo department of plant Breeding and seed Technology Federal University of Agriculture Abeokuta Nigeria College of Education and Liberal Art Wilmington University Delaware USA

This study explores the use of genetic variability for advancing the genetic improvement of Cowpea (Vigna unguiculata (L.) Walp), particularly in response to insect infestation stress. Over a period spanning 2015 to 2017, forty accessions of cowpeas were evaluated to determine their variability under both insecticide spray and no insecticide spray conditions at the Teachings and research Farms, Federal University of Agriculture, Abeokuta. The experimental design was a randomized complete block design in three replicates. The accessions were evaluated for plant height, leaf length, leaf width, number of days of 50% flowering, number of pods per plant, pod length, number of seeds per plant, 100-seed weight, and seed yield. Data collected were subjected to principal component and single linkage cluster analyses. Principal axis I (PCA1) accounted for 39% and 35% under insecticide spray and no insecticide spray respectively to the total variation in the accessions. plant height with a factor score of 0.38, leaf length (0.41), number of leaves (0.37), and 100-seed, weight (0.30) was related to PCAI under insecticide spray while leaf width (0.32). Pod length (0.37) and number of seeds/plant (0.38) were significant to PCA1 under no insecticide spray. Notably, accessions such as SAMPEA6, SAMPEA10, IFE-Brown, and IFE-BPE exhibited consistent performance across both conditions, while others displayed condition-specific attributes. For instance, NGB1063, NGB1152, and NGB1093 demonstrated distinct traits under insecticide spray, while NGB1146 and NGB1124 exhibited notable characteristics under no insecticide spray conditions. Therefore, identifying these forty accessions with desirable traits hold promise for future genetic improvement efforts of cowpea cultivation in Nigeria and beyond.

关键词： Cowpea Vigna Unguiculata Genetic Diversity Cowpea Accessions

Tomato CYP94C1 inactivates bioactive JA-lle to attenuate jasmonate-mediated defense during fruit ripening

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Molecular plant 2024年第4期17卷 509-512页

作者： Tianxia Yang Lei Deng Qinyang Wang Chuanlong Sun Muhammad Ali Fangming Wu Huawei Zhaj Qian Xu Peiyong Xin Shujing Cheng Jinfang Chu Tingting Huang Chang-Bao Li Chuanyou Li Key Laboratory of seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China College of Life Sciences Shandong Agricultural UniversityTai'an 271018China Taishan Academy of Tomato Innovation Tai'an 271018China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China College of Horticulture Science and Engineering Shandong Agricultural UniversityTaian 271018China Institute of Vegetable Qingdao Academy of Agricultural SciencesQingdao 266100China Key Laboratory of Biology and Genetic improvement of Horticultural Crops(North China) Ministry of AgricultureBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBejing 100097China Frontiers Science Center for Molecular Design Breeding(MOE) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Dear Editor,Fruit rot caused by necrotrophic pathogens results in substantial reductions in fruit yield and revenues worldwide(Petrasch et al.,2019).A widespread phenomenon in fleshy fruit species is the susceptibility of ripe fruits to necrotrophs(Silva et al.,2021),which facilitates seed dispersal(Forlani et al.,2019)but causes severe post-harvest losses in *** most of the nutritional and sensory qualities of fruits are elaborated at the ripening stage(Liu et al.,2015),balancing fruit ripening and pathogen resistance to maintain fruit quality has proven to be challenging.A deeper understanding of the mechanisms underlying the increased susceptibility of fruits to necrotrophs during ripening could lead to new strategies for producing necrotrophy-resistant fruits without compromising ripening-relatedquality.

关键词： susceptibility maintain fruit

Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

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Journal of Integrative plant Biology 2024年第2期66卷 228-251页

作者： Yezi Xiang Taikui Zhang Yiyong Zhao Hongjin Dong Hongyi Chen Yi Hu Chien-Hsun Huang Jun Xiang Hong Ma State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China department of Biology Howard Hughes Medical InstituteDuke UniversityDurhamNC 27708USA department of Biology the Eberly College of Scienceand the Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA 16802USA Hubei Key Laboratory of Economic Forest Germplasm improvement and Resources Comprehensive Utilization College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggang 438000China

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and *** we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain *** this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial *** robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and ***,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple *** of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and *** new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversificat

关键词： angiosperm fruit evolution MADS-box molecular clock nuclear phylogeny ovary and fruit developmental genes

A 1-bp deletion in the MC04g1399 is highly associated with failure to produce fruit wart in bitter gourd

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Horticultural plant Journal 2024年第1期10卷 171-180页

作者： Jia Liu Junjie Cui Jichi Dong Jian Zhong Chunfeng Zhong Fanchong Yuan Wendong Guan Fang Hu Jiaowen Cheng Kailin Hu College of Horticulture South China Agricultural UniversityGuangzhouGuangdong 510642China Key Laboratory of Biology and Genetic improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural AffairsGuangzhouGuangdong 510642China Guangdong Vegetables Engineering research Center GuangzhouGuangdong 510642China department of Horticulture Foshan UniversityFoshanGuangdong 528225China Henry Fok School of Biology and Agricultural Shaoguan UniversityShaoguanGuangdong 512023China

Fruit wart is an important appearance trait influencing consumer preferences of bitter gourd(Momordica charantia L.).The molecular genetic mechanisms underlying fruit wart formation in bitter gourd are largely *** this study,genetic analysis based on four generations showed that fruit wart formation in bitter gourd was controlled by a single dominant locus named as *** Fwa locus was initially mapped into a 4.82 Mb region on pseudochromosome 4 by BSA-seq analysis and subsequently narrowed down to a 286.30 kb region by linkage analysis.A large F2population consisting of 2360 individuals was used to screen recombinants,and the Fwa locus was finally fine mapped into a 22.70 kb region harboring four protein-coding genes through recombination ***04g1399,encoding an epidermal patterning factor 2-like protein,was proposed as the best candidate gene for Fwa via sequence variation and expression *** addition,a 1-bp insertion and deletion(InDel)variation within MC04g1399 was converted to a cleaved amplified polymorphic sequence(CAPS)marker that could precisely distinguish between the warty and non-warty types with an accuracy rate of 100%among a wide panel of 126 bitter gourd germplasm *** results not only provide a scientific basis for deciphering the molecular mechanisms underlying fruit wart formation but also provide a powerful tool for efficient genetic improvement of fruit wart via marker-assisted selection.

关键词： Bitter gourd Fruit wart Bulk segregant analysis Fine-mapping Candidate gene

Identification of P-type plasma membrane H^(+)-ATPases in common wheat and characterization of TaHA7 associated with seed dormancy and germination

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Journal of Integrative Agriculture 2024年第7期23卷 2164-2177页

作者： Bingli Jiang Wei Gao Yating Jiang Shengnan Yan Jiajia Cao Litian Zhang Yue Zhang Jie Lu Chuanxi Ma Cheng Chang Haiping Zhang Key Laboratory of Wheat Biology and Genetic improvement on Southern Yellow&Huai River Valley Ministry of Agriculture and Rural Affairs/College of AgronomyAnhui Agricultural UniversityHefei 230036China

The P-type plasma membrane(PM)H^(+)-ATPases(HAs)are crucial for plant development,growth,and *** HAs have been thoroughly characterized in many different ***,despite their importance,the functions of HAs in germination and seed dormancy(SD)have not been validated in ***,we identified 28 TaHA genes(TaHA1-28)in common wheat,which were divided into five *** examination of gene expression in strong-and weak-SD wheat varieties led to the discovery of six candidate genes(TaHA7/-12/-14/-16/-18/-20).Based on a single nucleotide polymorphism(SNP)mutation(C/T)in the TaHA7 coding region,a CAPS marker(HA7)was developed and validated in 168 wheat varieties and 171 Chinese mini-core collections that exhibit diverse germination and SD *** further verified the roles of the two allelic variations of TaHA7 in germination and SD using wheat mutants mutagenized with ethyl methane sulphonate(EMS)in‘Jimai 22’and‘Jing 411’backgrounds,and in transgenic Arabidopsis ***7 appears to regulate germination and SD by mediating gibberellic acid(GA)and abscisic acid(ABA)signaling,metabolism,and *** results presented here will enable future research regarding the TaHAs in wheat.

关键词： wheat P-type plasma membrane H^(+)-ATPase seed dormancy abscisic acid gibberellin

Integrating artificial intelligence and high-throughput phenotyping for crop improvement

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Journal of Integrative Agriculture 2024年第6期23卷 1787-1802页

作者： Mansoor Sheikh Farooq Iqra Hamadani Ambreen Kumar A Pravin Manzoor Ikra Yong Suk Chung Phenomics Laboratory Department of Plant Resources and EnvironmentJeju National UniversityJeju 63234Republic of Korea Council of Scientific&Industrial research Indian Institute of Integrative MedicinePulwamaJ&K 192301India Animal and Dairy Science University of WisconsinMadisonWI 530706United States of America Division of Fruit Science Faculty of HorticultureSher-e-Kashmir University of Agricultural Sciences and Technology of KashmirSrinagar 190025India

Crop improvement is crucial for addressing the global challenges of food security and sustainable *** advancements in high-throughput phenotyping(HTP)technologies and artificial intelligence(AI)have revolutionized the field,enabling rapid and accurate assessment of crop traits on a large *** integration of AI and machine learning algorithms with HTP data has unlocked new opportunities for crop *** algorithms can analyze and interpret large datasets,and extract meaningful patterns and correlations between phenotypic traits and genetic *** technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection,thereby reducing the time and cost required for variety ***,further research and collaboration are needed to overcome the existing challenges and fully unlock the power of HTP and AI in crop *** leveraging AI algorithms,researchers can efficiently analyze phenotypic data,uncover complex patterns,and establish predictive models that enable precise trait selection and crop *** aim of this review is to explore the transformative potential of integrating HTP and AI in crop *** review will encompass an in-depth analysis of recent advances and applications,highlighting the numerous benefits and challenges associated with HTP and AI.

关键词： artificial intelligence crop improvement data analysis high-throughput phenotyping machine learning precision agriculture trait selection

Evaluation of proline, chlorophyll, soluble sugar content and uptake of nutrients in the German chamomile (Matricaria chamomilla L.) under drought stress and organic fertilizer treatments

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Asian Pacific Journal of Tropical Biomedicine 2016年第10期6卷 886-891页

作者： Amin Salehi Hamidreza Tasdighi Majid Gholamhoseini Agronomy and plant Breeding department Yasouj University Oil seed Crops department Seed and Plant Improvement Institute Agricultural Research Education and Extension Organization (AREEO)

Objective: To investigate the effect of drought stress and organic fertilizer on German chamomile(Matricaria chamomilla) nutrient uptake, leaf chlorophyll content and osmotic adjustment under field ***: This experiment was carried out through a randomized complete block design with a split factorial arrangement of treatments in three replications. The main plots were subjected to the following irrigation treatments: irrigation after 60, 90, 120, 150 and180 mm evaporation from Class A pan. The sub-plots were treated with three vermicompost doses(0, 5 and 10 t/ha).Results: Although drought stress reduced the nutrient percentages in the shoots, application of vermicompost enhanced the nutrient percentages, particularly when the plants were subjected to moderate to severe drought stress conditions. Moreover, the results of this study showed that the interaction between irrigation treatments and vermicompost rates on leaf chlorophyll content was significant. Comparison between the combined treatments indicated that under normal irrigation and moderate drought stress conditions chamomile plants received 5 and 10 t/ha vermicompost showed significantly higher leaf chlorophyll content comparing to the control ***: Totally, organic fertilization by vermicompost could partly alleviate the effect of drought stress on chamomile by increasing N, P and K uptake and leaf soluble sugar, especially in stressed treatments.

关键词： German chamomile(Matricaria chamomilla) Drought stress Osmotic adjustment Organic fertilizer Vermicompost