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Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits

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Horticulture Research 2019年第1期6卷 568-584页

作者： Aliki Xanthopoulou Javier Montero-Pau Ifigeneia Mellidou Christos Kissoudis JoséBlanca Belén Picó Aphrodite Tsaballa Eleni Tsaliki Athanasios Dalakouras Harry S.Paris Maria Ganopoulou Theodoros Moysiadis Maslin Osathanunkul Athanasios Tsaftaris Panagiotis Madesis Apostolos Kalivas Ioannis Ganopoulos Department of Genetics and Plant Breeding Aristotle University of ThessalonikiThessaloniki 54124Greece Department of Biochemistry and Molecular Biology Universitat de València46022 ValenciaSpain Institute of Plant Breeding and Genetic Resources Hellenic Agricultural Organization DEMETER(ex NAGREF)ThermiMacedonia 57001Greece Perrotis College American Farm SchoolThessaloniki 57001Greece Institute for the Conservation and Breeding of Agricultural Biodiversity(COMAV-UPV) Universitat Politècnica de ValènciaCamino de Vera s/n46022 ValenciaSpain Department of Vegetable Crops and Plant Genetics Agricultural Research OrganizationNewe Ya’ar Research CenterRamat YishayIsrael Institute of Applied Biosciences(INAB) CERTHThermi-Thessaloniki 57001Greece Department of Biology Faculty of Science Chiang Mai UniversityChiang MaiThailand Center of Excellence in Bioresources for Agriculture Industry and MedicineChiang Mai UniversityChiang MaiThailand

Cucurbita pepo contains two cultivated subspecies,each of which encompasses four fruit-shape morphotypes(cultivar groups).The Pumpkin,Vegetable Marrow,Cocozelle,and Zucchini Groups are of subsp.pepo and the Acorn,Crookneck,Scallop,and Straightneck Groups are of subsp.ovifera.Recently,a de novo assembly of the C.pepo subsp.pepo Zucchini genome was published,providing insights into its evolution.To expand our knowledge of evolutionary processes within C.pepo and to identify variants associated with particular morphotypes,we performed wholegenome resequencing of seven of these eight C.pepo morphotypes.We report for the first time whole-genome resequencing of the four subsp.pepo(Pumpkin,Vegetable Marrow,Cocozelle,green Zucchini,and yellow Zucchini)morphotypes and three of the subsp.ovifera(Acorn,Crookneck,and Scallop)morphotypes.A high-depth resequencing approach was followed,using the BGISEQ-500 platform that enables the identification of rare variants,with an average of 33.5X.Approximately 94.5%of the clean reads were mapped against the reference Zucchini genome.In total,3,823,977 high confidence single-nucleotide polymorphisms(SNPs)were identified.Within each accession,SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck,and were distributed homogeneously along the chromosomes.Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted.In fact,comparison between subspecies pepo and ovifera indicated 5710 genes(22.5%)with Fst>0.80 and 1059 genes(4.1%)with Fst=1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies.Linkage disequilibrium was greater in subsp.ovifera than in subsp.pepo,perhaps reflective of the earlier differentiation of morphotypes within subsp.ovifera.Some morphotype-specific genes have been localized.Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication

关键词： cultivar traits Whole

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Selection for production-related traits in Pelargonium zonale: improved design and analysis make all the difference

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Horticulture Research 2017年第1期4卷 365-373页

作者： Heike Molenaar Martin Glawe Robert Boehm Hans-Peter Piepho Institute of Crop Science University of HohenheimBiostatistics UnitStuttgart70599Germany Klemm+Sohn GmbH&Co.KG Stuttgart70378Germany

Ornamental plant variety improvement is limited by current phenotyping approaches and neglected use of experimental designs.The present study was conducted to show the benefits of using an experimental design and corresponding analysis in ornamental breeding regarding simulated response to selection in Pelargonium zonale for production-related traits.This required establishment of phenotyping protocols for root formation and stem cutting counts,with which 974 genotypes were assessed in a two-phase experimental design.The present paper evaluates this protocol.The possibility of varietal improvement through indirect selection on secondary traits such as branch count and flower count was assessed by genetic correlations.Simulated response to selection varied greatly,depending on the genotypic variances of the breeding population and traits.A varietal improvement of over 20%is possible for stem cutting count,root formation,branch count and flower count.In contrast,indirect selection of stem cutting count by branch count or flower count was found to be ineffective.The established phenotypic protocols and two-phase experimental designs are valuable tools for breeding of P.zonale.

关键词： breeding traits branch

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High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry

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Horticulture Research 2021年第1期8卷 2391-2403页

作者： Molla F.Mengist Hamed Bostan Elisheba Young Kristine L.Kay Nicholas Gillitt James Ballington Colin D.Kay Mario G.Ferruzzi Hamid Ashrafi Mary Ann Lila Massimo Iorizzo Plants for Human Health Institute North Carolina State UniversityKannapolisNCUSA Department of Horticultural Science North Carolina State UniversityRaleighNCUSA David H.Murdock Research Institute KannapolisNCUSA Department of Food Bioprocessing and Nutrition Sciences North Carolina State UniversityRaleighNCUSA

Fruit quality traits play a significant role in consumer preferences and consumption in blueberry(Vaccinium corymbosum L).The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry.A total of 287 F_(1) individuals derived from a cross between two southern highbush blueberry cultivars,‘Reveille’and‘Arlen’,were phenotyped over three years(2016–2018)for fruit quality-related traits,including titratable acidity,pH,total soluble solids,and fruit weight.A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers.The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM.The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits,including seven loci for fruit weight,three loci for titratable acidity,five loci for pH,and three loci for total soluble solids.Ten of these loci were detected in more than one year.These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid,and 8-13% for pH.However,the loci identified for fruit weight did not explain more than 10%of the phenotypic variance.We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits.Organic acids,citric acid,and quinic acid were significantly(Ptraits and established an association between these fruit quality traits and metabolites.

关键词： cultivar linkage traits

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The Cymbidium genome reveals the evolution of unique morphological traits

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Horticulture Research 2021年第1期8卷 3449-3463页

作者： Ye Ai Zhen Li Wei-Hong Sun Juan Chen Diyang Zhang Liang Ma Qing-Hua Zhang Ming-Kun Chen Qing-Dong Zheng Jiang-Feng Liu Yu-Ting Jiang Bai-Jun Li Xuedie Liu Xin-Yu Xu Xia Yu Yu Zheng Xing-Yu Liao Zhuang Zhou Jie-Yu Wang Zhi-Wen Wang Tai-Xiang Xie Shan-Hu Ma Jie Zhou Yu-Jie Ke Yu-Zhen Zhou Hsiang-Chia Lu Ke-Wei Liu Feng-Xi Yang Gen-Fa Zhu Laiqiang Huang Dong-Hui Peng Shi-Pin Chen Siren Lan Yves Van de Peer Zhong-Jian Liu Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhouChina Department of Plant Biotechnology and Bioinfor matics Ghent UniversityGentBelgium VIB Center for Plant Systems Biology GentBelgium College of Forestry Fujian Agriculture and Forestry UniversityFuzhouChina Management Office of Yushan Scenic Area FuzhouChina College of Agriculture and Biotechnology Zhejiang UniversityHangzhouChina Key Laboratory of Plant Resource Conservation and Sustainable Utilization South China Botanical GardenChinese Academy of SciencesGuangzhouChina PubBio-Tech WuhanChina Tsinghua-Berkeley Shenzhen Institute(TBSI) Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody The rapyState Key Laboratory of Chemical OncogenomicsState Key Laboratory of Health Sciences and TechnologyInstitute of Biopha rmaceutical and Health Engineering(iBHE)Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization Environmental Horticulture Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina Department of Biochemistry Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa College of Horticulture Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina Henry Fok College of Biology and Agriculture Shaoguan UniversityShaoguanChina Institute of Vegetable and Flowers Shandong Academy of Agricultural SciencesJinanChina

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms.The genus Cymbidium in Orchidaceae is well known for its unique vegetation,floral morphology,and flower scent traits.Here,a chromosomescale assembly of the genome of Cymbidium ensifolium(Jianlan)is presented.Comparative genomic analysis showed that C.ensifolium has experienced two whole-genome duplication(WGD)events,the most recent of which was shared by all orchids,while the older event was the t event shared by most monocots.The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation,and flower shape mutations in C.ensifolium were shown to be associated with the abnormal expression of MADS-box genes.The most abundant floral scent components identi fied included methyl jasmonate,acacia alcohol and linalool,and the genes involved in the floral scent component network of C.ensifolium were determined.Furthermore,the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves,while the increased expression of MADS-box genes in leaves led to perianth-like leaves.Our results provide fundamental insights into orchid evolution and diversi fication.

关键词： traits evolution establishing

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Genome-wide association study of berryrelated traits in grape[Vitis vinifera L.]based on genotyping-by-sequencing markers

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Horticulture Research 2019年第1期6卷 1655-1667页

作者： Da-Long Guo Hui-Li Zhao Qiong Li Guo-Hai Zhang Jian-Fu Jiang Chong-Huai Liu Yi-He Yu College of Forestry Henan University of Science and TechnologyLuoyang 471023 Henan ProvinceChina Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhou 450009 Henan ProvinceChina

Deciphering the genetic control of grape berry traits is crucial for optimizing yield,fruit quality,and consumer acceptability.In this study,an association panel of 179 grape genotypes comprising a mixture of ancient cultivars,landraces,and modern varieties collected worldwide were genotyped with genotyping-by-sequencing using a genome-wide association approach based on 32,311 single-nucleotide polymorphism(SNP)markers.Genome-wide efficient mixed-model association was selected as the optimal statistical model based on the results of known control loci of grape berry color traits.Many of the associated SNPs identified in this study were in accordance with the previous QTL analyses using biparental mapping.The grape skin color locus was found to be associated with a mybA transcription factor on chromosome 2.Two strong and distinct association signals associated with berry development periods were found on chromosome 16.Most candidate genes of the interval were highlighted as receptor-like protein kinase.For berry weight,significant association loci were identified on chromosome 18,as previously known,and on chromosome 19 and chromosome 17,as newly mapped.Berry flesh texture was newly located on chromosome 16;candidate genes in the interval were related to calcium.Berry flavor was determined on chromosome 5.Genomic regions were further investigated to reveal candidate genes.In this work,we identified interesting genetic determinants of grape berry-related traits.The identification of the markers closely associated with these berry traits may be useful for grape molecular breeding.

关键词： cultivar traits Berry

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Morphological and Physiological traits of Assistance in the Selection of High Yielding Varieties of Durum Wheat (Triticum turgidumL. spp. Durum) for the Rainfed Mediterranean Environments of Central Chile

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American Journal of Plant Sciences 2012年第12期3卷 1809-1819页

作者： Gerlitt González Ribot Paola Silva Edmundo Acevedo Facultad de Ciencias Agronómicas Universidad de Chile Santiago Chile

Chile has high potential to produce quality durum wheat;however, it is not self-sufficient. It is necessary to increase durum grain yield in the Mediterranean rainfed areas which are characterized by adverse environmental conditions, mainly, water deficit. The criteria normally used by breeders to select varieties of wheat for these environments are yield under stress and early flowering. The objective of this monograph is to propose that the selection of high yielding genotypes of durum wheat, under Chilean Mediterranean rainfed conditions, be assisted by morphological and physiological traits associated with yield in order to increase its heritability.

关键词： Rainfed Mediterranean Durum Wheat Morphological Physiological traits

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Comparison between the Quality traits of Phosphate and Bicarbonate-Marinated Chicken Breast Fillets Cooked under Different Heat Treatments

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Food and Nutrition Sciences 2014年第1期5卷 35-44页

作者： Samer Mudalal Massimiliano Petracci Silvia Tappi Pietro Rocculi Claudio Cavani Department of Agricultural and Food Sciences Alma Mater Studiorum-University of Bologna Cesena Italy Department of Agricultural and Food Sciences Alma Mater Studiorum-University of Bologna Cesena Italy.

Because the use of phosphates has being recently diminished in meat industry due to the nutritional drawbacks of phosphates, some researchers started to evaluate sodium bicarbonate as phosphate replacer in meat products. The aim of this study was to evaluate the effect of different temperature combinations of dry air-cooking treatments (Air and Core temperatures: 160 - 76, 160 - 80, 200 - 76 and 200℃ - 80℃, respectively) on chemical composition, texture properties, water activity, freezable water and bound water, color, pH, and water binding capacity of phosphate and bicarbonate-marinated chicken breast. A batch of 24 h post-mortem broiler breast meat of 80 fillets was divided into two groups of marination treatments (0.3% sodium bicarbonate n = 40, 0.3% sodium tripolyphosphate n = 40) and was vacuum tumbled (45 min, ?0.95 mbar, 20 rpm). Different temperature-combinations cooking treatments significantly modified the chemical composition. Bicarbonate marinated fillets showed higher ability to retain water (67.3% vs. 65.7%, P 0.05) during severe heat treatment and lower cook losses (30.7% vs. 33.4%, P 0.05) when compared with phosphate-marinated fillets. The effect of changing the cooking temperatures on Texture Profile Analysis (hardness, cohesiveness, gumminess, springiness, and chewiness) was more tangible in phosphate marinated fillets than bicarbonate. Bicarbonate-marinated fillets showed significant differences in the percentage of bound water, latent heat, and water activity after cooking in comparison to phosphate-marinated fillets. The results of this study revealed that phosphate-marinated fillets interacted with heat treatments in different patterns in comparison with bicarbonate-marinated fillets.

关键词： Chicken Meat Marination Sodium Bicarbonate Heat Treatment Quality traits

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Study on Quality traits for Steamed Bread Made from 25 Representative Wheat Varieties in Shandong Province

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Agricultural Sciences 2019年第4期10卷 499-507页

作者： Juan Liu Jichun Tian Peng Wu Xiangyang Li Chao Li College of Food Science and Engineering Shandong Agricultural University/Key Laboratory of Food Processing Technology and Quality Control in Shandong Province Taian China Group of Quality Wheat Breading Shandong Agricultural University/State Key Laboratory of Crop Biology Taian China Agricultural Environment Protection Station Taian China

In order to study steamed bread quality traits and explore good wheat cultivars, 25 wheat cultivars grown in Shandong province were used through one-process fermentation procedure to examine the variability of steamed bread quality traits and the correlation between quality and score. The results showed that all the steamed bread quality traits expressed large variable coefficient except volume, L* value, l* value and cohesiveness traits, which suggested that the genetic diversity made from wheat in Shandong province was large. The average comprehensive score of the steamed bread was 76.8 for the tested 25 varieties, and ten varieties reached the good steamed bread level, which were Liangxing 99, Luyuan 205, Jimai 22, Jinan 17, Tainong 19, Wennong 17, Huaiyin 84137, and Huaimai 8. The main quality factors affecting the steamed bread score were volume, L* value, A* value, hardness, chewiness, and adhesiveness. Among these factors, the adhesiveness has a significantly positive correlation with the hardness and cohesive, and the volume has a significantly positive correlation with the A* value. The volume, L* value has a significantly positive correlation with score, A* value, hardness and chewiness, and gumminess has a significantly negative correlation with the score. There was no correlation between the score and other traits. The results will benefit the understanding of steamed bread quality in wheat cultivated in Shandong. l

关键词： Wheat Steamed Bread Quality traits Variable Coefficient Correlation Coefficient

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Ethical Ideologies, Personality traits, and Whistleblowing Intention in Public Sector: Mediating Role of Whistleblowing Judgment

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Journal of Modern Accounting and Auditing 2019年第5期15卷 241-248页

作者： Intan Salwani Mohamed Nabilah Rozzani Noor Hidayah Ab Aziz Richard Hicks Universiti Teknologi MARA Shah Alam Malaysia Management & Science University Shah Alam Malaysia Universiti Teknologi MARA Segamat Malaysia Bond University Queensland Australia

Whistleblowing decision by an individual employee has always been an interesting topic in the management of businesses and organizations. Whistleblowing can be an effective fraud detection mechanism if a person decided to whistleblow on the wrongdoings of other employees. In reality, however, individuals who are aware of unlawful activity of his or her peer group members would face a challenging dilemma if the company or organizations they are working with do not have a sound whistleblowing policy to ensure the confidentiality of whistleblower. Knowing the factors that could influence their whistleblowing judgement and intention would be an interesting topic to be studied. The present study attempts to discuss on factors which would influence whistleblowing intention on staffs from selected public sector organizations in Malaysia. These factors include three individual level factors of ethical ideology (idealism and relativism), personality traits (conscientiousness, openness to experience, extraversion, agreeableness, neuroticism), and whistleblowing judgment, all with regards to peer reporting. A theoretical model is developed in accordance to the issues discussed in this paper.

关键词： whistleblowing intention whistleblowing judgement ethical ideology personality traits

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Association analyses of single nucleotide polymorphisms in the leptinand leptin receptorgenes on milk and morphological traits in Holstein cows

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Open Journal of Animal Sciences 2012年第3期2卷 174-182页

作者： Giovanna De Matteis Maria Carmela Scatà Francesco Grandoni Francesca Petrera Fabio Abeni Gennaro Catillo Francesco Napolitano Bianca Moioli Agricultural Research Council-Animal Production Research Centre (CRA-PCM) Animal Production Research Centre Via Salaria Monterotondo Roma Italy Agricultural Research Council-Research Centre for Fodder Crops and Dairy Productions (CRA-FLC) Research Centre for Fodder Crops and Dairy Productions Via Porcellasco Cremona Italy

To date, only a few SNP in the leptin receptor gene have been detected and analyzed while the leptin gene has been extensively characterized and several polymorphisms were detected and associated to functional and productive traits in cattle. In this work, for the first time, the bovine leptin receptor gene was fully characterized by sequencing the whole coding region and part of the 5’ flanking region. A group of 95 Holstein cows was genotyped in order to search for SNP at both the LEPR and LEP genes, and to associate them with milk and morphological traits. Nine novel SNP in the leptin receptor gene and one novel SNP in the leptin gene were detected. Four SNP of the leptin receptor gene and one SNP of leptin gene showed a significant effect on one or more analyzed traits, and, in all cases, the greatest effect was observed on fat content. This study provided knowledge of the existence of further polymorphisms in the leptin receptor and leptin genes that have an influence on some important economic traits.

关键词： Polymorphis leptin Gene leptin Receptor Gene and Dairy traits

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