keyword
https://read.qxmd.com/read/38504885/plant-necrotrophic-bacterial-disease-resistance-phenotypes-qtl-and-metabolites-identified-through-integrated-genetic-mapping-and-metabolomics-in-solanum-species
#21
JOURNAL ARTICLE
Janak R Joshi, Dev Paudel, Ethan Eddy, Amy O Charkowski, Adam L Heuberger
Most food crops are susceptible to necrotrophic bacteria that cause rotting and wilting diseases in fleshy organs and foods. All varieties of cultivated potato ( Solanum tuberosum L.) are susceptible to diseases caused by Pectobacterium species, but resistance has been demonstrated in wild potato relatives including S. chacoense . Previous studies demonstrated that resistance is in part mediated by antivirulence activity of phytochemicals in stems and tubers. Little is known about the genetic basis of antivirulence traits, and the potential for inheritance and introgression into cultivated potato is unclear...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38504151/chromosome-level-genome-assembly-provides-insights-into-the-genome-evolution-and-functional-importance-of-the-phenylpropanoid-flavonoid-pathway-in-thymus-mongolicus
#22
JOURNAL ARTICLE
Zhenhua Dang, Ying Xu, Xin Zhang, Wentao Mi, Yuan Chi, Yunyun Tian, Yaling Liu, Weibo Ren
BACKGROUND: Thymus mongolicus (family Lamiaceae) is a Thyme subshrub with strong aroma and remarkable environmental adaptability. Limited genomic information limits the use of this plant. RESULTS: Chromosome-level 605.2 Mb genome of T. mongolicus was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified...
March 19, 2024: BMC Genomics
https://read.qxmd.com/read/38497586/chromosome-level-reference-genome-and-resequencing-of-322-accessions-reveal-evolution-genomic-imprint-and-key-agronomic-traits-in-adzuki-bean
#23
JOURNAL ARTICLE
Liwei Chu, Kai Yang, Chunhai Chen, Bo Zhao, Yanan Hou, Wanqiu Wang, Pu Zhao, Kaili Wang, Binhu Wang, Ying Xiao, Yongqiang Li, Yisong Li, Qijian Song, Biao Liu, Ruoxi Fan, Abhishek Bohra, Jianping Yu, Eva C Sonnenschein, Rajeev K Varshney, Zhixi Tian, Jianbo Jian, Ping Wan
Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated...
March 18, 2024: Plant Biotechnology Journal
https://read.qxmd.com/read/38495466/use-of-remote-sensing-for-linkage-mapping-and-genomic-prediction-for-common-rust-resistance-in-maize
#24
JOURNAL ARTICLE
Alexander Loladze, Francelino A Rodrigues, Cesar D Petroli, Carlos Muñoz-Zavala, Sergio Naranjo, Felix San Vicente, Bruno Gerard, Osval A Montesinos-Lopez, Jose Crossa, Johannes W R Martini
Breeding for disease resistance is a central component of strategies implemented to mitigate biotic stress impacts on crop yield. Conventionally, genotypes of a plant population are evaluated through a labor-intensive process of assigning visual scores (VS) of susceptibility (or resistance) by specifically trained staff, which limits manageable volumes and repeatability of evaluation trials. Remote sensing (RS) tools have the potential to streamline phenotyping processes and to deliver more standardized results at higher through-put...
March 15, 2024: Field Crops Research
https://read.qxmd.com/read/38493093/physiological-responses-to-drought-stress-of-three-pine-species-and-comparative-transcriptome-analysis-of-pinus-yunnanensis-var-pygmaea
#25
JOURNAL ARTICLE
Feng Xiao, Yang Zhao, Xiurong Wang, Xueyan Jian, Yao Yang
Drought stress can significantly affect plant growth, development, and yield. Fewer comparative studies have been conducted between different species of pines, particularly involving Pinus yunnanensis var. pygmaea (P. pygmaea). In this study, the physiological indices, photosynthetic pigment and related antioxidant enzyme changes in needles from P. pygmaea, P. elliottii and P. massoniana under drought at 0, 7, 14, 21, 28 and 35 d, as well as 7 days after rehydration, were measured. The PacBio single-molecule real-time (SMRT) and Illumina RNA sequencing were used to uncover the gene expression differences in P...
March 16, 2024: BMC Genomics
https://read.qxmd.com/read/38489164/genome-wide-association-study-gwas-reveals-polygenic-architecture-for-limber-pine-quantitative-disease-resistance-to-white-pine-blister-rust
#26
JOURNAL ARTICLE
Jun-Jun Liu, Richard A Sniezko, Sydney Houston, Jodie Krakowski, Genoa Alger, Andy Benowicz, Robert Sissons, Arezoo Zamany, Holly Williams, Angelia Kegley, Benjamin Rancourt
Development of durable resistance effective against a broad range of pathotypes is crucial for restoration of pathogen-damaged ecosystems. This study dissected the complex genetic architecture for limber pine quantitative disease resistance (QDR) to Cronartium ribicola using a genome-wide association study (GWAS). Eighteen-month-old seedlings were inoculated for resistance screening under controlled conditions. Disease development was quantitatively assessed for QDR-related traits over four years post inoculation...
March 15, 2024: Phytopathology
https://read.qxmd.com/read/38488269/genetic-underpinnings-of-arthropod-community-distributions-in-populus-trichocarpa
#27
JOURNAL ARTICLE
Sandra J Simon, Anna Furches, Hari Chhetri, Luke Evans, Chanaka Roshan Abeyratne, Piet Jones, Gina Wimp, David Macaya-Sanz, Daniel Jacobson, Timothy J Tschaplinski, Gerald A Tuskan, Stephen P DiFazio
Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition...
March 15, 2024: New Phytologist
https://read.qxmd.com/read/38487297/dissecting-the-complex-genetic-basis-of-pre-and-post-harvest-traits-in-vitis-vinifera-l-using-genome-wide-association-studies
#28
JOURNAL ARTICLE
Julian García-Abadillo, Paola Barba, Tiago Carvalho, Viviana Sosa-Zuñiga, Roberto Lozano, Humberto Fanelli Carvalho, Miguel Garcia-Rojas, Erika Salazar, Julio Isidro Y Sánchez
Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding...
February 2024: Horticulture Research
https://read.qxmd.com/read/38486454/dissecting-the-molecular-basis-of-spike-traits-by-integrating-gene-regulatory-network-and-genetic-variation-in-wheat
#29
JOURNAL ARTICLE
Guo Ai, Chao He, Siteng Bi, Ziru Zhou, Ankui Liu, Xin Hu, Yanyan Liu, Liujie Jin, JiaCheng Zhou, Heping Zhang, Dengxiang Du, Hao Chen, Xin Gong, Sulaiman Saeed, Handong Su, Caixia Lan, Wei Chen, Qiang Li, Hailiang Mao, Lin Li, Hao Liu, Dijun Chen, Kerstin Kaufmann, Khaled F Alazab, Wenhao Yan
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes affecting the spike traits. Here, we systematically identify genes involved in spike trait formation by integrating the information of genomic variation and gene regulatory network (GRN) controlling young spike development in wheat...
March 14, 2024: Plant communications
https://read.qxmd.com/read/38486452/the-super-pangenome-of-populus-unveil-genomic-facets-for-its-adaptation-and-diversification-in-widespread-forest-trees
#30
JOURNAL ARTICLE
Tingting Shi, Xinxin Zhang, Yukang Hou, Changfu Jia, Xuming Dan, Yulin Zhang, Yuanzhong Jiang, Qiang Lai, Jiajun Feng, Jianju Feng, Tao Ma, Jiali Wu, Shuyu Liu, Lei Zhang, Zhiqin Long, Liyang Chen, Nathaniel R Street, Pär K Ingvarsson, Jianquan Liu, Tongming Yin, Jing Wang
Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions...
March 13, 2024: Molecular Plant
https://read.qxmd.com/read/38486237/different-divergence-processes-of-isoglosses-of-folk-nomenclature-between-wild-trees-and-rice-landraces-imply-the-need-for-different-conservation-planning-based-on-the-type-of-plant-resources
#31
JOURNAL ARTICLE
Yoshinori Tokuoka, Mincheol Seo, Hiroshi Hayakawa, Fukuhiro Yamasaki, Kenichiro Kimura, Kenji Takashima, Kiyokazu Hashigoe, Hiromitsu Matsui, Mitsunori Oka
BACKGROUND: The intensification of production and socio-economic changes have accelerated the loss of local traditional knowledge and plant resources. Understanding the distribution and determinants of such biocultural diversity is essential in planning efficient surveys and conservation efforts. Because the concept of biocultural diversity in socio-ecological adaptive systems comprises biological, cultural, and linguistic diversity, linguistic information should serve as a surrogate for the distribution of local biological and cultural diversity...
March 14, 2024: Journal of Ethnobiology and Ethnomedicine
https://read.qxmd.com/read/38484681/potential-locus-w-and-candidate-gene-mcprr2-associated-with-pericarp-pigment-accumulation-in-bitter-gourd-momordica-charantia-l-revealed-via-bsa-seq-analysis
#32
JOURNAL ARTICLE
Jinju Guo, Xin Han, Tingquan Wu, Rui Wang, Junhong Zhao, Rufang Wang, Delong Tan, Shijuan Yan, Jie Gao, Wenjie Huang, Huiyao Zhang, Changyuan Zhang
Pericarp color is a prominent agronomic trait that exerts a significant impact on consumer and breeder preferences. Genetic analysis has revealed that the pericarp color of bitter gourd is a quantitative trait. However, the underlying mechanism for this trait in bitter gourd remains largely unknown. In the present study, we employed bulked segregant analysis (BSA) to identify the candidate genes responsible for bitter gourd pericarp color (specifically, dark green versus white) within F2 segregation populations resulting from the crossing of B07 (dark green pericarp) and A06 (white pericarp)...
March 8, 2024: Plant Physiology and Biochemistry: PPB
https://read.qxmd.com/read/38480216/updated-checklist-of-treehoppers-of-panama-hemiptera-membracidae-with-plant-associations
#33
JOURNAL ARTICLE
Dawn J Flynn
An updated checklist of treehoppers (Hemiptera: Membracidae) of Panama is provided with known province distribution data. The world catalogue of Membracoidea, through April, 1997, lists 68 genera, 162 species, and 1 subspecies from Panama (McKamey, 1998). Flynn (2012) listed all known species from Panama, documenting range extensions for 29 genera, 107 species, and 1 subspecies previously unknown from Panama, bringing the treehopper fauna from Panama to 97 genera, 269 species, and 2 subspecies. Inspection of 768 additional specimens since 2012 (new total of 3,595 specimens for the study), in addition to published literature, has added 2 new genera and 40 new species bringing the treehopper fauna to 100 genera (increase of 3 genera), 313 species (increase of 44 species) from 2012, and 2 subspecies...
February 20, 2024: Zootaxa
https://read.qxmd.com/read/38479175/integrating-socio-economic-vulnerability-factors-improves-neighborhood-scale-wastewater-based-epidemiology-for-public-health-applications
#34
JOURNAL ARTICLE
Prakit Saingam, Tanisha Jain, Addie Woicik, Bo Li, Pieter Candry, Raymond Redcorn, Sheng Wang, Jonathan Himmelfarb, Andrew Bryan, Mari K H Winkler
Wastewater Based Epidemiology (WBE) of COVID-19 is a low-cost, non-invasive, and inclusive early warning tool for disease spread. Previously studied WBE focused on sampling at wastewater treatment plant scale, limiting the level at which demographic and geographic variations in disease dynamics can be incorporated into the analysis of certain neighborhoods. This study demonstrates the integration of demographic mapping to improve the WBE of COVID-19 and associated post-COVID disease prediction (here kidney disease) at the neighborhood level using machine learning...
March 6, 2024: Water Research
https://read.qxmd.com/read/38478699/n6-methyladenosine-m6a-sequencing-reveals-heterodera-glycines-induced-dynamic-methylation-promoting-soybean-defense
#35
JOURNAL ARTICLE
Ruifeng Qin, Minghui Huang, Ye Jiang, Dan Jiang, Doudou Chang, Yifan Xie, Yuewen Dou, Lili Wu, Liuli Wei, Mingze Wang, Zhongyan Tian, Chunjie Li, Congli Wang
Unraveling the intricacies of soybean cyst nematode ( Heterodera glycines ) race 4 resistance and susceptibility in soybean breeding lines-11-452 (highly resistant) and Dongsheng1 (DS1, highly susceptible)-was the focal point of this study. Employing cutting-edge N6-methyladenosine (m6A)-seq and RNA-seq techniques, we delved into the impact of m6A modification on gene expression and plant defense responses. Through the evaluation of nematode development in both resistant and susceptible roots, a pivotal time point (3 days post inoculation) for m6A methylation sequencing was identified...
March 13, 2024: Phytopathology
https://read.qxmd.com/read/38476683/a-high-density-linkage-map-construction-in-guava-psidium-guajava-l-using-genotyping-by-sequencing-and-identification-of-qtls-for-leaf-peel-and-pulp-color-in-an-intervarietal-mapping-population
#36
JOURNAL ARTICLE
Malarvizhi Mathiazhagan, Dayanandhi Elangovan, Vasugi Chinnaiyan, Kodthalu Seetharamaiah Shivashankara, Darisi Venkata Sudhakar Rao, Kundapura Venkataramana Ravishankar
Psidium guajava L. is an important fruit crop in the tropical and subtropical regions of the world. The advanced breeding methods are not employed for important commercial traits like peel and pulp color, seed hardiness, fruit size, etc., due to the scarcity of genome-wide molecular markers and high-density linkage maps. In this study, we employed single-nucleotide polymorphism (SNP) markers and identified quantitative trait loci (QTL) regions that are associated with color traits of leaf, peel, and pulp in the guava intervarietal mapping population...
2024: Frontiers in Plant Science
https://read.qxmd.com/read/38475425/hybrid-rice-production-a-worldwide-review-of-floral-traits-and-breeding-technology-with-special-emphasis-on-china
#37
REVIEW
Humera Ashraf, Fozia Ghouri, Faheem Shehzad Baloch, Muhammad Azhar Nadeem, Xuelin Fu, Muhammad Qasim Shahid
Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level...
February 21, 2024: Plants (Basel, Switzerland)
https://read.qxmd.com/read/38474104/construction-of-genetic-map-and-qtl-mapping-for-seed-size-and-quality-traits-in-soybean-glycine-max-l
#38
JOURNAL ARTICLE
Weiran Gao, Ronghan Ma, Xi Li, Jiaqi Liu, Aohua Jiang, Pingting Tan, Guoxi Xiong, Chengzhang Du, Jijun Zhang, Xiaochun Zhang, Xiaomei Fang, Zelin Yi, Jian Zhang
Soybean ( Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. The quantitative trait loci (QTL) mapping for yield and quality traits, as well as for the identification of mining-related candidate genes, is of great significance for the molecular breeding and understanding the genetic mechanism. In this study, 186 individual plants of the F2 generation derived from crosses between Changjiangchun 2 and Yushuxian 2 were selected as the mapping population to construct a molecular genetic linkage map...
March 1, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38473942/joint-gwas-linkage-mapping-and-transcriptome-analysis-to-reveal-the-genetic-basis-of-plant-architecture-related-traits-in-maize
#39
JOURNAL ARTICLE
Xuefeng Lu, Pengfei Liu, Liang Tu, Xiangyang Guo, Angui Wang, Yunfang Zhu, Yulin Jiang, Chunlan Zhang, Yan Xu, Zehui Chen, Xun Wu
Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant density. In this study, one natural panel of 226 inbred lines and 150 family lines derived from the offspring of T32 crossed with Qi319 were genotyped by using the MaizeSNP50 chip and the genotyping by sequence (GBS) method and phenotyped under three different environments...
February 26, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38463846/modern-day-breeding-approaches-for-improvement-of-castor
#40
REVIEW
Rumit Patel, Juned Menon, Sushil Kumar, Márcia B M Nóbrega, Dipak A Patel, Amar A Sakure, Mahesh B Vaja
Castor ( Ricinus communis L.) is an industrially important oil producing crop belongs to Euphorbiaceae family. Castor oil has unique chemical properties make it industrially important crop. It is a member of monotypic genus even though it has ample amount of variability. Using this variability, conventionally many varieties and hybrids have been developed. But, like other crops, the modern and unconventional methods of crop improvement has not fully explored in castor. This article discusses the use of polyploidy induction, distant/wide hybridization and mutation breeding as tools for generating variety...
March 15, 2024: Heliyon
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