Tree Genetics & Genomes最新文献

{"title":"Phenotyping and genotyping of Pistacia atlantica Desf. subsp. kurdica along an environmental gradient in the semi-arid forests of western and southern Iran","authors":"Mohammad-Shafie Rahmani, Mohammad-Reza Naghavi, Ali-Akbar Shahnejat Bushehri, Naghi Shabanian, Lars-Gernot Otto","doi":"10.1007/s11295-023-01621-x","DOIUrl":"https://doi.org/10.1007/s11295-023-01621-x","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135833141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The domestication and breeding history of Castanea crenata Siebold et Zucc. estimated by direction of gene flow and approximate Bayesian computation","authors":"Sogo Nishio, Norio Takada, Yukie Takeuchi, Atsushi Imai, Megumi K. Kimura, Hiroyuki Iketani","doi":"10.1007/s11295-023-01620-y","DOIUrl":"https://doi.org/10.1007/s11295-023-01620-y","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135385453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demographic history and conservation aspects of two relict shrubs (Daphnimorpha spp., Thymelaeaceae) showing disjunct and restricted distribution in the southern part of Japan","authors":"Daiki Takahashi, Yoshihisa Suyama","doi":"10.1007/s11295-023-01618-6","DOIUrl":"https://doi.org/10.1007/s11295-023-01618-6","url":null,"abstract":"Abstract Climate relicts are of particular importance in evolutionary biology because of the strategies they may adopt for long-term survival despite climatic oscillations. However, because their current distribution is usually restricted and fragmented, many climatic relicts are at risk of extinction. Daphnimorpha (Thymelaeaceae) is a genus endemic to Japan that comprises two species ( D. capitellata and D. kudoi ) with a disjunct distribution in southern Japan. These two shrub species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphisms obtained from multiplexed inter-simple sequence repeats genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed that these two species may have been isolated since the Tertiary period, supporting their status as climate relicts. In addition, D. kudoi showed clear genetic differentiation between the two mountains where it occurred (Mt. Nagata and Mt. Kuromi), with a decline in the effective population sizes inferred during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure, and its effective population size was relatively stable. These differences could result in contrasting light tolerance between species. For conservation, we recommend managing these species as three evolutionarily significant units (ESUs): D. capitellata , D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi. Considering the limited gene flow among subpopulations and small population census, all ESUs require conservation attention to maintain or increase their effective population sizes.","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135059832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pleistocene-dated genomic divergence of avocado trees supports cryptic diversity in the Colombian germplasm","authors":"Jhon A. Berdugo-Cely, Andrés J. Cortés, Felipe López-Hernández, Paola Delgadillo-Durán, Ivania Cerón-Souza, Paula H. Reyes-Herrera, Alejandro A. Navas-Arboleda, Roxana Yockteng","doi":"10.1007/s11295-023-01616-8","DOIUrl":"https://doi.org/10.1007/s11295-023-01616-8","url":null,"abstract":"Abstract Genomic characterization of ex situ plant collections optimizes the utilization of genetic resources by identifying redundancies among accessions, capturing cryptic variation, establishing reference collections, and ultimately assisting pre-breeding and breeding efforts. Yet, the integration of evolutionary genomic analyses is often lacking when studying the biodiversity of crop gene pools. Such is the case in the avocado, Persea americana Mill., an iconic American fruit tree crop that has seen an unprecedented expansion worldwide because of its nutritional properties. However, given a very restricted number of commercial clones, avocado plantations are becoming more vulnerable to diseases and climate change. Therefore, exploring new sources of evolutionary novelty and genetic diversity beyond the commercial varieties derived from traditional genetic pools in Mexico and Central America is imperative. To fill this gap, we aimed to characterize the genomic diversity of Colombian avocado trees. Specifically, we constructed reduced representation genomic libraries to genotype by sequencing 144 accessions from the Colombian National genebank and 240 materials from local commercial orchards in the Colombian northwest Andes. We merged the resulting reads with available sequences of reference genotypes from known avocado groups (also named as races), Mexican, Guatemalan, and West Indian, to discover 4931 SNPs. We then analyzed the population structure and phylogenetic diversity, and reconstructed evolutionary scenarios, possibly leading to new genetic groups in Colombian germplasm. We detected demographic stratification despite evidence of intergroup gene flow. Besides the classical three avocado groups, we found an exclusive Colombian group with a possible genetic substructure related to the geographical origin (Andean and Caribbean). Phylogenetic and ABC demographic modeling suggested that the Colombian group evolved in the Pleistocene before human agriculture started, and its closest relative from the three recognized races would be the West Indian group. We conclude that northwest South America offers a cryptic source of allelic novelty capable of boosting avocado pre-breeding strategies to select rootstock candidates well adapted to specific eco-geographical regions in Colombia and abroad.","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134911992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Range shift and introgression of three Japanese Abies species: insights from population genetic data and species distribution modeling","authors":"K. Uchiyama, Sayaka Fujii, Ikutaro Tsuyama, Nobuyuki Tanaka, S. Setsuko, Megumi K. Kimura, Y. Suyama, Y. Tsumura","doi":"10.1007/s11295-023-01617-7","DOIUrl":"https://doi.org/10.1007/s11295-023-01617-7","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43689734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent advances in genomics, conservation, and breeding of pistachio","authors":"S. Choulak, K. Chatti, S. Rhouma","doi":"10.1007/s11295-023-01615-9","DOIUrl":"https://doi.org/10.1007/s11295-023-01615-9","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44549718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and structure in wild and cultivated populations of an emblematic African tree species, Garcinia kola (Clusiaceae)","authors":"Boniface Tientcheu Yogom, M. Avana-Tientcheu, Franck K. Monthe, P. Bissiengou, J. Loumeto, L. Zekraoui, C. Hervouet, T. Fonkou, C. Mariac, J. Duminil","doi":"10.1007/s11295-023-01614-w","DOIUrl":"https://doi.org/10.1007/s11295-023-01614-w","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49511226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association genetics of wood traits in European black poplar (Populus nigra L.)","authors":"Z. Kaya, Bircan Taşkıran, Asiye Uluğ, Aysun D. Güvendiren, J. Wegrzyn, D. Neale","doi":"10.1007/s11295-023-01612-y","DOIUrl":"https://doi.org/10.1007/s11295-023-01612-y","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43719055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of a high-density genetic linkage map and QTL analysis using an interspecific F1 population in pistachio","authors":"M. Islam, Habibullah Tevfik, H. Topçu, H. Karcı, S. Kafkas","doi":"10.1007/s11295-023-01613-x","DOIUrl":"https://doi.org/10.1007/s11295-023-01613-x","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47831387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterochromatic patterns of Citrus revisited: a new look at species origins and karyotype evolution","authors":"Claudio Montenegro, F. Roa, W. S. Soares Filho, A. E. Barros e Silva","doi":"10.1007/s11295-023-01610-0","DOIUrl":"https://doi.org/10.1007/s11295-023-01610-0","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45389670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}