{"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}
Pub Date : 2023-09-19DOI: 10.1007/s11295-023-01618-6
Daiki Takahashi, Yoshihisa Suyama
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.
{"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}
Pub Date : 2023-09-14DOI: 10.1007/s11295-023-01616-8
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
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.
迁地植物的基因组鉴定可以通过鉴定遗传资源的冗余性、捕获隐性变异、建立参考资料、最终辅助育种和育种工作来优化遗传资源的利用。然而，在研究作物基因库的生物多样性时，往往缺乏进化基因组分析的整合。这就是鳄梨Persea americana Mill的情况。这是一种标志性的美国果树作物，由于其营养特性，在全球范围内得到了前所未有的扩张。然而，由于商业克隆数量非常有限，牛油果种植园越来越容易受到疾病和气候变化的影响。因此，在墨西哥和中美洲传统基因库衍生的商业品种之外，探索进化新颖性和遗传多样性的新来源是势在必行的。为了填补这一空白，我们的目标是表征哥伦比亚鳄梨树的基因组多样性。具体来说，我们通过对来自哥伦比亚国家基因库的144份材料和来自哥伦比亚西北部安第斯山脉当地商业果园的240份材料进行测序，构建了减少代表性的基因组文库。我们将结果读取与已知鳄梨群体(也称为种族)，墨西哥，危地马拉和西印度的可用参考基因型序列合并，发现4931个snp。然后，我们分析了种群结构和系统发育多样性，并重建了进化情景，可能导致哥伦比亚种质资源中新的遗传群。尽管存在群体间基因流动的证据，我们还是发现了人口分层。除了经典的三个鳄梨类群外，我们还发现了一个独特的哥伦比亚类群，其遗传亚结构可能与地理起源(安第斯和加勒比)有关。系统发育和ABC人口统计学模型表明，哥伦比亚人在更新世进化，早于人类农业的开始，在三个已知的种族中，与他们最近的亲戚是西印度人。我们得出结论，南美洲西北部提供了一个神秘的等位基因新颖性来源，能够促进鳄梨的预育种策略，以选择适合哥伦比亚和国外特定生态地理区域的候选砧木。
{"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}
Pub Date : 2023-09-09DOI: 10.1007/s11295-023-01617-7
K. Uchiyama, Sayaka Fujii, Ikutaro Tsuyama, Nobuyuki Tanaka, S. Setsuko, Megumi K. Kimura, Y. Suyama, Y. Tsumura
{"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}
Pub Date : 2023-08-24DOI: 10.1007/s11295-023-01615-9
S. Choulak, K. Chatti, S. Rhouma
{"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}
Pub Date : 2023-08-14DOI: 10.1007/s11295-023-01614-w
Boniface Tientcheu Yogom, M. Avana-Tientcheu, Franck K. Monthe, P. Bissiengou, J. Loumeto, L. Zekraoui, C. Hervouet, T. Fonkou, C. Mariac, J. Duminil
{"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}
Pub Date : 2023-07-31DOI: 10.1007/s11295-023-01612-y
Z. Kaya, Bircan Taşkıran, Asiye Uluğ, Aysun D. Güvendiren, J. Wegrzyn, D. Neale
{"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}
Pub Date : 2023-07-29DOI: 10.1007/s11295-023-01613-x
M. Islam, Habibullah Tevfik, H. Topçu, H. Karcı, S. Kafkas
{"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}
Pub Date : 2023-07-19DOI: 10.1007/s11295-023-01610-0
Claudio Montenegro, F. Roa, W. S. Soares Filho, A. E. Barros e Silva
{"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}
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