Pub Date : 2023-11-27DOI: 10.1007/s11295-023-01632-8
Siqin Liu, Tao Long, Zihao Chen, Jikai Liu, Wenli Cui, Haiqin Leng, Yuhang Xing, Lucas Gutierrez Rodriguez, Yongfeng Gao, Yinan Yao
{"title":"Correction to: Genome‑wide identification of NRAMP family genes in Populus trichocarpa and their roles in transport of heavy metals","authors":"Siqin Liu, Tao Long, Zihao Chen, Jikai Liu, Wenli Cui, Haiqin Leng, Yuhang Xing, Lucas Gutierrez Rodriguez, Yongfeng Gao, Yinan Yao","doi":"10.1007/s11295-023-01632-8","DOIUrl":"https://doi.org/10.1007/s11295-023-01632-8","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139229739","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 : 2023-11-20DOI: 10.1007/s11295-023-01630-w
Shashi N. Goonetilleke, Michelle G. Wirthensohn, Diane E. Mather
In almond (Prunus dulcis L.), the physical characteristics of nuts and kernels underpin both crop yield and processing quality. In this research, the objective was to investigate whether quantitative trait locus (QTL) mapping could identify genomic regions that affect nut and kernel traits in the almond varieties Nonpareil and Lauranne and to investigate whether these regions have effects in two other almond populations (Nonpareil × Constantí and Nonpareil × Tarraco). Linkage mapping and QTL analysis were carried out using single-nucleotide polymorphisms (SNPs) that had previously been discovered using a set of 180 Nonpareil × Lauranne F1 progeny. With the Nonpareil × Lauranne population, QTLs were detected in ten regions on the Nonpareil map and 16 regions on the Lauranne map. Each Nonpareil QTL region and most Lauranne QTL regions were also detected using the Constantí and/or Tarraco populations. Most QTLs had small effects, indicating that the traits investigated here may be more suitable for genomic selection than for marker-assisted selection. With anchoring of QTL regions to genome sequence assemblies for Nonpareil and Lauranne, some candidate genes were identified that could be evaluated in future research.
{"title":"Genetic analysis of quantitative variation in almond nut traits","authors":"Shashi N. Goonetilleke, Michelle G. Wirthensohn, Diane E. Mather","doi":"10.1007/s11295-023-01630-w","DOIUrl":"https://doi.org/10.1007/s11295-023-01630-w","url":null,"abstract":"<p>In almond (<i>Prunus dulcis</i> L.), the physical characteristics of nuts and kernels underpin both crop yield and processing quality. In this research, the objective was to investigate whether quantitative trait locus (QTL) mapping could identify genomic regions that affect nut and kernel traits in the almond varieties Nonpareil and Lauranne and to investigate whether these regions have effects in two other almond populations (Nonpareil × Constantí and Nonpareil × Tarraco). Linkage mapping and QTL analysis were carried out using single-nucleotide polymorphisms (SNPs) that had previously been discovered using a set of 180 Nonpareil × Lauranne F<sub>1</sub> progeny. With the Nonpareil × Lauranne population, QTLs were detected in ten regions on the Nonpareil map and 16 regions on the Lauranne map. Each Nonpareil QTL region and most Lauranne QTL regions were also detected using the Constantí and/or Tarraco populations. Most QTLs had small effects, indicating that the traits investigated here may be more suitable for genomic selection than for marker-assisted selection. With anchoring of QTL regions to genome sequence assemblies for Nonpareil and Lauranne, some candidate genes were identified that could be evaluated in future research.</p>","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138534039","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 : 2023-11-18DOI: 10.1007/s11295-023-01624-8
Ana Usié, Octávio Serra, Pedro M. Barros, Pedro Barbosa, Célia Leão, Tiago Capote, Tânia Almeida, Leandra Rodrigues, Isabel Carrasquinho, Joana B. Guimarães, Diogo Mendoça, Filomena Nóbrega, Conceição Egas, Inês Chaves, Isabel A. Abreu, Nelson J. M. Saibo, Liliana Marum, Maria Carolina Varela, José Matos, Fernanda Simões, Célia M. Miguel, M. Margarida Oliveira, Cândido P. Ricardo, Sónia Gonçalves, António Marcos Ramos
Cork oak (Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that Q. suber is closely related to Quercus variabilis, two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.
{"title":"An improved reference genome and first organelle genomes of Quercus suber","authors":"Ana Usié, Octávio Serra, Pedro M. Barros, Pedro Barbosa, Célia Leão, Tiago Capote, Tânia Almeida, Leandra Rodrigues, Isabel Carrasquinho, Joana B. Guimarães, Diogo Mendoça, Filomena Nóbrega, Conceição Egas, Inês Chaves, Isabel A. Abreu, Nelson J. M. Saibo, Liliana Marum, Maria Carolina Varela, José Matos, Fernanda Simões, Célia M. Miguel, M. Margarida Oliveira, Cândido P. Ricardo, Sónia Gonçalves, António Marcos Ramos","doi":"10.1007/s11295-023-01624-8","DOIUrl":"https://doi.org/10.1007/s11295-023-01624-8","url":null,"abstract":"<p>Cork oak (<i>Quercus suber</i> L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that <i>Q. suber</i> is closely related to <i>Quercus variabilis</i>, two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.</p>","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138534041","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 : 2023-11-06DOI: 10.1007/s11295-023-01628-4
Xue-Mei Lu, Yan-Chang Wang, Chuang Liu, Li Liao, Yongbo Liu, Jian-Wen Zhang, Cai-Hong Zhong, Zuo-Zhou Li
{"title":"Full-scale genetic pattern and environmental association of Actinidia chinensis populations across ten mountain systems in China, and its significance for conservation","authors":"Xue-Mei Lu, Yan-Chang Wang, Chuang Liu, Li Liao, Yongbo Liu, Jian-Wen Zhang, Cai-Hong Zhong, Zuo-Zhou Li","doi":"10.1007/s11295-023-01628-4","DOIUrl":"https://doi.org/10.1007/s11295-023-01628-4","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135678958","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 : 2023-11-01DOI: 10.1007/s11295-023-01629-3
Siqin Liu, Tao Long, Zihao Chen, Jikai Liu, Wenli Cui, Haiqin Leng, Yuhang Xing, Lucas Gutierrez Rodriguez, Víctor Resco de Dios, Yongfeng Gao, Yinan Yao
{"title":"Genome-wide identification of NRAMP family genes in Populus trichocarpa and their roles in transport of heavy metals","authors":"Siqin Liu, Tao Long, Zihao Chen, Jikai Liu, Wenli Cui, Haiqin Leng, Yuhang Xing, Lucas Gutierrez Rodriguez, Víctor Resco de Dios, Yongfeng Gao, Yinan Yao","doi":"10.1007/s11295-023-01629-3","DOIUrl":"https://doi.org/10.1007/s11295-023-01629-3","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135271725","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 : 2023-10-23DOI: 10.1007/s11295-023-01626-6
Richard Tegtmeier, Della Cobb-Smith, Gan-Yuan Zhong, Awais Khan
{"title":"Identification and marker development of a moderate-effect fire blight resistance QTL in M. sieversii, the primary progenitor of domesticated apples","authors":"Richard Tegtmeier, Della Cobb-Smith, Gan-Yuan Zhong, Awais Khan","doi":"10.1007/s11295-023-01626-6","DOIUrl":"https://doi.org/10.1007/s11295-023-01626-6","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135413266","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 : 2023-10-19DOI: 10.1007/s11295-023-01625-7
Guillaume Otis-Prud’homme, Josianne DeBlois, Martin Perron
Abstract Genetic parameters for growth, trunk quality, and susceptibility to frost and Sphaerulina musiva attack were estimated from 34 half-sib families of hybrid poplar from the crossing of non-native parents, Populus maximowiczii A. Henry, and Populus trichocarpa Torr. & Gray, 3 and 6 years after planting. The use of spatial analysis proved to be the best method for quantitative growth data. The proportion of the among-family variance to the total (phenotypic) variance as well as the high heritabilities of growth and susceptibility to frost and Spaherulina musiva showed a high potential for selection for these traits while the quality traits were under low genetic control. Some families showed gains for several traits, suggesting the possibility of developing a selection index to obtain superior families that show gain for not only growth but quality and adaptive traits as well. Type B correlations were high, suggesting that families responded in the same way regardless of the site. High type A correlation between growth traits at 3 and 6 years showed early selection potential, although these relationships should be confirmed with future measurements to evaluate this effect at maturity. These results can be integrated into the strategy for improving hybrid poplar parental populations and, in the longer term, will make it possible to optimize the selection of individuals with traits of interest for the operational deployment of hybrid poplar clones.
摘要以非本地亲本杨杨(Populus maximowiczii A. Henry)和杨杨(Populus trichocarpa Torr)杂交的34个半同胞家系为材料，分析了其生长、树干品质、对霜冻和霉病的敏感性等遗传参数。,灰色，种植后3年和6年。采用空间分析方法是定量分析增长数据的最佳方法。家族间方差占总(表型)方差的比例以及生长、霜冻敏感性和草叶的高遗传力表明，这些性状具有较高的选择潜力，而品质性状的遗传控制较低。有些家族在几个性状上都有增益，这表明有可能建立一种选择指数，以获得不仅在生长性状上有增益，而且在品质和适应性状上也有增益的优良家族。B型相关性很高，这表明无论地点如何，家庭的反应都是一样的。3岁和6岁时生长性状之间的高A型相关性显示了早期选择潜力，尽管这些关系应该通过未来的测量来确认，以评估成熟时的影响。这些结果可作为杨树杂交亲本群体改良策略的参考，并为杨树杂交无性系的操作部署优化选择具有感兴趣性状的个体提供了可能。
{"title":"Preliminary estimates of genetic parameters and familial selection for non-native poplars show good potential for genetic gains on growth, cold hardiness, trunk quality and Sphaerulina musiva susceptibility","authors":"Guillaume Otis-Prud’homme, Josianne DeBlois, Martin Perron","doi":"10.1007/s11295-023-01625-7","DOIUrl":"https://doi.org/10.1007/s11295-023-01625-7","url":null,"abstract":"Abstract Genetic parameters for growth, trunk quality, and susceptibility to frost and Sphaerulina musiva attack were estimated from 34 half-sib families of hybrid poplar from the crossing of non-native parents, Populus maximowiczii A. Henry, and Populus trichocarpa Torr. & Gray, 3 and 6 years after planting. The use of spatial analysis proved to be the best method for quantitative growth data. The proportion of the among-family variance to the total (phenotypic) variance as well as the high heritabilities of growth and susceptibility to frost and Spaherulina musiva showed a high potential for selection for these traits while the quality traits were under low genetic control. Some families showed gains for several traits, suggesting the possibility of developing a selection index to obtain superior families that show gain for not only growth but quality and adaptive traits as well. Type B correlations were high, suggesting that families responded in the same way regardless of the site. High type A correlation between growth traits at 3 and 6 years showed early selection potential, although these relationships should be confirmed with future measurements to evaluate this effect at maturity. These results can be integrated into the strategy for improving hybrid poplar parental populations and, in the longer term, will make it possible to optimize the selection of individuals with traits of interest for the operational deployment of hybrid poplar clones.","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135667793","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 : 2023-10-13DOI: 10.1007/s11295-023-01622-w
Nianqin Jiang, Linna Wang, Yangang Lan, Hongxia Liu, Xiaoyue Zhang, Wei He, Min Wu, Hanwei Yan, Yan Xiang
{"title":"Genome-wide identification of the Carya illinoinensis bZIP transcription factor and the potential function of S1-bZIPs in abiotic stresses","authors":"Nianqin Jiang, Linna Wang, Yangang Lan, Hongxia Liu, Xiaoyue Zhang, Wei He, Min Wu, Hanwei Yan, Yan Xiang","doi":"10.1007/s11295-023-01622-w","DOIUrl":"https://doi.org/10.1007/s11295-023-01622-w","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135853928","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 : 2023-10-02DOI: 10.1007/s11295-023-01619-5
Ana Albarrán-Lara, Maried Ochoa-Zavala, Andres Torres-Miranda, Ivan M. De-la-Cruz, Patricia Dávila-Aranda, Juan M. Peñaloza-Ramírez, Hernando Rodríguez-Correa, Ken Oyama
Abstract While hybridization and introgression can have a strong adaptive importance, it can impede divergence of species. Quercus magnoliifolia and Q. resinosa are two endemic oak species distributed across the Mexican highlands. These species diverged ecological and morphologically; however, no nuclear genetic differentiation is evident. In this study, we determined the mechanisms that shape patterns of genetic variation and establish the role of migration and hybridization in the evolutionary history of these two oak species. To do this, Bayesian approaches were used for inference on migration rates and directionality and timing of divergence between species using chloroplast microsatellites. We then integrated species distribution models to infer the geographic distribution of Q. magnoliifolia and Q. resinosa during Last Interglacial, Last Glacial Maximum, and Mid-Holocene time frames. We failed in distinguishing a unique genetic composition for each species. Chloroplast differentiation was more congruent with geography than the taxonomic status of each species. Our study revealed that after the divergence ( c . 10 Mya) of these two oak species, high rates of introgression took place at the end of the Pleistocene. Furthermore, past distribution models predicted that Q. magnoliifolia and Q. resinosa have likely been in sympatry presumable since Last Glacial Maximum and Q. resinosa probably expanded geographically towards its current distribution around Mid-Holocene. This expansion was supported by testing migration models, suggesting recent establishment of Q. resinosa to the north of Trans-Mexican Volcanic Belt. We hypothesized that after Q. magnoliifolia and Q. resinosa diverged, colonization events followed by hybridization between oaks and long-distance seed dispersal occurred, explaining the present-day patterns of distribution of chloroplast diversity. We propose that divergence of species remains mainly on loci under natural selection, providing evidence on the “porous” nature of species boundaries among oaks.
{"title":"Long-distance dispersal drives the genetic variation and historical demography of Quercus magnoliifolia and Quercus resinosa (Fagaceae) in the Mexican highlands","authors":"Ana Albarrán-Lara, Maried Ochoa-Zavala, Andres Torres-Miranda, Ivan M. De-la-Cruz, Patricia Dávila-Aranda, Juan M. Peñaloza-Ramírez, Hernando Rodríguez-Correa, Ken Oyama","doi":"10.1007/s11295-023-01619-5","DOIUrl":"https://doi.org/10.1007/s11295-023-01619-5","url":null,"abstract":"Abstract While hybridization and introgression can have a strong adaptive importance, it can impede divergence of species. Quercus magnoliifolia and Q. resinosa are two endemic oak species distributed across the Mexican highlands. These species diverged ecological and morphologically; however, no nuclear genetic differentiation is evident. In this study, we determined the mechanisms that shape patterns of genetic variation and establish the role of migration and hybridization in the evolutionary history of these two oak species. To do this, Bayesian approaches were used for inference on migration rates and directionality and timing of divergence between species using chloroplast microsatellites. We then integrated species distribution models to infer the geographic distribution of Q. magnoliifolia and Q. resinosa during Last Interglacial, Last Glacial Maximum, and Mid-Holocene time frames. We failed in distinguishing a unique genetic composition for each species. Chloroplast differentiation was more congruent with geography than the taxonomic status of each species. Our study revealed that after the divergence ( c . 10 Mya) of these two oak species, high rates of introgression took place at the end of the Pleistocene. Furthermore, past distribution models predicted that Q. magnoliifolia and Q. resinosa have likely been in sympatry presumable since Last Glacial Maximum and Q. resinosa probably expanded geographically towards its current distribution around Mid-Holocene. This expansion was supported by testing migration models, suggesting recent establishment of Q. resinosa to the north of Trans-Mexican Volcanic Belt. We hypothesized that after Q. magnoliifolia and Q. resinosa diverged, colonization events followed by hybridization between oaks and long-distance seed dispersal occurred, explaining the present-day patterns of distribution of chloroplast diversity. We propose that divergence of species remains mainly on loci under natural selection, providing evidence on the “porous” nature of species boundaries among oaks.","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":"135834703","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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