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Lytkin K, Nosulchak V, Agakhanov M, Matveikina E, Lushchay E, Karzhaev D, Raines E, Vasylyk I, Rybachenko N, Grigoreva E, Volkov V, Volynkin V, Gentzbittel L, Potokina E. Development of a High-Density Genetic Map for Muscadine Grape Using a Mapping Population from Selfing of the Perfect-Flowered Vine 'Dixie'. PLANTS (BASEL, SWITZERLAND) 2022; 11:3231. [PMID: 36501271 PMCID: PMC9738875 DOI: 10.3390/plants11233231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Intraspecific diversity of the immune grape Muscadinia rotundifolia Michaux. can serve as a rich source of valuable resistance loci to the most widespread pathogens and pests of grapevine. While only one Run1/Rpg1 resistance locus has been introgressed from M. rotundifolia to the Vitis vinifera gene pool, a number of other genes conferring resistance to powdery mildew and downy mildew have been identified in various Muscadinia cultivars. A larger introduction of Muscadinia varieties to the European continent would greatly facilitate experiments of interspecific crosses as well as stimulate biotechnological efforts to overcome the main barrier to F1 fertility caused by the differences in chromosome number. For the successful introduction of Muscadinia into the new European environment, it is necessary to overcome the difficulties associated with the physiological characteristics of the species, such as insufficient cold tolerance and very late fruit ripening. To facilitate the further discovery of valuable loci in Muscadinia and their transfer to grapevine breeding programs, we constructed a high-density linkage map using an S1 mapping population obtained from the self-pollination of M. rotundifolia cv. Dixie maintained on the southern coast of Crimea. Using ddRADseq, 3730 SNPs were ordered across 20 linkage groups spanning 2753.6 cM of the total map length. No segregation in resistance to diseases and pests was observed among the 'Dixie' S1 population, suggesting the presence of homozygous non-segregating resistant loci in the genetic background of 'Dixie'. Markers with high segregation distortion showed a bias towards chromosomal intervals on linkage groups 10 and 20, where loci affecting the survival of 'Dixie' S1 progeny may be localized. QTLs with significant additive and dominance effects were discovered on LG14 and LG18, affecting the morphological traits associated with the vigor of growth and adaptability of young Muscadinia vines in the conditions of Crimea.
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Affiliation(s)
- Kirill Lytkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vasily Nosulchak
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Magamedgusein Agakhanov
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Elena Matveikina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Evgenii Raines
- Information Technologies and Programming Faculty, ITMO University, St. Petersburg 197101, Russia
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Nataliya Rybachenko
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | | | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
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A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii. Genes (Basel) 2022; 13:genes13101731. [PMID: 36292616 PMCID: PMC9601732 DOI: 10.3390/genes13101731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic linkage maps of the traditional F2 population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F2 population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F1 hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map.
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Chen W, Yu W, Dong A, Zeng Y, Yuan H, Zheng B, Wu R. The Genetic Architecture of Juvenile Growth Traits in the Conifer Torreya grandis as Revealed by Joint Linkage and Linkage Disequilibrium Mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:858187. [PMID: 35832218 PMCID: PMC9271899 DOI: 10.3389/fpls.2022.858187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Despite its high economical and ornamental values, Torreya grandis, a dioecious non-timber coniferous species, has long been an underrepresented species. However, the advent and application of advanced genotyping technologies have stimulated its genetic research, making it possible to gain new insight into the genetic architecture of complex traits that may not be detected for model species. We apply an open-pollination (OP) mapping strategy to conduct a QTL mapping experiment of T. grandis, in which nearly 100 unrelated trees randomly chosen from the species' natural distribution and their half-sib progeny are simultaneously genotyped. This strategy allows us to simultaneously estimate the recombination fractions and linkage disequilibrium (LD) coefficients between each pair of markers. We reconstruct a high-density linkage map of 4,203 SNPs covering a total distance of 8,393.95 cM and plot pairwise normalized LD values against genetic distances to build up a linkage-LD map. We identify 13 QTLs for stem basal diameter growth and 4 QTLs for stem height growth in juvenile seedlings. From the linkage-LD map, we infer the evolutionary history of T. grandis and each of its QTLs. The slow decay of QTL-related LDs indicates that these QTLs and their harboring genomic regions are evolutionarily relatively young, suggesting that they can better utilized by clonal propagation rather than through seed propagation. Genetic results from the OP sampling strategy could provide useful guidance for genetic studies of other dioecious species.
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Affiliation(s)
- Wenchong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiwu Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yanru Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Huwei Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Rongling Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Center for Statistical Genetics, Department of Public Health Sciences, Department of Statistics, The Pennsylvania State University, Hershey, PA, United States
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Li M, Sang M, Wen Z, Meng J, Cheng T, Zhang Q, Sun L. Mapping Floral Genetic Architecture in Prunus mume, an Ornamental Woody Plant. FRONTIERS IN PLANT SCIENCE 2022; 13:828579. [PMID: 35211141 PMCID: PMC8860970 DOI: 10.3389/fpls.2022.828579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Floral traits are both evolutionarily and economically relevant for ornamental plants. However, their underlying genetic architecture, especially in woody ornamental plants, is still poorly understood. We perform mapping experiments aimed at identifying specific quantitative trait loci (QTLs) that control the size, shape, architecture, color, and timing of flowers in mei (Prunus mume). We find that the narrow region of chromosome 1 (5-15 Mb) contains a number of floral QTLs. Most QTLs detected from this mapping study are annotated to candidate genes that regulate various biological functions toward the floral formation. We identify strong pleiotropic control on different aspects of flower morphology (including shape, petal number, pistil number, petal color, and calyx color) and flower timing, but find different genetic systems that mediate whether a flower produces pistils and how many pistils a flower produces. We find that many floral QTLs display pleiotropic effects on shoot length growth but shoot radial growth, implicating a possible association of floral display with light capture. We conduct a transcriptomic study to characterize the genomic signature of floral QTLs expressed in mei. Our mapping results about the genetic control of floral features make it promising to select superior varieties for mei carrying flowers of ornamental value.
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Affiliation(s)
- Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- School Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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Wang Z, Ren H, Pang C, Lu G, Xu F, Cheng W, Que Y, Xu L. An autopolyploid-suitable polyBSA-seq strategy for screening candidate genetic markers linked to leaf blight resistance in sugarcane. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:623-636. [PMID: 34775519 DOI: 10.1007/s00122-021-03989-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
An autopolyploid-suitable polyBSA-seq strategy was developed for screening candidate genetic markers linked to leaf blight resistance in sugarcane. Due to the complex genome architecture, the quantitative trait loci mappings and linkage marker selections for agronomic traits of autopolyploid crops were mainly limited to the time-consuming and cost intensive construction of genetic maps. To map resistance-linked markers for sugarcane leaf blight (SLB) caused by Stagonospora tainanensis, the autopolyploid-suitable bulk-segregant analysis based on the sequencing (polyBSA-seq) strategy was successfully applied for the first time. Resistant- and susceptible-bulks (R- and S-bulks) constructed from the extreme-phenotypic sugarcane F1 lines of YT93-159 × ROC22 were deep sequenced with 195.0 × for bulks and 74.4 × for parents. Informative single-dose variants (ISDVs) present as one copy in one parent and null in the other parent were detected based on the genome sequence of LA Purple, an autooctoploid Saccharum officinarum, to screen candidate linkage markers (CLMs). The proportion of the number of short reads harboring ISDVs in the total short reads covering a given genomic position was defined as ISDV index and the ISDVs with indices met the threshold set in this study (0.04-0.14) were selected as CLMs. In total, three resistance- and one susceptibility-related CLMs for SLB resistance were identified by the polyBSA-seq. Among them, two markers on chromosome 10 were less than 300 Kb apart. Furthermore, the RNA-seq was used to calculate the expression level of genes within 1.0 Mb from the aforementioned four CLMs, which demonstrated that twelve genes were differentially expressed between resistant and susceptible clones, including a receptor-like kinase and an ethylene-responsive transcription factor. This is the first reported polyBSA-seq in autopolyploid sugarcane, which specifically tailored for the fast selection of the CLMs and causal genes associated with important agronomic traits.
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Affiliation(s)
- Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, 661600, China
| | - Hui Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guilong Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Cheng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Zhu X, Weng Q, Bush D, Zhou C, Zhao H, Wang P, Li F. High-density genetic linkage mapping reveals low stability of QTLs across environments for economic traits in Eucalyptus. FRONTIERS IN PLANT SCIENCE 2022; 13:1099705. [PMID: 37082511 PMCID: PMC10112524 DOI: 10.3389/fpls.2022.1099705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 05/03/2023]
Abstract
Introduction Eucalyptus urophylla, E. tereticornis and their hybrids are the most important commercial forest tree species in South China where they are grown for pulpwood and solid wood production. Construction of a fine-scale genetic linkage map and detecting quantitative trait loci (QTL) for economically important traits linked to these end-uses will facilitate identification of the main candidate genes and elucidate the regulatory mechanisms. Method A high-density consensus map (a total of 2754 SNPs with 1359.18 cM) was constructed using genotyping by sequencing (GBS) on clonal progenies of E. urophylla × tereticornis hybrids. QTL mapping of growth and wood property traits were conducted in three common garden experiments, resulting in a total of 108 QTLs. A total of 1052 candidate genes were screened by the efficient combination of QTL mapping and transcriptome analysis. Results Only ten QTLs were found to be stable across two environments, and only one (qSG10Stable mapped on chromosome 10, and associated with lignin syringyl-to-guaiacyl ratio) was stable across all three environments. Compared to other QTLs, qSG10Stable explained a very high level of phenotypic variation (18.4-23.6%), perhaps suggesting that QTLs with strong effects may be more stably inherited across multiple environments. Screened candidate genes were associated with some transcription factor families, such as TALE, which play an important role in the secondary growth of plant cell walls and the regulation of wood formation. Discussion While QTLs such as qSG10Stable, found to be stable across three sites, appear to be comparatively uncommon, their identification is likely to be a key to practical QTL-based breeding. Further research involving clonally-replicated populations, deployed across multiple target planting sites, will be required to further elucidate QTL-by-environment interactions.
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Affiliation(s)
- Xianliang Zhu
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qijie Weng
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - David Bush
- Commonwealth Scientific and Industrial Research Organisation (CRISO) Australian Tree Seed Centre, Canberra, ACT, Australia
| | - Changpin Zhou
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Haiwen Zhao
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Ping Wang
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Fagen Li
- Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- *Correspondence: Fagen Li,
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Amadeu RR, Muñoz PR, Zheng C, Endelman JB. QTL mapping in outbred tetraploid (and diploid) diallel populations. Genetics 2021; 219:iyab124. [PMID: 34740237 PMCID: PMC8570786 DOI: 10.1093/genetics/iyab124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/24/2021] [Indexed: 11/14/2022] Open
Abstract
Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multiallelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and nonadditive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with three tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher-order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.
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Affiliation(s)
- Rodrigo R Amadeu
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Patricio R Muñoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Chaozhi Zheng
- Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
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Kay KM, Surget-Groba Y. The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understorey herbs. Mol Ecol 2021; 31:4351-4363. [PMID: 34487383 DOI: 10.1111/mec.16165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many co-adapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.
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Affiliation(s)
- Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yann Surget-Groba
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Département de Biologie, Université du Québec en Outaouais, Ripon, QC, Canada
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Structural and Functional Genomics of the Resistance of Cacao to Phytophthora palmivora. Pathogens 2021; 10:pathogens10080961. [PMID: 34451425 PMCID: PMC8398157 DOI: 10.3390/pathogens10080961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/17/2022] Open
Abstract
Black pod disease, caused by Phytophthora spp., is one of the main diseases that attack cocoa plantations. This study validated, by association mapping, 29 SSR molecular markers flanking to QTL (Quantitative Trait Loci) associated with Phytophthora palmivora Butler (Butler) (PP) resistance, in three local ancient varieties of the Bahia (Comum, Pará, and Maranhão), varieties that have a high potential in the production of gourmet chocolate. Four SSR loci associated with resistance to PP were detected, two on chromosome 8, explaining 7.43% and 3.72% of the Phenotypic Variation (%PV), one on chromosome 2 explaining 2.71%PV and one on chromosome 3 explaining 1.93%PV. A functional domains-based annotation was carried out, in two Theobroma cacao (CRIOLLO and MATINA) reference genomes, of 20 QTL regions associated with cocoa resistance to the pathogen. It was identified 164 (genome CRIOLLO) and 160 (genome MATINA) candidate genes, hypothetically involved in the recognition and activation of responses in the interaction with the pathogen. Genomic regions rich in genes with Coiled-coils (CC), nucleotide binding sites (NBS) and Leucine-rich repeat (LRR) domains were identified on chromosomes 1, 3, 6, 8, and 10, likewise, regions rich in Receptor-like Kinase domain (RLK) and Ginkbilobin2 (GNK2) domains were identified in chromosomes 4 and 6.
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de Almeida CP, de Carvalho Paulino JF, Bonfante GFJ, Perseguini JMKC, Santos IL, Gonçalves JGR, Patrício FRA, Taniguti CH, Gesteira GDS, Garcia AAF, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:647043. [PMID: 33927738 PMCID: PMC8078856 DOI: 10.3389/fpls.2021.647043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Angular leaf spot (ALS) is a disease that causes major yield losses in the common bean crop. Studies based on different isolates and populations have already been carried out to elucidate the genetic mechanisms of resistance to ALS. However, understanding of the interaction of this resistance with the reproductive stages of common bean is lacking. The aim of the present study was to identify ALS resistance loci at different plant growth stages (PGS) by association and linkage mapping approaches. An BC2F3 inter-gene pool cross population (AND 277 × IAC-Milênio - AM population) profiled with 1,091 SNPs from genotyping by sequencing (GBS) was used for linkage mapping, and a carioca diversity panel (CDP) genotyped by 5,398 SNPs from BeadChip assay technology was used for association mapping. Both populations were evaluated for ALS resistance at the V2 and V3 PGSs (controlled conditions) and R8 PGS (field conditions). Different QTL (quantitative trait loci) were detected for the three PGSs and both populations, showing a different quantitative profile of the disease at different plant growth stages. For the three PGS, multiple interval mapping (MIM) identified seven significant QTL, and the Genome-wide association study (GWAS) identified fourteen associate SNPs. Several loci validated regions of previous studies, and Phg-1, Phg-2, Phg-4, and Phg-5, among the 5 loci of greatest effects reported in the literature, were detected in the CDP. The AND 277 cultivar contained both the Phg-1 and the Phg-5 QTL, which is reported for the first time in the descendant cultivar CAL143 as ALS10.1UC. The novel QTL named ALS11.1AM was located at the beginning of chromosome Pv11. Gene annotation revealed several putative resistance genes involved in the ALS response at the three PGSs, and with the markers and loci identified, new specific molecular markers can be developed, representing a powerful tool for common bean crop improvement and for gain in ALS resistance.
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Affiliation(s)
| | | | | | | | - Isabella Laporte Santos
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico - IAC, Campinas, Brazil
| | | | | | - Cristiane Hayumi Taniguti
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriel de Siqueira Gesteira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Antônio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, United States
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11
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Quezada M, Amadeu RR, Vignale B, Cabrera D, Pritsch C, Garcia AAF. Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:626811. [PMID: 33708232 PMCID: PMC7940835 DOI: 10.3389/fpls.2021.626811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.
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Affiliation(s)
- Marianella Quezada
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Rodrigo Rampazo Amadeu
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Beatriz Vignale
- Mejoramiento Genético, Departamento de Producción Vegetal, Estación Experimental de la Facultad de Agronomía, Universidad de la República, Salto, Uruguay
| | - Danilo Cabrera
- Programa de Investigación en Producción Fruticola, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental “Wilson Ferreira Aldunate”, Canelones, Uruguay
| | - Clara Pritsch
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Antonio Augusto Franco Garcia
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
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12
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Curtolo M, Granato LM, Soratto TAT, Curtolo M, Gazaffi R, Takita MA, Cristofani-Yaly M, Machado MA. Expression Quantitative Trait Loci (eQTL) mapping for callose synthases in intergeneric hybrids of Citrus challenged with the bacteria Candidatus Liberibacter asiaticus. Genet Mol Biol 2020; 43:e20190133. [PMID: 32568357 PMCID: PMC7295156 DOI: 10.1590/1678-4685-gmb-2019-0133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 01/07/2020] [Indexed: 11/21/2022] Open
Abstract
Citrus plants have been extremely affected by Huanglongbing (HLB) worldwide, causing
economic losses. HLB disease causes disorders in citrus plants, leading to callose
deposition in the phloem vessel sieve plates. Callose is synthesized by callose
synthases, which are encoded by 12 genes (calS1–
calS12)in Arabidopsis thaliana. We evaluated the
expression of eight callose synthase genes from Citrus in hybrids between
Citrus sunki and Poncirus trifoliata infected
with HLB. The objective of this work was to identify possible tolerance loci
combining the expression quantitative trait loci (eQTL) of different callose
synthases and genetic Single-Nucleotide Polymorphism (SNP) maps of C.
sunki and P. trifoliata. The expression data from all
CscalS ranged widely among the hybrids. Furthermore, the data
allowed the detection of 18 eQTL in the C. sunki map and 34 eQTL in
the P. trifoliata map. In both maps, some eQTL for different
CscalS were overlapped; thus, a single region could be associated
with the regulation of more than one CscalS. The regions identified
in this work can be interesting targets for future studies of Citrus
breeding programs to manipulate callose synthesis during HLB infection.
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Affiliation(s)
- Maiara Curtolo
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil.,Universidade Estadual de Campinas, Programa de Pós-Graduação em Genética e Biologia Molecular, Campinas, SP, Brazil
| | - Laís Moreira Granato
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Maisa Curtolo
- Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Programa de Pós-Graduação em Genética e Melhoramento de Plantas, Piracicaba, SP, Brazil
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos, Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Marcos Antonio Machado
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
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13
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Marshall MM, Remington DL, Lacey EP. Two reproductive traits show contrasting genetic architectures in Plantago lanceolata. Mol Ecol 2019; 29:272-291. [PMID: 31793079 DOI: 10.1111/mec.15320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022]
Abstract
In many species, temperature-sensitive phenotypic plasticity (i.e., an individual's phenotypic response to temperature) displays a positive correlation with latitude, a pattern presumed to reflect local adaptation. This geographical pattern raises two general questions: (a) Do a few large-effect genes contribute to latitudinal variation in a trait? (b) Is the thermal plasticity of different traits regulated pleiotropically? To address the questions, we crossed individuals of Plantago lanceolata derived from northern and southern European populations. Individuals naturally exhibited high and low thermal plasticity in floral reflectance and flowering time. We grew parents and offspring in controlled cool- and warm-temperature environments, mimicking what plants would encounter in nature. We obtained genetic markers via genotype-by-sequencing, produced the first recombination map for this ecologically important nonmodel species, and performed quantitative trait locus (QTL) mapping of thermal plasticity and single-environment values for both traits. We identified a large-effect QTL that largely explained the reflectance plasticity differences between northern and southern populations. We identified multiple smaller-effect QTLs affecting aspects of flowering time, one of which affected flowering time plasticity. The results indicate that the genetic architecture of thermal plasticity in flowering is more complex than for reflectance. One flowering time QTL showed strong cytonuclear interactions under cool temperatures. Reflectance and flowering plasticity QTLs did not colocalize, suggesting little pleiotropic genetic control and freedom for independent trait evolution. Such genetic information about the architecture of plasticity is environmentally important because it informs us about the potential for plasticity to offset negative effects of climate change.
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Affiliation(s)
- Matthew M Marshall
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - David L Remington
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Elizabeth P Lacey
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, USA
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14
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Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3-GENES GENOMES GENETICS 2019; 9:3297-3314. [PMID: 31405891 PMCID: PMC6778803 DOI: 10.1534/g3.119.400378] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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15
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Mollinari M, Garcia AAF. Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3 (BETHESDA, MD.) 2019. [PMID: 31405891 DOI: 10.1101/415232v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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Affiliation(s)
- Marcelo Mollinari
- Department of Horticultural Science, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, and
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16
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Miller JT, Reid NM, Nacci DE, Whitehead A. Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus. G3 (BETHESDA, MD.) 2019; 9:2851-2862. [PMID: 31289021 PMCID: PMC6723127 DOI: 10.1534/g3.119.400262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022]
Abstract
Killifish (Fundulus heteroclitus) are widely distributed among different aquatic environments where they demonstrate an impressive range of highly-plastic and locally adaptive phenotypes. High-throughput sequencing has begun to unravel the mechanisms and evolutionary history of these interesting features by establishing relationships in the genotype-phenotype map. However, some genotype-phenotype analyses require a higher order of contiguity than what initial scaffolded (fragmented genome assembly where contigs have been assemble into scaffolds) genome assemblies can provide. Here, we used 5,685 high-quality RAD-Seq markers from a single mapping family to order 84% of the scaffolded genome assembly to 24 chromosomes. This serves to: 1) expand the killifish genomic toolkit, 2) estimate genome-wide recombination rates, and 3) compare genome synteny to humans and other fishes. After initially building our map, we found that the selection of thresholds for sequence data filtration highly impacted scaffold placement in the map. We outline each step of the approach that dramatically improved our map to help guide others toward more effective linkage mapping for genome assembly. Our final map supports strong conservation of genomic synteny among closely related fish species and reveals previously described chromosomal rearrangements between more distantly related clades. However, we also commonly found minor scaffold misorientations in F. heteroclitus and in other assemblies, suggesting that further mapping (such as optical mapping) is necessary for finer scale resolution of genome structure. Lastly, we discuss the problems that would be expected from misoriented/unplaced scaffolds and stress the importance of a quality mapped genome as a key feature for further investigating population and comparative genomic questions with F. heteroclitus and other taxa.
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Affiliation(s)
- Jeffrey T Miller
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
| | - Noah M Reid
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, and
| | - Diane E Nacci
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
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17
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Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGDA, Vincentz M, Berges H, de Souza AP. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE 2019; 10:553. [PMID: 31134109 PMCID: PMC6514446 DOI: 10.3389/fpls.2019.00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
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Affiliation(s)
| | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | - Mônica Conte
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arnaud Bellec
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nair Dahmer
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Joelle Fourment
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nathalie Rodde
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | | | - Hermann Paulo Hoffmann
- Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCAR), Araras, Brazil
| | | | | | - Michel Vincentz
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Helene Berges
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
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18
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Bernhardsson C, Vidalis A, Wang X, Scofield DG, Schiffthaler B, Baison J, Street NR, García-Gil MR, Ingvarsson PK. An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies). G3 (BETHESDA, MD.) 2019; 9:1623-1632. [PMID: 30898899 PMCID: PMC6505157 DOI: 10.1534/g3.118.200840] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/15/2019] [Indexed: 12/30/2022]
Abstract
Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.
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Affiliation(s)
- Carolina Bernhardsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Amaryllis Vidalis
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Xi Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Douglas G Scofield
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, Sweden
- Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - Bastian Schiffthaler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - John Baison
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - M Rosario García-Gil
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
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19
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Sang M, Shi H, Wei K, Ye M, Jiang L, Sun L, Wu R. A dissection model for mapping complex traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1168-1182. [PMID: 30536697 DOI: 10.1111/tpj.14185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/26/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Many quantitative traits are composites of other traits that contribute differentially to genetic variation. Quantitative trait locus (QTL) mapping of these composite traits can benefit by incorporating the mechanistic process of how their formation is mediated by the underlying components. We propose a dissection model by which to map these interconnected components traits under a joint likelihood setting. The model can test how a composite trait is determined by pleiotropic QTLs for its component traits or jointly by different sets of QTLs each responsible for a different component. The model can visualize the pattern of time-varying genetic effects for individual components and their impacts on composite traits. The dissection model was used to map two composite traits, stemwood volume growth decomposed into its stem height, stem diameter and stem form components for Euramerican poplar adult trees, and total lateral root length constituted by its average lateral root length and lateral root number components for Euphrates poplar seedlings. We found the pattern of how QTLs for different components contribute to phenotypic variation in composite traits. The detailed understanding of the genetic machineries of composite traits will not only help in the design of molecular breeding in plants and animals, but also shed light on the evolutionary processes of quantitative traits under natural selection.
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Affiliation(s)
- Mengmeng Sang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hexin Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kun Wei
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Meixia Ye
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, Pennsylvania State University, Hershey, PA, 17033, USA
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Research and partnership in studies of sugarcane using molecular markers: a scientometric approach. Scientometrics 2019. [DOI: 10.1007/s11192-019-03047-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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21
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Jiang L, Shi H, Sang M, Zheng C, Cao Y, Zhu X, Zhuo X, Cheng T, Zhang Q, Wu R, Sun L. A Computational Model for Inferring QTL Control Networks Underlying Developmental Covariation. FRONTIERS IN PLANT SCIENCE 2019; 10:1557. [PMID: 31921232 PMCID: PMC6930182 DOI: 10.3389/fpls.2019.01557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/07/2019] [Indexed: 05/02/2023]
Abstract
How one trait developmentally varies as a function of others shapes a spectrum of biological phenomena. Despite its importance to trait dissection, the understanding of whether and how genes mediate such developmental covariation is poorly understood. We integrate developmental allometry equations into the functional mapping framework to map specific QTLs that govern the correlated development of different traits. Based on evolutionary game theory, we assemble and contextualize these QTLs into an intricate but organized network coded by bidirectional, signed, and weighted QTL-QTL interactions. We use this approach to map shoot height-diameter allometry QTLs in an ornamental woody species, mei (Prunus mume). We detect "pioneering" QTLs (piQTLs) and "maintaining" QTLs (miQTLs) that determine how shoot height varies with diameter and how shoot diameter varies with height, respectively. The QTL networks inferred can visualize how each piQTL regulates others to promote height growth at a cost of diameter growth, how miQTL regulates others to benefit radial growth at a cost of height growth, and how piQTLs and miQTLs regulate each other to form a pleiotropic web of primary and secondary growth in trees. Our approach provides a unique gateway to explore the genetic architecture of developmental covariation, a widespread phenomenon in nature.
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Affiliation(s)
- Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hexin Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Mengmeng Sang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chenfei Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yige Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
| | - Lidan Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, China
- *Correspondence: Lidan Sun,
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Sun L, Sang M, Zheng C, Wang D, Shi H, Liu K, Guo Y, Cheng T, Zhang Q, Wu R. The genetic architecture of heterochrony as a quantitative trait: lessons from a computational model. Brief Bioinform 2018; 19:1430-1439. [PMID: 28575183 DOI: 10.1093/bib/bbx056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Indexed: 11/14/2022] Open
Abstract
Heterochrony is known as a developmental change in the timing or rate of ontogenetic events across phylogenetic lineages. It is a key concept synthesizing development into ecology and evolution to explore the mechanisms of how developmental processes impact on phenotypic novelties. A number of molecular experiments using contrasting organisms in developmental timing have identified specific genes involved in heterochronic variation. Beyond these classic approaches that can only identify single genes or pathways, quantitative models derived from current next-generation sequencing data serve as a more powerful tool to precisely capture heterochronic variation and systematically map a complete set of genes that contribute to heterochronic processes. In this opinion note, we discuss a computational framework of genetic mapping that can characterize heterochronic quantitative trait loci that determine the pattern and process of development. We propose a unifying model that charts the genetic architecture of heterochrony that perceives and responds to environmental perturbations and evolves over geologic time. The new model may potentially enhance our understanding of the adaptive value of heterochrony and its evolutionary origins, providing a useful context for designing new organisms that can best use future resources.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Mengmeng Sang
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Chenfei Zheng
- Computational Genetics in the Center for Computational Biology at Beijing Forestry University
| | - Dongyang Wang
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Hexin Shi
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Kaiyue Liu
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Yanfang Guo
- Computational Biology Center for Computational Biology at Beijing Forestry University
| | - Tangren Cheng
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Qixiang Zhang
- National Engineering Research Center for Floriculture at Beijing Forestry University
| | - Rongling Wu
- Center for Computational Biology at Beijing Forestry University
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23
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Xue H, Wang S, Yao JL, Deng CH, Wang L, Su Y, Zhang H, Zhou H, Sun M, Li X, Yang J. Chromosome level high-density integrated genetic maps improve the Pyrus bretschneideri 'DangshanSuli' v1.0 genome. BMC Genomics 2018; 19:833. [PMID: 30463521 PMCID: PMC6249763 DOI: 10.1186/s12864-018-5224-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/06/2018] [Indexed: 01/23/2023] Open
Abstract
Background Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far. Results To anchor the scaffolds of P. bretschneideri ‘DangshanSuli’ (DS) v1.0 genome into pseudo-chromosomes, two genetic maps (MH and YM maps) were constructed using half sibling populations of Chinese pear crosses, ‘Mantianhong’ (MTH) × ‘Hongxiangsu’ (HXS) and ‘Yuluxiang’ (YLX) × MTH, from 345 and 162 seedlings, respectively, which were prepared for SNP discovery using genotyping-by-sequencing (GBS) technology. The MH and YM maps, each with 17 linkage groups (LGs), were constructed from 2606 and 2489 SNP markers and spanned 1847 and 1668 cM, respectively, with average marker intervals of 0.7. The two maps were further merged with a previously published genetic map (BD) based on the cross ‘Bayuehong’ (BYH) × ‘Dangshansuli’ (DS) to build a new integrated MH-YM-BD map. By using 7757 markers located on the integrated MH-YM-BD map, 898 scaffolds (400.57 Mb) of the DS v1.0 assembly were successfully anchored into 17 pseudo-chromosomes, accounting for 78.8% of the assembled genome size. About 88.31% of them (793 scaffolds) were directionally anchored with two or more markers on the pseudo-chromosomes. Furthermore, the errors in each pseudo-chromosome (especially 1, 5, 7 and 11) were manually corrected and pseudo-chromosomes 1, 5 and 7 were extended by adding 19, 12 and 14 scaffolds respectively in the newly constructed DS v1.1 genome. Synteny analyses revealed that the DS v1.1 genome had high collinearity with the apple genome, and the homologous fragments between pseudo-chromosomes were similar to those found in previous studies. Moreover, the red-skin trait of Asian pear was mapped to an identical locus as identified previously. Conclusions The accuracy of DS v1.1 genome was improved by using larger mapping populations and merged genetic map. With more than 400 MB anchored to 17 pseudo-chromosomes, the new DS v1.1 genome provides a critical tool that is essential for studies of pear genetics, genomics and molecular breeding. Electronic supplementary material The online version of this article (10.1186/s12864-018-5224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huabai Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Suke Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Jia-Long Yao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.,The New Zealand Institute for Plant and Food Research Limited, Auckland, 1025, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, 1025, New Zealand
| | - Long Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Yanli Su
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Huirong Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China
| | - Huangkai Zhou
- Guangzhou Gene Denovo Biotechnology Co., Ltd, Guangzhou, 510320, China
| | - Minshan Sun
- Guangzhou Gene Denovo Biotechnology Co., Ltd, Guangzhou, 510320, China
| | - Xiugen Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.
| | - Jian Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Fruit Breeding Technology of Ministry of Agriculture, Zhengzhou, 450009, China.
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24
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Yao D, Wu H, Chen Y, Yang W, Gao H, Tong C. gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population. Brief Bioinform 2018; 21:329-337. [PMID: 30445432 DOI: 10.1093/bib/bby114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/21/2018] [Accepted: 10/23/2018] [Indexed: 11/14/2022] Open
Abstract
Restriction site-associated DNA sequencing (RADseq) is a powerful technology that has been extensively applied in population genetics, phylogenetics and genetic mapping. Although many software packages are available for ecological and evolutionary studies, a few effective tools are available for extracting genotype data with RADseq for genetic mapping, a prerequisite for quantitative trait locus mapping, comparative genomics and genome scaffold assembly. Here, we present an integrated pipeline called gmRAD for generating single nucleotide polymorphism (SNP) genotypes from RADseq data, de novo, across a genetic mapping population derived by crossing two parents. As an analytical strategy, the software takes five steps to implement the whole algorithms, including clustering the first (forward) reads of each parent, building two parental references, generating parental SNP catalogs, calling SNP genotypes across all individuals and filtering the genotype data for genetic linkage mapping. All the steps can be completed with a simple command line, but they can be also performed optionally if prerequisite files are available. To validate its application, we also performed a real data analysis with RADseq data from an F1 hybrid population derived by crossing Populus deltoides and Populus simonii. The software gmRAD is freely available at https://github.com/tongchf/gmRAD.
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Affiliation(s)
- Dan Yao
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hainan Wu
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuhua Chen
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenguo Yang
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hua Gao
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Chunfa Tong
- Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China
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A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids. BMC Bioinformatics 2018; 19:398. [PMID: 30382832 PMCID: PMC6211426 DOI: 10.1186/s12859-018-2433-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/15/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heterozygous classes based on allele dosage. RESULTS VCF2SM is a Python script that integrates sequencing depth information of polymorphisms in variant call format (VCF) files and SUPERMASSA software for quantitative genotype calling. VCFs can be obtained from any variant discovery software that outputs exact allele sequencing depth, such as a modified version of the TASSEL-GBS pipeline provided here. VCF2SM was successfully applied in analyzing GBS data from diverse panels (alfalfa and potato) and full-sib mapping populations (alfalfa and switchgrass) of polyploid species. CONCLUSIONS We demonstrate that our approach can help plant geneticists working with autopolyploid species to advance their studies by distinguishing allele dosage from GBS data.
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26
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Rosa JRBF, Mantello CC, Garcia D, de Souza LM, da Silva CC, Gazaffi R, da Silva CC, Toledo-Silva G, Cubry P, Garcia AAF, de Souza AP, Le Guen V. QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions. BMC PLANT BIOLOGY 2018; 18:223. [PMID: 30305095 PMCID: PMC6180592 DOI: 10.1186/s12870-018-1450-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 09/27/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rubber tree is cultivated in mainly Southeast Asia and is by far the most significant source of natural rubber production worldwide. However, the genetic architecture underlying the primary agronomic traits of this crop has not been widely characterized. This study aimed to identify quantitative trait loci (QTLs) associated with growth and latex production using a biparental population established in suboptimal growth conditions in Brazil. RESULTS A full-sib population composed of 251 individuals was developed from crossing two high-producing Asiatic rubber tree cultivars, PR 255 and PB 217. This mapping population was genotyped with microsatellite markers from enriched genomic libraries or transcriptome datasets and single-nucleotide polymorphism (SNP) markers, leading to construction of a saturated multipoint integrated genetic map containing 354 microsatellite and 151 SNP markers. Height and circumference measurements repeated over a six-year period and registration of cumulative latex production during six consecutive months on the same individuals allowed in-depth characterization of the genetic values of several growth traits and precocious latex production. Growth traits, circumference and height, were overall positively correlated, whereas latex production was not correlated or even negatively correlated with growth traits. A total of 86 distinct QTLs were identified, most of which were detected for only one trait. Among these QTLs, 15 were linked to more than one phenotypic trait (up to 4 traits simultaneously). Latex production and circumference increments during the last wintering period were associated with the highest numbers of identified QTLs (eleven and nine, respectively), jointly explaining the most significantly observed phenotypic variances (44.1% and 44.4%, respectively). The most important QTL for latex production, located on linkage group 16, had an additive effect of the male parent PB 217 and corresponded to a QTL at the same position detected in a previous study carried out in Thailand for the biparental population RRIM 600 x PB 217. CONCLUSIONS Our results identified a set of significant QTLs for rubber tree, showing that the performance of modern Asiatic cultivars can still be improved and paving the way for further marker-assisted selection, which could accelerate breeding programs.
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Affiliation(s)
- João Ricardo Bachega Feijó Rosa
- Department of Genetics, Luiz de Queiros College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Pircacicaba, SP 13400-970 Brazil
- FTS Sementes S.A., Avenida Newton Slaviero, Ponta Grossa, PR 84043-560 Brazil
| | - Camila Campos Mantello
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0 LE UK
| | - Dominique Garcia
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
| | - Lívia Moura de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Carla Cristina da Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Rodrigo Gazaffi
- Center of Agronomic Sciences, Department of Biotechnology and Vegetal and Animal Production, Federal University of São Carlos (UFSCAR), Jardim Residencial Pedras Preciosas, Araras, SP 13604900 Brazil
| | - Cícero Casimiro da Silva
- Plantation E. Michelin, R&D Department, Rua João de Barro quadra 22 lote 16, Ouro Branco do Sul, Itiquira, MT 78790-000 Brazil
| | - Guilherme Toledo-Silva
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry - LABCAI, Biochemistry Department, Federal University Santa Catarina, Florianópolis, Brazil
| | - Philippe Cubry
- IRD, UMR DiADE, 911 avenue Agropolis, BP 64501, 34394, Montpellier cedex 5, France
| | - Antonio Augusto Franco Garcia
- Department of Genetics, Luiz de Queiros College of Agriculture (ESALQ), University of São Paulo (USP), Avenida Pádua Dias, 11, Pircacicaba, SP 13400-970 Brazil
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Vincent Le Guen
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, INRIA, Montpellier SupAgro, Montpellier, France
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Furman BLS, Evans BJ. Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems. Genome Biol Evol 2018; 10:742-755. [PMID: 29608717 PMCID: PMC5841384 DOI: 10.1093/gbe/evy045] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 02/02/2023] Open
Abstract
There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.
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Affiliation(s)
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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28
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Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, de Souza AP. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1255. [PMID: 30197655 PMCID: PMC6117502 DOI: 10.3389/fpls.2018.01255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/08/2018] [Indexed: 06/02/2023]
Abstract
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.
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Affiliation(s)
- André R. O. Conson
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Cristiane H. Taniguti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Livia M. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - João R. B. F. Rosa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Camila C. Mantello
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Carla C. da Silva
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vincent Le Guen
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Montpellier, France
| | - Antonio A. F. Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Anete P. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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Gutierrez AF, Hoy JW, Kimbeng CA, Baisakh N. Identification of Genomic Regions Controlling Leaf Scald Resistance in Sugarcane Using a Bi-parental Mapping Population and Selective Genotyping by Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:877. [PMID: 29997640 PMCID: PMC6028728 DOI: 10.3389/fpls.2018.00877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/05/2018] [Indexed: 05/23/2023]
Abstract
Leaf scald, caused by Xanthomonas albilineans, is a major sugarcane disease worldwide. The disease is managed primarily with resistant cultivars obtained through classical breeding. However, erratic symptom expression hinders the reliability and reproducibility of selection for resistance. The development and use of molecular markers associated with incompatible/compatible reactions could overcome this limitation. The aim of the present work was to find leaf scald resistance-associated molecular markers in sugarcane to facilitate marker-assisted breeding. A genetic linkage map was constructed by selective genotyping of 89 pseudo F2 progenies of a cross between LCP 85-384 (resistant) and L 99-226 (susceptible) using 1,948 single dose (SD) markers generated from SSR, eSSR, and SNPs. Of these, 1,437 SD markers were mapped onto 294 linkage groups, which covered 19,464 cM with 120 and 138 LGs assigned to the resistant and susceptible parent, respectively. Composite interval mapping identified 8 QTLs associated with the disease response with LOD scores ranging from 3.0 to 7.6 and explained 5.23 to 16.93% of the phenotypic variance. Comparative genomics analysis with Sorghum bicolor allowed us to pinpoint three SNP markers that explained 16% phenotypic variance. In addition, representative stress-responsive genes close to the major effect QTLs showed upregulation in their expression in response to the bacterial infection in leaf/meristem tissue.
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Affiliation(s)
- Andres F. Gutierrez
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Jeffrey W. Hoy
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Collins A. Kimbeng
- Sugar Research Station, Louisiana State University Agricultural Center, St. Gabriel, LA, United States
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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30
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Genome-Wide Association Mapping Uncovers Fw1, a Dominant Gene Conferring Resistance to Fusarium Wilt in Strawberry. G3-GENES GENOMES GENETICS 2018; 8:1817-1828. [PMID: 29602808 PMCID: PMC5940171 DOI: 10.1534/g3.118.200129] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae, threatens strawberry (Fragaria × ananassa) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance. Here, we report the discovery of Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. The Fw1 locus was uncovered in a genome-wide association study of 565 historically and commercially important strawberry accessions genotyped with 14,408 SNP markers. Fourteen SNPs in linkage disequilibrium with Fw1 physically mapped to a 2.3 Mb segment on chromosome 2 in a diploid F. vesca reference genome. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid segregating populations. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested-broad-sense heritability was 0.96. Several disease resistance and defense-related gene homologs, including a small cluster of genes encoding nucleotide-binding leucine-rich-repeat proteins, were identified in the 0.7 Mb genomic segment predicted to harbor Fw1 DNA variants and candidate genes identified in the present study should facilitate the development of high-throughput genotyping assays for accurately predicting Fusarium wilt phenotypes and applying marker-assisted selection.
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Gui S, Peng J, Wang X, Wu Z, Cao R, Salse J, Zhang H, Zhu Z, Xia Q, Quan Z, Shu L, Ke W, Ding Y. Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:721-734. [PMID: 29575237 DOI: 10.1111/tpj.13894] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 05/11/2023]
Abstract
Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of 'Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the 'Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the 'China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.
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Affiliation(s)
- Songtao Gui
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhihua Wu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Cao
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jérôme Salse
- Paleogenomics & Evolution (PaleoEvo) Group, Génétique Diversité & Ecophysiologie des Céréales (GDEC), Institut National de la Recherché Agronomique UMR 1095, Clermont-Ferrand, 63100, France
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhixuan Zhu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiuju Xia
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Zhiwu Quan
- Key Laboratory of Genomics, BGI-Shenzhen, Chinese Ministry of Agriculture, Shenzhen, 518083, China
| | - Liping Shu
- Wuhan Ice-Harbor Biological Technology Co. Ltd, Wuhan, 430040, China
| | - Wedong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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High-Throughput Sequencing and Linkage Mapping of a Clownfish Genome Provide Insights on the Distribution of Molecular Players Involved in Sex Change. Sci Rep 2018; 8:4073. [PMID: 29511241 PMCID: PMC5840384 DOI: 10.1038/s41598-018-22282-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/16/2018] [Indexed: 11/18/2022] Open
Abstract
Clownfishes are an excellent model system for investigating the genetic mechanism governing hermaphroditism and socially-controlled sex change in their natural environment because they are broadly distributed and strongly site-attached. Genomic tools, such as genetic linkage maps, allow fine-mapping of loci involved in molecular pathways underlying these reproductive processes. In this study, a high-density genetic map of Amphiprion bicinctus was constructed with 3146 RAD markers in a full-sib family organized in 24 robust linkage groups which correspond to the haploid chromosome number of the species. The length of the map was 4294.71 cM, with an average marker interval of 1.38 cM. The clownfish linkage map showed various levels of conserved synteny and collinearity with the genomes of Asian and European seabass, Nile tilapia and stickleback. The map provided a platform to investigate the genomic position of genes with differential expression during sex change in A. bicinctus. This study aims to bridge the gap of genome-scale information for this iconic group of species to facilitate the study of the main gene regulatory networks governing social sex change and gonadal restructuring in protandrous hermaphrodites.
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Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations. Genetics 2018; 209:65-76. [PMID: 29487138 PMCID: PMC5937187 DOI: 10.1534/genetics.117.300627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/25/2018] [Indexed: 01/06/2023] Open
Abstract
Next-generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which facilitate the development of nonmodel species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sibling family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sibling populations of diploid species, implemented in a package called GUSMap. Our model is based on the Lander-Green hidden Markov model but extended to account for errors present in sequencing data. We were able to obtain accurate estimates of the recombination fractions and overall map distance using GUSMap, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model.
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O'Leary SJ, Hollenbeck CM, Vega RR, Gold JR, Portnoy DS. Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma. BMC Genomics 2018; 19:163. [PMID: 29471804 PMCID: PMC5824557 DOI: 10.1186/s12864-018-4541-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome. RESULTS The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map. CONCLUSIONS The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.
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Affiliation(s)
- Shannon J O'Leary
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA.
| | - Christopher M Hollenbeck
- Scottish Oceans Institute, University of St. Andrews, East Sands, St. Andrews, Fife, KY16 8LB, UK
| | - Robert R Vega
- Texas Parks and Wildlife Department, CCA Marine Development Center, 4300 Waldron Road, Corpus Christi, TX, 78418, USA
| | - John R Gold
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA
| | - David S Portnoy
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA
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Liu J, Ye M, Zhu S, Jiang L, Sang M, Gan J, Wang Q, Huang M, Wu R. Two-stage identification of SNP effects on dynamic poplar growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:286-296. [PMID: 29168265 DOI: 10.1111/tpj.13777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 05/23/2023]
Abstract
This project proposes an approach to identify significant single nucleotide polymorphism (SNP) effects, both additive and dominant, on the dynamic growth of poplar in diameter and height. The annual changes in yearly phenotypes based on regular observation periods are considered to represent multiple responses. In total 156,362 candidate SNPs are studied, and the phenotypes of 64 poplar trees are recorded. To address this ultrahigh dimensionality issue, this paper adopts a two-stage approach. First, the conventional genome-wide association studies (GWAS) and the distance correlation sure independence screening (DC-SIS) methods (Li et al., 2012) were combined to reduce the model dimensions at the sample size; second, a grouped penalized regression was applied to further refine the model and choose the final sparse SNPs. The multiple response issue was also carefully addressed. The SNP effects on the dynamic diameter and height growth patterns of poplar were systematically analyzed. In addition, a series of intensive simulation studies was performed to validate the proposed approach.
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Affiliation(s)
- Jingyuan Liu
- Department of Statistics in School of Economics, Wang Yanan Institute for Studies in Economics, Fujian Key Laboratory of Statistical Science, Xiamen University, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China
| | - Sheng Zhu
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China
| | - Jingwen Gan
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China
| | - Qian Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China
| | - Minren Huang
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100081, China
- Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, PA17033, USA
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Schiffthaler B, Bernhardsson C, Ingvarsson PK, Street NR. BatchMap: A parallel implementation of the OneMap R package for fast computation of F1 linkage maps in outcrossing species. PLoS One 2017; 12:e0189256. [PMID: 29261725 PMCID: PMC5738033 DOI: 10.1371/journal.pone.0189256] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/22/2017] [Indexed: 11/24/2022] Open
Abstract
With the rapid advancement of high throughput sequencing, large numbers of genetic markers can be readily and cheaply acquired, but most current software packages for genetic map construction cannot handle such dense input. Modern computer architectures and server farms represent untapped resources that can be used to enable higher marker densities to be processed in tractable time. Here we present a pipeline using a modified version of OneMap that parallelizes over bottleneck functions and achieves substantial speedups for producing a high density linkage map (N = 20,000). Using simulated data we show that the outcome is as accurate as the traditional pipeline. We further demonstrate that there is a direct relationship between the number of markers used and the level of deviation between true and estimated order, which in turn impacts the final size of a genetic map.
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Affiliation(s)
- Bastian Schiffthaler
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden
- * E-mail:
| | | | - Pär K. Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nathaniel R. Street
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden
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Wang J, Sun L, Jiang L, Sang M, Ye M, Cheng T, Zhang Q, Wu R. A high-dimensional linkage analysis model for characterizing crossover interference. Brief Bioinform 2017; 18:382-393. [PMID: 27113727 DOI: 10.1093/bib/bbw033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 12/19/2022] Open
Abstract
Linkage analysis has played an important role in understanding genome structure and evolution. However, two-point linkage analysis widely used for genetic map construction can rarely chart a detailed picture of genome organization because it fails to identify the dependence of crossovers distributed along the length of a chromosome, a phenomenon known as crossover interference. Multi-point analysis, proven to be more advantageous in gene ordering and genetic distance estimation for dominant markers than two-point analysis, is equipped with a capacity to discern and quantify crossover interference. Here, we review a statistical model for four-point analysis, which, beyond three-point analysis, can characterize crossover interference that takes place not only between two adjacent chromosomal intervals, but also over multiple successive intervals. This procedure provides an analytical tool to elucidate the detailed landscape of crossover interference over the genome and further infer the evolution of genome structure and organization.
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Liu F, Tong C, Tao S, Wu J, Chen Y, Yao D, Li H, Shi J. MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F 1 population of outbred species. BMC Bioinformatics 2017; 18:515. [PMID: 29169342 PMCID: PMC5701343 DOI: 10.1186/s12859-017-1908-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/01/2017] [Indexed: 01/02/2023] Open
Abstract
Background With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines. Results We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi’s information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F1 population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations. Conclusions We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F1 population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim. Electronic supplementary material The online version of this article (10.1186/s12859-017-1908-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fenxiang Liu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.,College of Department of Computer Science and Engineering, Sanjiang University, Nanjing, 210012, China
| | - Chunfa Tong
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
| | - Shentong Tao
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiyan Wu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuhua Chen
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Dan Yao
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jisen Shi
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
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Zhu X, Li H, Ye M, Jiang L, Sang M, Wu R. AlloMap6: an R package for genetic linkage analysis in allohexaploids. Brief Bioinform 2017; 18:919-927. [PMID: 27651481 DOI: 10.1093/bib/bbw085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Indexed: 11/13/2022] Open
Abstract
Allopolyploids are a group of polyploids with more than two sets of chromosomes derived from different species. Previous linkage analysis of allopolyploids is based on the assumption that different chromosomes pair randomly during meiosis. A more sophisticated model to relax this assumption has been developed for allotetraploids by incorporating the preferential pairing behavior of homologous over homoeologous chromosomes. Here, we show that the basic principle of this model can be extended to perform linkage analysis of higher-ploidy allohexaploids, where multiple preferential pairing factors are used to characterize chromosomal-pairing meiotic features between different constituent species. We implemented the extended model into an R package, called AlloMap6, allowing the recombination fractions and preferential pairing factors to be estimated simultaneously. Allomap6 has two major functionalities, computer simulation and real-data analysis. By analyzing a real data from a full-sib family of allohexaploid persimmon, we tested and validated the usefulness and utility of this package. AlloMap6 lays a foundation for allohexaploid genetic mapping and provides a new horizon to explore the chromosomal kinship of allohexaploids.
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Sun L, Wang J, Sang M, Jiang L, Zhao B, Cheng T, Zhang Q, Wu R. Landscaping Crossover Interference Across a Genome. TRENDS IN PLANT SCIENCE 2017; 22:894-907. [PMID: 28822625 DOI: 10.1016/j.tplants.2017.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 05/14/2023]
Abstract
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations. We further discuss the crucial role of CO interference in amplifying and maintaining genetic diversity through sex-, stress-, and age-induced differentiation.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Libo Jiang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tangran Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA.
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da Costa ZP, Munhoz CDF, Vieira MLC. Report on the development of putative functional SSR and SNP markers in passion fruits. BMC Res Notes 2017; 10:445. [PMID: 28874179 PMCID: PMC5585897 DOI: 10.1186/s13104-017-2771-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). RESULTS A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. CONCLUSIONS Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
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Affiliation(s)
- Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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Sutherland BJG, Rico C, Audet C, Bernatchez L. Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis. G3 (BETHESDA, MD.) 2017; 7:2749-2762. [PMID: 28626004 PMCID: PMC5555479 DOI: 10.1534/g3.117.040915] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/13/2017] [Indexed: 02/06/2023]
Abstract
Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.
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Affiliation(s)
- Ben J G Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Ciro Rico
- School of Marine Studies, Molecular Diagnostics Laboratory, University of the South Pacific, Suva, Fiji
- Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Quebec G5L 3A1, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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Li L, Deng CH, Knäbel M, Chagné D, Kumar S, Sun J, Zhang S, Wu J. Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome. DNA Res 2017; 24:289-301. [PMID: 28130382 PMCID: PMC5499846 DOI: 10.1093/dnares/dsw063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 12/16/2016] [Indexed: 01/14/2023] Open
Abstract
Genetic maps are essential tools for pear genetics and genomics research. In this study, we first constructed an integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic map for pear based on common SSR markers between nine published maps. A total of 5,085 markers, including 1,232 SSRs and 3,853 SNPs, were localized on a consensus map spanning 3,266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date. Using three sets of high-density SNP-based genetic maps with European pear genetic backgrounds, we anchored a total of 291.5 Mb of the ‘Bartlett’ v1.0 (Pyrus communis L.) genome scaffolds into 17 pseudo-chromosomes. This accounted for 50.5% of the genome assembly, which was a great improvement on the 29.7% achieved originally. Intra-genome and inter-genome synteny analyses of the new ‘Bartlett’ v1.1 genome assembly with the Asian pear ‘Dangshansuli’ (Pyrus bretschneideri Rehd.) and apple (Malus × domestica Borkh.) genomes uncovered four new segmental duplication regions. The integrated high-density SSR and SNP-based consensus genetic map provided new insights into the genetic structure patterns of pear and assisted in the genome assembly of ‘Bartlett’ through further exploration of different pear genetic maps.
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Affiliation(s)
- Leiting Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - Mareike Knäbel
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - Satish Kumar
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - Jiangmei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
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Zhang M, Bo W, Xu F, Li H, Ye M, Jiang L, Shi C, Fu Y, Zhao G, Huang Y, Gosik K, Liang D, Wu R. The genetic architecture of shoot-root covariation during seedling emergence of a desert tree, Populus euphratica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:918-928. [PMID: 28244225 DOI: 10.1111/tpj.13518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 05/12/2023]
Abstract
The coordination of shoots and roots is critical for plants to adapt to changing environments by fine-tuning energy production in leaves and the availability of water and nutrients from roots. To understand the genetic architecture of how these two organs covary during developmental ontogeny, we conducted a mapping experiment using Euphrates poplar (Populus euphratica), a so-called hero tree able to grow in the desert. We geminated intraspecific F1 seeds of Euphrates Poplar individually in a tube to obtain a total of 370 seedlings, whose shoot and taproot lengths were measured repeatedly during the early stage of growth. By fitting a growth equation, we estimated asymptotic growth, relative growth rate, the timing of inflection point and duration of linear growth for both shoot and taproot growth. Treating these heterochronic parameters as phenotypes, a univariate mapping model detected 19 heterochronic quantitative trait loci (hQTLs), of which 15 mediate the forms of shoot growth and four mediate taproot growth. A bivariate mapping model identified 11 pleiotropic hQTLs that determine the covariation of shoot and taproot growth. Most QTLs detected reside within the region of candidate genes with various functions, thus confirming their roles in the biochemical processes underlying plant growth.
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Affiliation(s)
- Miaomiao Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Fang Xu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Huan Li
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chaozhong Shi
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaru Fu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Guomiao Zhao
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuejiao Huang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kirk Gosik
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA
| | - Dan Liang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA
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Curtolo M, Cristofani-Yaly M, Gazaffi R, Takita MA, Figueira A, Machado MA. QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genomics 2017; 18:289. [PMID: 28403819 PMCID: PMC5389163 DOI: 10.1186/s12864-017-3629-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/14/2017] [Indexed: 11/24/2022] Open
Abstract
Background Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits. A controlled Murcott x Pera crossing was conducted at the Citrus Germplasm Repository at the Sylvio Moreira Citrus Centre of the Agronomic Institute (IAC) located in Cordeirópolis, SP, in 1997. In 2012, 278 F1 individuals out of a family of 312 confirmed hybrid individuals were analyzed for fruit traits and genotyped using the DArTseq markers. Using OneMap software to obtain the integrated genetic map, we considered only the DArT loci that showed no segregation deviation. The likelihood ratio and the genomic information from the available Citrus sinensis L. Osbeck genome were used to determine the linkage groups (LGs). Results The resulting integrated map contained 661 markers in 13 LGs, with a genomic coverage of 2,774 cM and a mean density of 0.23 markers/cM. The groups were assigned to the nine Citrus haploid chromosomes; however, some of the chromosomes were represented by two LGs due the lack of information for a single integration, as in cases where markers segregated in a 3:1 fashion. A total of 19 QTLs were identified through composite interval mapping (CIM) of the 12 analyzed fruit characteristics: fruit diameter (cm), height (cm), height/diameter ratio, weight (g), rind thickness (cm), segments per fruit, total soluble solids (TSS, %), total titratable acidity (TTA, %), juice content (%), number of seeds, TSS/TTA ratio and number of fruits per box. The genomic sequence (pseudochromosomes) of C. sinensis was compared to the genetic map, and synteny was clearly identified. Further analysis of the map regions with the highest LOD scores enabled the identification of putative genes that could be associated with the fruit quality characteristics. Conclusion An integrated linkage map of Murcott tangor and Pera sweet orange using DArTseq™ molecular markers was established and it was useful to perform QTL mapping of twelve fruit quality traits. The next generation sequences data allowed the comparison between the linkage map and the genomic sequence (pseudochromosomes) of C. sinensis and the identification of genes that may be responsible for phenotypic traits in Citrus. The obtained linkage map was used to assign sequences that had not been previously assigned to a position in the reference genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3629-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maiara Curtolo
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil.,Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Mariângela Cristofani-Yaly
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil.
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos (UFSCar) - Centro de Ciências Agrárias, Rodovia Anhanguera, km 174, 13600-970, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - Marcos Antonio Machado
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
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Khanal S, Kim C, Auckland SA, Rainville LK, Adhikari J, Schwartz BM, Paterson AH. SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:819-839. [PMID: 28168408 DOI: 10.1007/s00122-017-2854-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/04/2017] [Indexed: 05/20/2023]
Abstract
We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x = 9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.
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Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31793, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
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Sun L, Wang J, Zhu X, Jiang L, Gosik K, Sang M, Sun F, Cheng T, Zhang Q, Wu R. HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly. Brief Bioinform 2017; 19:603-612. [DOI: 10.1093/bib/bbx011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Indexed: 01/19/2023] Open
Affiliation(s)
- Lidan Sun
- Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
| | - Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kirk Gosik
- Statistical Genetics, Department of Public Health Sciences, Pennsylvania State University, Pennsylvania, USA
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Fengsuo Sun
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Ornamental Genetics, National Engineering Research, Center for Floriculture, Beijing Forestry University Beijing, China
| | - Qixiang Zhang
- Ornamental Genetics, National Engineering Research, Center for Floriculture, Beijing Forestry University Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, Pennsylvania State University, Pennsylvania, PA, USA
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Fu L, Sun L, Hao H, Jiang L, Zhu S, Ye M, Tang S, Huang M, Wu R. How trees allocate carbon for optimal growth: insight from a game-theoretic model. Brief Bioinform 2017; 19:593-602. [DOI: 10.1093/bib/bbx003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 01/20/2023] Open
Affiliation(s)
- Liyong Fu
- Center for Computational Biology at Beijing Forestry University, China
- Institute of Forest Resource Information Techniques at Chinese Academy of Forestry, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture at Beijing Forestry University, Beijing, China
| | - Han Hao
- Department of Statistics at The Pennsylvania State University, USA
- Department of Mathematics at the University of North Texas, Denton, USA
| | - Libo Jiang
- Center for Computational Biology at Beijing Forestry University, Beijing, China
| | - Sheng Zhu
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement at Nanjing Forestry University, Nanjing, China
| | - Meixia Ye
- Center for Computational Biology at Beijing Forestry University, Beijing, China
| | - Shouzheng Tang
- Forest Management in the Institute of Forest Resource Information Techniques at Chinese Academy of Forestry, Beijing, China
| | - Minren Huang
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement at Nanjing Forestry University, Nanjing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Balsalobre TWA, da Silva Pereira G, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP, de Souza AP, Garcia AAF, Carneiro MS. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 2017; 18:72. [PMID: 28077090 PMCID: PMC5225503 DOI: 10.1186/s12864-016-3383-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. RESULTS We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. CONCLUSIONS This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.
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Affiliation(s)
- Thiago Willian Almeida Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Guilherme da Silva Pereira
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Rodrigo Gazaffi
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Fernanda Zatti Barreto
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Carina Oliveira Anoni
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Cláudio Benício Cardoso-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Estela Araújo Costa
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Melina Cristina Mancini
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Hermann Paulo Hoffmann
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Antonio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
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Sutherland BJG, Gosselin T, Normandeau E, Lamothe M, Isabel N, Audet C, Bernatchez L. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps. Genome Biol Evol 2016; 8:3600-3617. [PMID: 28173098 PMCID: PMC5381510 DOI: 10.1093/gbe/evw262] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 12/13/2022] Open
Abstract
Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/
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Affiliation(s)
- Ben J. G. Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Thierry Gosselin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Manuel Lamothe
- Centre de Foresterie des Laurentides, Ressources Naturelles Canada, Québec, QC, Canada
| | - Nathalie Isabel
- Centre de Foresterie des Laurentides, Ressources Naturelles Canada, Québec, QC, Canada
| | - Céline Audet
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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