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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Silva A, Montoya ME, Quintero C, Cuasquer J, Tohme J, Graterol E, Cruz M, Lorieux M. Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach. G3 (BETHESDA, MD.) 2023; 13:jkad223. [PMID: 37766452 PMCID: PMC10700108 DOI: 10.1093/g3journal/jkad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
Rice hoja blanca (RHB) is one of the most serious diseases in rice-growing areas in tropical Americas. Its causal agent is RHB virus (RHBV), transmitted by the planthopper Tagosodes orizicolus Müir. Genetic resistance is the most effective and environment-friendly way of controlling the disease. So far, only 1 major quantitative trait locus (QTL) of Oryza sativa ssp. japonica origin, qHBV4.1, that alters the incidence of the virus symptoms in 2 Colombian cultivars has been reported. This resistance has already started to be broken, stressing the urgent need for diversifying the resistance sources. In the present study, we performed a search for new QTLs of O. sativa indica origin associated with RHB resistance. We used 4 F2:3-segregating populations derived from indica-resistant varieties crossed with a highly susceptible japonica pivot parent. Besides the standard method for measuring disease incidence, we developed a new method based on computer-assisted image processing to determine the affected leaf area (ALA) as a measure of symptom severity. Based on the disease severity and incidence scores in the F3 families under greenhouse conditions and SNP genotyping of the F2 individuals, we identified 4 new indica QTLs for RHB resistance on rice chromosomes 4, 6, and 11, namely, qHBV4.2WAS208, qHBV6.1PTB25, qHBV11.1, and qHBV11.2, respectively. We also confirmed the wide-range action of qHBV4.1. Among the 5 QTLs, qHBV4.1 and qHBV11.1 had the largest effects on incidence and severity, respectively. These results provide a more complete understanding of the genetic bases of RHBV resistance in the cultivated rice gene pool and can be used to develop marker-aided breeding strategies to improve RHB resistance. The power of joint- and meta-analyses allowed precise mapping and candidate gene identification, providing the basis for positional cloning of the 2 major QTLs qHBV4.1 and qHBV11.1.
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Affiliation(s)
- Alexander Silva
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - María Elker Montoya
- FLAR-The Latin American Fund for Irrigated Rice, Valle del Cauca CP 763537, Colombia
| | - Constanza Quintero
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - Juan Cuasquer
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - Joe Tohme
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
| | - Eduardo Graterol
- FLAR-The Latin American Fund for Irrigated Rice, Valle del Cauca CP 763537, Colombia
| | - Maribel Cruz
- FLAR-The Latin American Fund for Irrigated Rice, Valle del Cauca CP 763537, Colombia
| | - Mathias Lorieux
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Palmira, Valle del Cauca CP 763537, Colombia
- DIADE, University of Montpellier, Cirad, IRD.IRD Occitanie, 911 Ave Agropolis, 34394 Montpellier Cedex 5, France
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Anshakov DV, Fisinin VI, Narushin VG, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail ( Coturnix japonica) Breeds. Animals (Basel) 2023; 13:3439. [PMID: 38003057 PMCID: PMC10668688 DOI: 10.3390/ani13223439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center Zagorsk Experimental Breeding Farm—Branch of the Federal Research Centre, All-Russian Poultry Research and Technological Institute, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Valeriy G. Narushin
- Research Institute for Environment Treatment, 69032 Zaporizhya, Ukraine;
- Vita-Market Co., Ltd., 69032 Zaporizhya, Ukraine
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.)
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Arantes LS, Caccavo JA, Sullivan JK, Sparmann S, Mbedi S, Höner OP, Mazzoni CJ. Scaling-up RADseq methods for large datasets of non-invasive samples: Lessons for library construction and data preprocessing. Mol Ecol Resour 2023. [PMID: 37646753 DOI: 10.1111/1755-0998.13859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Genetic non-invasive sampling (gNIS) is a critical tool for population genetics studies, supporting conservation efforts while imposing minimal impacts on wildlife. However, gNIS often presents variable levels of DNA degradation and non-endogenous contamination, which can incur considerable processing costs. Furthermore, the use of restriction-site-associated DNA sequencing methods (RADseq) for assessing thousands of genetic markers introduces the challenge of obtaining large sets of shared loci with similar coverage across multiple individuals. Here, we present an approach to handling large-scale gNIS-based datasets using data from the spotted hyena population inhabiting the Ngorongoro Crater in Tanzania. We generated 3RADseq data for more than a thousand individuals, mostly from faecal mucus samples collected non-invasively and varying in DNA degradation and contamination level. Using small-scale sequencing, we screened samples for endogenous DNA content, removed highly contaminated samples, confirmed overlap fragment length between libraries, and balanced individual representation in a sequencing pool. We evaluated the impact of (1) DNA degradation and contamination of non-invasive samples, (2) PCR duplicates and (3) different SNP filters on genotype accuracy based on Mendelian error estimated for parent-offspring trio datasets. Our results showed that when balanced for sequencing depth, contaminated samples presented similar genotype error rates to those of non-contaminated samples. We also showed that PCR duplicates and different SNP filters impact genotype accuracy. In summary, we showed the potential of using gNIS for large-scale genetic monitoring based on SNPs and demonstrated how to improve control over library preparation by using a weighted re-pooling strategy that considers the endogenous DNA content.
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Affiliation(s)
- Larissa S Arantes
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Jilda A Caccavo
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
- Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques, LOCEAN/IPSL, UPMC-CNRS-IRD-MNHN, Sorbonne Université, Paris, France
| | - James K Sullivan
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Freie Universität, Berlin, Germany
| | - Sarah Sparmann
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Berlin, Germany
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Museum für Naturkunde, Berlin, Germany
| | - Oliver P Höner
- Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
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Wu N, Wang S, Dujsebayeva TN, Chen D, Ali A, Guo X. Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia. Mol Phylogenet Evol 2023; 184:107781. [PMID: 37044189 DOI: 10.1016/j.ympev.2023.107781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.
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Affiliation(s)
- Na Wu
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wang
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China
| | - Tatjana N Dujsebayeva
- Laboratory of Ornithology and Herpetology, Institute of Zoology, Ministry of Sciences and High Education of Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Abid Ali
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguang Guo
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China.
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Li J, Chang X, Huang Q, Liu P, Zhao X, Li F, Wang Y, Chang C. Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1080691. [PMID: 36938035 PMCID: PMC10017979 DOI: 10.3389/fpls.2023.1080691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The flower buds of Lonicera japonica Thunb. are widely used in Chinese medicine for their anti-inflammatory properties, and they have played an important role in the fight against SARS COVID-19 and other major epidemics. However, due to the lack of scientific and accurate variety identification methods and national unified standards, scattered and non-standardized management in flower bud production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new L. japonica varieties. METHODS In this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of Lonicera in China using simplified genome sequencing technology. RESULTS A total of 13,143,268 single nucleotide polymorphisms (SNPs) were identified. Thirty-nine samples of Lonicera were divided into four subgroups, and the population structure and genetic relationships among existing Lonicera germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 39 Lonicera varieties. DISCUSSION To our knowledge, this is the first comprehensive study measuring the diversity and population structure of a large collection of Lonicera varieties in China. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of Lonicera. The results may enhance the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding by providing a scientific basis and reference data for these efforts.
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Affiliation(s)
- Jianjun Li
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiaopei Chang
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Qian Huang
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Pengfei Liu
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiting Zhao
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Fengmei Li
- School of Life Science and Basic Medicine, Xinxiang University, Xinxiang, China
| | - Yungang Wang
- Foresty Seeding Service Station of XinXiang, Xinxiang, Henan, China
| | - Cuifang Chang
- State Key Laboratory Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, China
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Shen Y, Wang J, Shaw RK, Yu H, Sheng X, Zhao Z, Li S, Gu H. Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli ( Brassica oleracea L. var. italica) in China. FRONTIERS IN PLANT SCIENCE 2021; 12:655254. [PMID: 34149754 PMCID: PMC8213352 DOI: 10.3389/fpls.2021.655254] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.
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Affiliation(s)
- Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ranjan K. Shaw
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Kausch AP, Nelson-Vasilchik K, Hague J, Mookkan M, Quemada H, Dellaporta S, Fragoso C, Zhang ZJ. Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:186-205. [PMID: 30824051 DOI: 10.1016/j.plantsci.2019.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/07/2018] [Accepted: 01/10/2019] [Indexed: 05/21/2023]
Abstract
The combination of advanced genomics, genome editing and plant transformation biology presents a powerful platform for basic plant research and crop improvement. Together these advances provide the tools to identify genes as targets for direct editing as single base pair changes, deletions, insertions and site specific homologous recombination. Recent breakthrough technologies using morphogenic regulators in plant transformation creates the ability to introduce reagents specific toward their identified targets and recover stably transformed and/or edited plants which are genotype independent. These technologies enable the possibility to alter a trait in any variety, without genetic disruption which would require subsequent extensive breeding, but rather to deliver the same variety with one trait changed. Regulatory issues regarding this technology will predicate how broadly these technologies will be implemented. In addition, education will play a crucial role for positive public acceptance. Taken together these technologies comprise a platform for advanced breeding which is an imperative for future world food security.
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Affiliation(s)
- Albert P Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, RI 02892, USA.
| | | | - Joel Hague
- Department of Cell and Molecular Biology, University of Rhode Island, RI 02892, USA
| | - Muruganantham Mookkan
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Stephen Dellaporta
- Yale University, New Haven, CT 06520, USA; Verinomics Inc., New Haven, CT 06520, USA
| | | | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
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10
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Worthington M, Ebina M, Yamanaka N, Heffelfinger C, Quintero C, Zapata YP, Perez JG, Selvaraj M, Ishitani M, Duitama J, de la Hoz JF, Rao I, Dellaporta S, Tohme J, Arango J. Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola. BMC Genomics 2019. [PMID: 30642244 DOI: 10.1186/s12864-018-5392-5394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species. RESULTS Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F1 mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F1 mapping population, despite its location on a different carrier chromosome than B. decumbens. CONCLUSIONS The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.
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Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.
- Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR, 72701, USA.
| | - Masumi Ebina
- National Agriculture and Food Research Organization (NARO), Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, 392-2793, Japan
| | - Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Constanza Quintero
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | | | | | - Michael Selvaraj
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Manabu Ishitani
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jorge Duitama
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- Present address: Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Juan Fernando de la Hoz
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- Present address: Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Idupulapati Rao
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- Present address: Plant Polymer Research Unit (PPL), National Center for Agricultural Utilization Research (NCAUR), Agricultural Research Service, United States Department of Agriculture (ARS-USDA), 1815 N. University St., Peoria, IL, 61604, USA
| | - Stephen Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
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11
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Worthington M, Ebina M, Yamanaka N, Heffelfinger C, Quintero C, Zapata YP, Perez JG, Selvaraj M, Ishitani M, Duitama J, de la Hoz JF, Rao I, Dellaporta S, Tohme J, Arango J. Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola. BMC Genomics 2019; 20:41. [PMID: 30642244 PMCID: PMC6332668 DOI: 10.1186/s12864-018-5392-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 12/18/2018] [Indexed: 12/05/2022] Open
Abstract
Background The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species. Results Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F1 mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F1 mapping population, despite its location on a different carrier chromosome than B. decumbens. Conclusions The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis. Electronic supplementary material The online version of this article (10.1186/s12864-018-5392-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia. .,Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR, 72701, USA.
| | - Masumi Ebina
- National Agriculture and Food Research Organization (NARO), Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, 392-2793, Japan
| | - Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Constanza Quintero
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | | | | | - Michael Selvaraj
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Manabu Ishitani
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jorge Duitama
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.,Present address: Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Juan Fernando de la Hoz
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.,Present address: Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Idupulapati Rao
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.,Present address: Plant Polymer Research Unit (PPL), National Center for Agricultural Utilization Research (NCAUR), Agricultural Research Service, United States Department of Agriculture (ARS-USDA), 1815 N. University St., Peoria, IL, 61604, USA
| | - Stephen Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
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12
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Discovery of Anthocyanin Acyltransferase1 (AAT1) in Maize Using Genotyping-by-Sequencing (GBS). G3-GENES GENOMES GENETICS 2018; 8:3669-3678. [PMID: 30257861 PMCID: PMC6222571 DOI: 10.1534/g3.118.200630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The reduced acylation phenotype describes the inability of certain accessions of maize (Zea mays [L.]) to produce significant amounts of acylated anthocyanins, which are typically the most abundant pigments. Acylated anthocyanins are important for their association with stability and are therefore important for the various industries using anthocyanins as natural colorants to replace synthetic dyes. Many anthocyanin acyltransferases have been characterized in other species; however, no anthocyanin acyltransferases have been characterized in maize. Therefore, a mapping population was developed from a cross between mutant stock 707G and wild-type acylation line B73 to identify the locus associated with the reduced acylation trait. High-performance liquid chromatography was used to assay the pigment content and composition of 129 F2 lines generated in the mapping population. Recessive alleles of Colorless1, Colored1, and the reduced acylation mutant all decreased anthocyanin content while Intensifier1 increased anthocyanin content in aleurone tissue. The association of increased proportions of acylation with increased anthocyanin content indicates acylation may be important for increasing the stability of anthocyanins in vivo. Genotyping-by-sequencing was used to create SNP markers to map the reduced acylation locus. In the QTL analysis, a segment of Chromosome 1 containing transferase family protein GRMZM2G387394 was found to be significant. A UniformMu Mu transposon knockout of GRMZM2G387394 demonstrated this gene has anthocyanidin malonyltransferase activity and will therefore be named Anthocyanin Acyltransferase1 (AAT1). AAT1 is the first anthocyanin acyltransferase characterized in a monocot species and will increase our knowledge of all acyltransferase family members.
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13
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Zheng C, Boer MP, van Eeuwijk FA. Accurate Genotype Imputation in Multiparental Populations from Low-Coverage Sequence. Genetics 2018; 210:71-82. [PMID: 30045858 PMCID: PMC6116951 DOI: 10.1534/genetics.118.300885] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/21/2018] [Indexed: 11/18/2022] Open
Abstract
Many different types of multiparental populations have recently been produced to increase genetic diversity and resolution in QTL mapping. Low-coverage, genotyping-by-sequencing (GBS) technology has become a cost-effective tool in these populations, despite large amounts of missing data in offspring and founders. In this work, we present a general statistical framework for genotype imputation in such experimental crosses from low-coverage GBS data. Generalizing a previously developed hidden Markov model for calculating ancestral origins of offspring DNA, we present an imputation algorithm that does not require parental data and that is applicable to bi- and multiparental populations. Our imputation algorithm allows heterozygosity of parents and offspring as well as error correction in observed genotypes. Further, our approach can combine imputation and genotype calling from sequencing reads, and it also applies to called genotypes from SNP array data. We evaluate our imputation algorithm by simulated and real data sets in four different types of populations: the F2, the advanced intercross recombinant inbred lines, the multiparent advanced generation intercross, and the cross-pollinated population. Because our approach uses marker data and population design information efficiently, the comparisons with previous approaches show that our imputation is accurate at even very low ([Formula: see text]) sequencing depth, in addition to having accurate genotype phasing and error detection.
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Affiliation(s)
- Chaozhi Zheng
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Martin P Boer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
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14
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Salas‐Lizana R, Oono R. Double-digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles. Ecol Evol 2018; 8:6638-6651. [PMID: 30038763 PMCID: PMC6053583 DOI: 10.1002/ece3.4147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/14/2018] [Accepted: 03/29/2018] [Indexed: 12/24/2022] Open
Abstract
The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low-cost double-digest restriction site-associated DNA sequencing (ddRADseq) protocol to reveal among- and within-species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded adapters and incorporates universal indexes for multiplexing. We tested for reproducibility and functionality by comparing shared loci from sample replicates and assessed the effects of numbers of ambiguous sites and clustering thresholds on coverage depths, number of shared loci among samples, and phylogenetic reconstruction. Errors between technical replicates were minimal. Relaxing the quality-filtering criteria increased the mean coverage depth per locus and the number of loci recovered within a sample, but had little effect on the number of shared loci across samples. Increasing clustering threshold decreased the mean coverage depth per cluster and increased the number of loci recovered within a sample but also decreased the number of shared loci across samples, especially among distantly related species. The combination of low similarity clustering (70%) and relaxed quality-filtering (allowing up to 30 ambiguous sites per read) performed the best in phylogenetic analyses at both recent and deep genetic divergences. Hence, this method generated sufficient number of shared homologous loci to investigate the evolutionary relationships among divergent fungal lineages with small haploid genomes. The greater genetic resolution also revealed new structure within species that correlated with ecological traits, providing valuable insights into their cryptic life histories.
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Affiliation(s)
- Rodolfo Salas‐Lizana
- Department of Ecology, Evolution, and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
- Present address:
Departamento de Biología ComparadaFacultad de CienciasUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
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15
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Heffelfinger C, Fragoso CA, Lorieux M. Constructing linkage maps in the genomics era with MapDisto 2.0. Bioinformatics 2018; 33:2224-2225. [PMID: 28369214 DOI: 10.1093/bioinformatics/btx177] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/25/2017] [Indexed: 01/10/2023] Open
Abstract
Motivation Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). Results MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. Availability and Implementation The program is available free of charge at mapdisto.free.fr. Contact mapdisto@gmail.com. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Christopher A Fragoso
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Mathias Lorieux
- DIADE Research Unit, Institut de Recherche pour le Développement (IRD), Montpellier, France.,Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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16
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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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17
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Yang X, Song J, You Q, Paudel DR, Zhang J, Wang J. Mining sequence variations in representative polyploid sugarcane germplasm accessions. BMC Genomics 2017; 18:594. [PMID: 28793856 PMCID: PMC5551020 DOI: 10.1186/s12864-017-3980-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes. Results To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. Conclusions The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.
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Affiliation(s)
- Xiping Yang
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Jian Song
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Qian You
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Dev R Paudel
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute of Science and Techonology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA. .,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute of Science and Techonology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. .,Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA.
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18
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FRAGMATIC: in silico locus prediction and its utility in optimizing ddRADseq projects. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0814-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize. G3-GENES GENOMES GENETICS 2017; 7:2161-2170. [PMID: 28526729 PMCID: PMC5499125 DOI: 10.1534/g3.117.042036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of issues encountered with GBS be considered, including the sequencing of nonoverlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation. We addressed these issues while developing and validating a new, comprehensive platform for GBS. This study supports the notion that GBS can be tailored to particular aims, and using Zea mays our results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. Optimizing size selection to sequence a high proportion of shared loci among individuals in different libraries and using simple in silico filters, a GBS procedure was established that produces high call rates per marker (>85%) with accuracy exceeding 99.4%. Furthermore, by capitalizing on the sequence-read structure of GBS data (stacks of reads), a new tool for resolving local haplotypes and scoring phased genotypes was developed, a feature that is not available in many GBS pipelines. Using local haplotypes reduces the marker dimensionality of the genotype matrix while increasing the informativeness of the data. Phased GBS in maize also revealed the existence of reproducibly inaccurate (apparent accuracy) genotypes that were due to divergent copy number variants (CNVs) unobservable in the underlying single nucleotide polymorphism (SNP) data.
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Fragoso CA, Moreno M, Wang Z, Heffelfinger C, Arbelaez LJ, Aguirre JA, Franco N, Romero LE, Labadie K, Zhao H, Dellaporta SL, Lorieux M. Genetic Architecture of a Rice Nested Association Mapping Population. G3 (BETHESDA, MD.) 2017; 7:1913-1926. [PMID: 28450374 PMCID: PMC5473768 DOI: 10.1534/g3.117.041608] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022]
Abstract
Describing the genetic diversity in the gene pool of crops will provide breeders with novel resources for varietal improvement. Nested Association Mapping (NAM) populations are uniquely suited for characterizing parental diversity through the shuffling and fixation of parental haplotypes. Here, we describe a set of 1879 rice NAM lines created through the selfing and single-seed descent of F1 hybrids derived from elite IR64 indica crossed with 10 diverse tropical japonica lines. Genotyping data indicated tropical japonica alleles were captured at every queried locus despite the presence of segregation distortion factors. Several distortion loci were mapped, both shared and unique, among the 10 populations. Using two-point and multi-point genetic map calculations, our datasets achieved the ∼1500 cM expected map size in rice. Finally, we highlighted the utility of the NAM lines for QTL mapping, including joint analysis across the 10 populations, by confirming known QTL locations for the trait days to heading.
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Affiliation(s)
- Christopher A Fragoso
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Maria Moreno
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Zuoheng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511
- Department of Biostatistics, Yale University, New Haven, Connecticut 06511
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Lady J Arbelaez
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - John A Aguirre
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - Natalia Franco
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - Luz E Romero
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | - Karine Labadie
- Commissariat à L'énergie Atomique et aux Énergies Alternatives, Institut de Génomique, Genoscope, 91000 Evry, France
| | - Hongyu Zhao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511
- Department of Biostatistics, Yale University, New Haven, Connecticut 06511
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Mathias Lorieux
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
- Diversité, Adaptation, Développement des Plantes Research Unit, Institut de Recherche pour le Développement, F-34394 Montpellier, France
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Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S. Adapting Genotyping-by-Sequencing for Rice F2 Populations. G3 (BETHESDA, MD.) 2017; 7:881-893. [PMID: 28082325 PMCID: PMC5345719 DOI: 10.1534/g3.116.038190] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.
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Affiliation(s)
- Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Kshirod K Jena
- Plant Breeding Division, International Rice Research Institute, 1301 Manila, Philippines
| | - Kazuyuki Doi
- Associated Field Science and Research Center, Nagoya University, 470-0151, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
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22
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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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Triplett LR, Cohen SP, Heffelfinger C, Schmidt CL, Huerta A, Tekete C, Verdier V, Bogdanove AJ, Leach JE. A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL effectors with diverse predicted targets and is effective against African strains of Xanthomonas oryzae pv. oryzicola. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:472-83. [PMID: 27197779 PMCID: PMC5030141 DOI: 10.1111/tpj.13212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 05/19/2023]
Abstract
The rice pathogens Xanthomonas oryzae pathovar (pv.) oryzae and pv. oryzicola produce numerous transcription activator-like (TAL) effectors that increase bacterial virulence by activating expression of host susceptibility genes. Rice resistance mechanisms against TAL effectors include polymorphisms that prevent effector binding to susceptibility gene promoters, or that allow effector activation of resistance genes. This study identifies, in the heirloom variety Carolina Gold Select, a third mechanism of rice resistance involving TAL effectors. This resistance manifests through strong suppression of disease development in response to diverse TAL effectors from both X. oryzae pathovars. The resistance can be triggered by an effector with only 3.5 central repeats, is independent of the composition of the repeat variable di-residues that determine TAL effector binding specificity, and is independent of the transcriptional activation domain. We determined that the resistance is conferred by a single dominant locus, designated Xo1, that maps to a 1.09 Mbp fragment on chromosome 4. The Xo1 interval also confers complete resistance to the strains in the African clade of X. oryzae pv. oryzicola, representing the first dominant resistance locus against bacterial leaf streak in rice. The strong phenotypic similarity between the TAL effector-triggered resistance conferred by Xo1 and that conferred by the tomato resistance gene Bs4 suggests that monocots and dicots share an ancient or convergently evolved mechanism to recognize analogous TAL effector epitopes.
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Affiliation(s)
- Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
| | - Stephen P. Cohen
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520
| | - Clarice L. Schmidt
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Alejandra Huerta
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
| | - Cheick Tekete
- Université des Sciences Techniques et Technologiques, Faculté des Sciences et Techniques, LBMA, Bamako, Mali
| | - Valerie Verdier
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177
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24
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Clark LV, Sacks EJ. TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. SOURCE CODE FOR BIOLOGY AND MEDICINE 2016; 11:11. [PMID: 27408618 PMCID: PMC4940913 DOI: 10.1186/s13029-016-0057-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/06/2016] [Indexed: 01/24/2023]
Abstract
BACKGROUND In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. RESULTS We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user-supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. CONCLUSIONS TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.
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Affiliation(s)
- Lindsay V Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802 USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802 USA
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25
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A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens. Genetics 2016; 203:1117-32. [PMID: 27206716 PMCID: PMC4937464 DOI: 10.1534/genetics.116.190314] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/14/2016] [Indexed: 12/19/2022] Open
Abstract
Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR–BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR–BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR–BBML as candidate genes for the apomictic function of parthenogenesis.
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26
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Fu YB, Peterson GW, Dong Y. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes. G3 (BETHESDA, MD.) 2016; 6:845-56. [PMID: 26818077 PMCID: PMC4825655 DOI: 10.1534/g3.115.025775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/22/2016] [Indexed: 12/15/2022]
Abstract
Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0-16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - Gregory W Peterson
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - Yibo Dong
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
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27
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Abstract
High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
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28
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Jiang Z, Wang H, Michal JJ, Zhou X, Liu B, Woods LCS, Fuchs RA. Genome Wide Sampling Sequencing for SNP Genotyping: Methods, Challenges and Future Development. Int J Biol Sci 2016; 12:100-8. [PMID: 26722221 PMCID: PMC4679402 DOI: 10.7150/ijbs.13498] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/07/2015] [Indexed: 12/04/2022] Open
Abstract
Genetic polymorphisms, particularly single nucleotide polymorphisms (SNPs), have been widely used to advance quantitative, functional and evolutionary genomics. Ideally, all genetic variants among individuals should be discovered when next generation sequencing (NGS) technologies and platforms are used for whole genome sequencing or resequencing. In order to improve the cost-effectiveness of the process, however, the research community has mainly focused on developing genome-wide sampling sequencing (GWSS) methods, a collection of reduced genome complexity sequencing, reduced genome representation sequencing and selective genome target sequencing. Here we review the major steps involved in library preparation, the types of adapters used for ligation and the primers designed for amplification of ligated products for sequencing. Unfortunately, currently available GWSS methods have their drawbacks, such as inconsistency in the number of reads per sample library, the number of sites/targets per individual, and the number of reads per site/target, all of which result in missing data. Suggestions are proposed here to improve library construction, genotype calling accuracy, genome-wide marker density and read mapping rate. In brief, optimized GWSS library preparation should generate a unique set of target sites with dense distribution along chromosomes and even coverage per site across all individuals.
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Affiliation(s)
- Zhihua Jiang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA
| | - Hongyang Wang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA; ; 2. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jennifer J Michal
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA
| | - Xiang Zhou
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620, USA
| | - Bang Liu
- 2. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Leah C Solberg Woods
- 3. Department of Pediatrics, Human and Molecular Genetics Center and Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rita A Fuchs
- 4. Department of Integrative Physiology and Neuroscience, Washington State University College of Veterinary Medicine, Pullman, WA 99164-7620, USA
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Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data. Genetics 2015; 202:487-95. [PMID: 26715670 DOI: 10.1534/genetics.115.182071] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/16/2015] [Indexed: 12/31/2022] Open
Abstract
Low-coverage next-generation sequencing methodologies are routinely employed to genotype large populations. Missing data in these populations manifest both as missing markers and markers with incomplete allele recovery. False homozygous calls at heterozygous sites resulting from incomplete allele recovery confound many existing imputation algorithms. These types of systematic errors can be minimized by incorporating depth-of-sequencing read coverage into the imputation algorithm. Accordingly, we developed Low-Coverage Biallelic Impute (LB-Impute) to resolve missing data issues. LB-Impute uses a hidden Markov model that incorporates marker read coverage to determine variable emission probabilities. Robust, highly accurate imputation results were reliably obtained with LB-Impute, even at extremely low (<1×) average per-marker coverage. This finding will have implications for the design of genotype imputation algorithms in the future. LB-Impute is publicly available on GitHub at https://github.com/dellaporta-laboratory/LB-Impute.
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30
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Hilario E, Barron L, Deng CH, Datson PM, De Silva N, Davy MW, Storey RD. Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome. PLoS One 2015; 10:e0143193. [PMID: 26633193 PMCID: PMC4669186 DOI: 10.1371/journal.pone.0143193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/02/2015] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED Genotyping by sequencing (GBS) is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al. METHOD some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS). By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS) method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145) of BamH I sites shared with the reference genome, compared to only 14% (11,513) by stdGBS.
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Affiliation(s)
- Elena Hilario
- The New Zealand Institute for Plant & Food Research Ltd, Priv. Bag 92–169, Auckland, 1025, New Zealand
- * E-mail:
| | - Lorna Barron
- The New Zealand Institute for Plant & Food Research Ltd, Priv. Bag 92–169, Auckland, 1025, New Zealand
| | - Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Ltd, Priv. Bag 92–169, Auckland, 1025, New Zealand
| | - Paul M. Datson
- The New Zealand Institute for Plant & Food Research Ltd, Priv. Bag 92–169, Auckland, 1025, New Zealand
| | - Nihal De Silva
- The New Zealand Institute for Plant & Food Research Ltd, Priv. Bag 92–169, Auckland, 1025, New Zealand
| | - Marcus W. Davy
- The New Zealand Institute for Plant & Food Research Ltd, 412 No 1 Road RD 2, Te Puke, 3182, New Zealand
| | - Roy D. Storey
- The New Zealand Institute for Plant & Food Research Ltd, 412 No 1 Road RD 2, Te Puke, 3182, New Zealand
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Fierst JL. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools. Front Genet 2015; 6:220. [PMID: 26150829 PMCID: PMC4473057 DOI: 10.3389/fgene.2015.00220] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/08/2015] [Indexed: 01/05/2023] Open
Abstract
Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.
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Affiliation(s)
- Janna L. Fierst
- Department of Biological Sciences, University of AlabamaTuscaloosa, AL, USA
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