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Feng Y, Yang C, Zhang J, Qiao J, Wang B, Zhao Y. Construction of a High-Density Paulownia Genetic Map and QTL Mapping of Important Phenotypic Traits Based on Genome Assembly and Whole-Genome Resequencing. Int J Mol Sci 2023; 24:15647. [PMID: 37958630 PMCID: PMC10647314 DOI: 10.3390/ijms242115647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative trait locus (QTL) mapping based on a genetic map is a very effective method of marker-assisted selection in breeding, and whole-genome resequencing is one of the useful methods to obtain high-density genetic maps. In this study, the hybrid assembly of Illumina, PacBio, and chromatin interaction mapping data was used to construct high-quality chromosomal genome sequences of Paulownia fortunei, with a size of 476.82 Mb, a heterozygosity of 0.52%, and a contig and scaffold N50s of 7.81 Mb and 21.81 Mb, respectively. Twenty scaffolds with a total length of 437.72 Mb were assembled into 20 pseudochromosomes. Repeat sequences with a total length of 243.96 Mb accounted for 51.16% of the entire genome. In all, 26,903 protein-coding gene loci were identified, and 26,008 (96.67%) genes had conserved functional motifs. Further comparative genomics analysis preliminarily showed that the split of P. fortunei with Tectona grandis likely occurred 38.8 (33.3-45.1) million years ago. Whole-genome resequencing was used to construct a merged genetic map of 20 linkage groups, with 2993 bin markers (3,312,780 SNPs), a total length of 1675.14 cm, and an average marker interval of 0.56 cm. In total, 73 QTLs for important phenotypic traits were identified (19 major QTLs with phenotypic variation explained ≥ 10%), including 10 for the diameter at breast height, 7 for the main trunk height, and 56 for branch-related traits. These results not only enrich P. fortunei genomic data but also form a solid foundation for fine QTL mapping and key marker/gene mining of Paulownia, which is of great significance for the directed genetic improvement of these species.
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Affiliation(s)
- Yanzhi Feng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Chaowei Yang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jiajia Zhang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jie Qiao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Baoping Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Yang Zhao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
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Pan Z, Zhang J, Bai S, Li Z, Tong C. InDelGT: An integrated pipeline for extracting indel genotypes for genetic mapping in a hybrid population using next-generation sequencing data. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11499. [PMID: 36518944 PMCID: PMC9742820 DOI: 10.1002/aps3.11499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/04/2022] [Accepted: 05/25/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Although several software packages are available for genotyping insertion/deletion (indel) polymorphisms in genomes using next-generation sequencing data, simultaneously calling indel genotypes across many individuals for use in genetic mapping remains challenging. METHODS AND RESULTS We present an integrated pipeline, InDelGT, for the extraction of indel genotypes from a segregating population such as backcross or F2 lines, or from an F1 cross between outbred species. The InDelGT algorithm is implemented in three steps: generating an indel catalog, calling indel genotypes, and analyzing indel segregation. We demonstrated the use of the pipeline with an example data set from an F1 hybrid population of Populus and successfully constructed the two parental genetic linkage maps. CONCLUSIONS InDelGT is a practical tool that can quickly genotype a large number of indel markers within a population following Mendelian segregation. The InDelGT pipeline is freely available on GitHub (https://github.com/tongchf/InDelGT).
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Affiliation(s)
- Zhiliang Pan
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjing210037China
| | - Jinpeng Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjing210037China
| | - Shengjun Bai
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjing210037China
| | - Zhiting Li
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjing210037China
| | - Chunfa Tong
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjing210037China
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A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii. Genes (Basel) 2022; 13:genes13101731. [PMID: 36292616 PMCID: PMC9601732 DOI: 10.3390/genes13101731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic linkage maps of the traditional F2 population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F2 population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F1 hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map.
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Li Z, Zhao W, Zhang J, Pan Z, Bai S, Tong C. A Novel Strategy to Reveal the Landscape of Crossovers in an F1 Hybrid Population of Populus deltoides and Populus simonii. PLANTS 2022; 11:plants11081046. [PMID: 35448774 PMCID: PMC9025136 DOI: 10.3390/plants11081046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/03/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022]
Abstract
Although the crossover (CO) patterns of different species have been extensively investigated, little is known about the landscape of CO patterns in Populus because of its high heterozygosity and long-time generation. A novel strategy was proposed to reveal the difference of CO rate and interference between Populus deltoides and Populus simonii using their F1 hybrid population. We chose restriction site-associated DNA (RAD) tags that contained two SNPs, one only receiving the CO information from the female P. deltoides and the other from the male P. simonii. These RAD tags allowed us to investigate the CO patterns between the two outbred species, instead of using the traditional backcross populations in inbred lines. We found that the CO rate in P. deltoides was generally greater than that in P. simonii, and that the CO interference was a common phenomenon across the two genomes. The COs landscape of the different Populus species facilitates not only to understand the evolutionary mechanism for adaptability but also to rebuild the statistical model for precisely constructing genetic linkage maps that are critical in genome assembly in Populus. Additionally, the novel strategy could be applied in other outbred species for investigating the CO patterns.
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Affiliation(s)
| | | | | | | | | | - Chunfa Tong
- Correspondence: ; Tel.: +86-025-85428817 (ext. 815)
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Yang W, Yao D, Wu H, Zhao W, Chen Y, Tong C. Multivariate genome-wide association study of leaf shape in a Populus deltoides and P. simonii F1 pedigree. PLoS One 2021; 16:e0259278. [PMID: 34710178 PMCID: PMC8553126 DOI: 10.1371/journal.pone.0259278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/16/2021] [Indexed: 11/19/2022] Open
Abstract
Leaf morphology exhibits tremendous diversity between and within species, and is likely related to adaptation to environmental factors. Most poplar species are of great economic and ecological values and their leaf morphology can be a good predictor for wood productivity and environment adaptation. It is important to understand the genetic mechanism behind variation in leaf shape. Although some initial efforts have been made to identify quantitative trait loci (QTLs) for poplar leaf traits, more effort needs to be expended to unravel the polygenic architecture of the complex traits of leaf shape. Here, we performed a genome-wide association analysis (GWAS) of poplar leaf shape traits in a randomized complete block design with clones from F1 hybrids of Populus deltoides and Populus simonii. A total of 35 SNPs were identified as significantly associated with the multiple traits of a moderate number of regular polar radii between the leaf centroid and its edge points, which could represent the leaf shape, based on a multivariate linear mixed model. In contrast, the univariate linear mixed model was applied as single leaf traits for GWAS, leading to genomic inflation; thus, no significant SNPs were detected for leaf length, measures of leaf width, leaf area, or the ratio of leaf length to leaf width under genomic control. Investigation of the candidate genes showed that most flanking regions of the significant leaf shape-associated SNPs harbored genes that were related to leaf growth and development and to the regulation of leaf morphology. The combined use of the traditional experimental design and the multivariate linear mixed model could greatly improve the power in GWAS because the multiple trait data from a large number of individuals with replicates of clones were incorporated into the statistical model. The results of this study will enhance the understanding of the genetic mechanism of leaf shape variation in Populus. In addition, a moderate number of regular leaf polar radii can largely represent the leaf shape and can be used for GWAS of such a complicated trait in Populus, instead of the higher-dimensional regular radius data that were previously considered to well represent leaf shape.
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Affiliation(s)
- Wenguo Yang
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Dan Yao
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Hainan Wu
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Wei Zhao
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Yuhua Chen
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Chunfa Tong
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
- * E-mail:
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Exploring the genomic resources and analysing the genetic diversity and population structure of Chinese indigenous rabbit breeds by RAD-seq. BMC Genomics 2021; 22:573. [PMID: 34311701 PMCID: PMC8314496 DOI: 10.1186/s12864-021-07833-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/23/2021] [Indexed: 12/30/2022] Open
Abstract
Background Chinese indigenous rabbits have distinct characteristics, such as roughage resistance, stress resistance and environmental adaptability, which are of great significance to the sustainable development of the rabbit industry in China. Therefore, it is necessary to study the genetic diversity and population structure of this species and develop genomic resources. Results In this study, we used restriction site-associated DNA sequencing (RAD-seq) to obtain 1,006,496 SNP markers from six Chinese indigenous rabbit breeds and two imported rabbit breeds. Jiuyishan and Fujian Yellow rabbits showed the highest nucleotide diversity (π) and decay of linkage disequilibrium (LD), as well as higher observed heterozygosity (Ho) and expected heterozygosity (He), indicating higher genetic diversity than other rabbits. The inbreeding coefficient (FIS) of New Zealand rabbits and Belgian rabbits was higher than that of other rabbits. The neighbour-joining (NJ) tree, principal component analysis (PCA), and population structure analysis of autosomes and Y chromosomes showed that Belgian, New Zealand, Wanzai, Sichuan White, and Minxinan Black rabbits clustered separately, and Fujian Yellow, Yunnan Colourful, and Jiuyishan rabbits clustered together. Wanzai rabbits were clearly separated from other populations (K = 3), which was consistent with the population differentiation index (FST) analysis. The selection signature analysis was performed in two populations with contrasting coat colours. With Sichuan White and New Zealand rabbits as the reference populations and Minxinan Black and Wanzai rabbits as the target populations, 408, 454, 418, and 518 genes with a selection signature, respectively, were obtained. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the genes with a selection signature. The results showed that the genes with a selection signature were enriched in the melanogenesis pathway in all four sets of selection signature analyses. Conclusions Our study provides the first insights into the genetics and genomics of Chinese indigenous rabbit breeds and serves as a valuable resource for the further effective utilization of the species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07833-6.
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Bai S, Wu H, Zhang J, Pan Z, Zhao W, Li Z, Tong C. Genome Assembly of Salicaceae Populus deltoides (Eastern Cottonwood) I-69 Based on Nanopore Sequencing and Hi-C Technologies. J Hered 2021; 112:303-310. [PMID: 33730157 PMCID: PMC8141683 DOI: 10.1093/jhered/esab010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Populus deltoides has important ecological and economic values, widely used in poplar breeding programs due to its superior characteristics such as rapid growth and resistance to disease. Although the genome sequence of P. deltoides WV94 is available, the assembly is fragmented. Here, we reported an improved chromosome-level assembly of the P. deltoides cultivar I-69 by combining Nanopore sequencing and chromosome conformation capture (Hi-C) technologies. The assembly was 429.3 Mb in size and contained 657 contigs with a contig N50 length of 2.62 Mb. Hi-C scaffolding of the contigs generated 19 chromosome-level sequences, which covered 97.4% (418 Mb) of the total assembly size. Moreover, repetitive sequences annotation showed that 39.28% of the P. deltoides genome was composed of interspersed elements, including retroelements (23.66%), DNA transposons (6.83%), and unclassified elements (8.79%). We also identified a total of 44 362 protein-coding genes in the current P. deltoides assembly. Compared with the previous genome assembly of P. deltoides WV94, the current assembly had some significantly improved qualities: the contig N50 increased 3.5-fold and the proportion of gaps decreased from 3.2% to 0.08%. This high-quality, well-annotated genome assembly provides a reliable genomic resource for identifying genome variants among individuals, mining candidate genes that control growth and wood quality traits, and facilitating further application of genomics-assisted breeding in populations related to P. deltoides.
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Affiliation(s)
- Shengjun Bai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hainan Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jinpeng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhiliang Pan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wei Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhiting Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Chunfa Tong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Liu G, Yang Q, Gao J, Wu Y, Feng Z, Huang J, Zou H, Zhu X, Chen Y, Yu C, Lian B, Zhong F, Zhang J. Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in Salix matsudana (Koidz). Front Genet 2021; 12:596749. [PMID: 33868361 PMCID: PMC8044533 DOI: 10.3389/fgene.2021.596749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
The study on the fast-growing traits of trees, mainly valued by tree height (TH) and diameter at breast height (DBH), is of great significance to promote the development of the forest industry. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for fast-growing traits. In our study, a high-density genetic map for the F1 population was constructed. The genetic map had a total size of 5,484.07 centimorgan (cM), containing 5,956 single nucleotide polymorphisms (SNPs) based on Specific Length Amplified Fragment sequencing. Six fast-growing related stable QTL were identified on six chromosomes, and five stable QTL were identified by a principal component analysis (PCA). By combining the RNA-seq analysis for the two parents and two progenies with the qRT-PCR analysis, four candidate genes, annotated as DnaJ, 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), Caffeic acid 3-O-methyltransferase 1 (COMT1), and Dirigent protein 6 (DIR6), that may regulate height growth were identified. Several lignin biosynthesis-related genes that may take part in height growth were detected. In addition, 21 hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of TH and DBH.
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Affiliation(s)
- Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | | | - Junfeng Gao
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Yuwei Wu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Zhicong Feng
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Jingke Huang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Hang Zou
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Xingzhao Zhu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Bolin Lian
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
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Chen Y, Wu H, Yang W, Zhao W, Tong C. Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design. G3-GENES GENOMES GENETICS 2021; 11:6064171. [PMID: 33604666 PMCID: PMC8022933 DOI: 10.1093/g3journal/jkaa053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/01/2020] [Indexed: 01/09/2023]
Abstract
With the advances in high-throughput sequencing technologies, it is not difficult to extract tens of thousands of single-nucleotide polymorphisms (SNPs) across many individuals in a fast and cheap way, making it possible to perform genome-wide association studies (GWAS) of quantitative traits in outbred forest trees. It is very valuable to apply traditional breeding experiments in GWAS for identifying genome variants associated with ecologically and economically important traits in Populus. Here, we reported a GWAS of tree height measured at multiple time points from a randomized complete block design (RCBD), which was established with clones from an F1 hybrid population of Populus deltoides and Populus simonii. A total of 22,670 SNPs across 172 clones in the RCBD were obtained with restriction site-associated DNA sequencing (RADseq) technology. The multivariate mixed linear model was applied by incorporating the pedigree relationship matrix of individuals to test the association of each SNP to the tree heights over 8 time points. Consequently, 41 SNPs were identified significantly associated with the tree height under the P-value threshold determined by Bonferroni correction at the significant level of 0.01. These SNPs were distributed on all but two chromosomes (Chr02 and Chr18) and explained the phenotypic variance ranged from 0.26% to 2.64%, amounting to 63.68% in total. Comparison with previous mapping studies for poplar height as well as the candidate genes of these detected SNPs were also investigated. We therefore showed that the application of multivariate linear mixed model to the longitudinal phenotypic data from the traditional breeding experimental design facilitated to identify far more genome-wide variants for tree height in poplar. The significant SNPs identified in this study would enhance understanding of molecular mechanism for growth traits and would accelerate marker-assisted breeding programs in Populus.
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Affiliation(s)
- Yuhua Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.,School of Animal Science and Technology, Jingling Institute of Technology, Nanjing 210038, China
| | - Hainan Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenguo Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Zhao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Chunfa Tong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Tong C, Yao D, Wu H, Chen Y, Yang W, Zhao W. High-Quality SNP Linkage Maps Improved QTL Mapping and Genome Assembly in Populus. J Hered 2020; 111:515-530. [PMID: 32930789 PMCID: PMC7751148 DOI: 10.1093/jhered/esaa039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
With the advances in high-throughput sequencing technologies and the development of new software for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality genetic maps with thousands of SNPs in outbred forest trees. Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing data from an F1 hybrid population derived from Populus deltoides and Populus simonii, and applied in QTL mapping and genome assembly. The female P. deltoides map contained 4018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55. The male P. simonii map showed similar characteristics, consisting of 2097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP order of each linkage group was optimal among different ordering results from several available software. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height. In addition, the linkage maps improved the anchoring of 689 contigs of P. simonii to chromosomes. The 2 parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus, as well as the excellent performances in QTL mapping and genome assembly. Both approaches for extracting and ordering SNPs could be applied to other species for constructing high-quality genetic maps.
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Affiliation(s)
- Chunfa Tong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Dan Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hainan Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuhua Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenguo Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wei Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Liu X, Zhang Z, Bian W, Duan A, Zhang H. Enhancing the expression of ARK1 genes in poplar leads to multiple branches and transcriptomic changes. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201201. [PMID: 33047064 PMCID: PMC7540752 DOI: 10.1098/rsos.201201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 05/22/2023]
Abstract
The ARBORKNOX1 (ARK1) gene is an important gene for regulating plant growth and development; however, transcriptomic responses of enhancing expression of ARK1 gene in poplar are poorly investigated. To provide insight into the gene function of the ARK1 gene in poplar, the ARK1 transgenic poplar '717' and '84 K' lines were obtained, the morphology of transgenic plants was observed, and transcriptome profiles were compared. The results showed that there were multiple branches in ARK1 transgenic seedlings compared with non-transgenic seedlings. The results of transcriptome analysis showed that there were significant differences in transcriptome profiles between the transgenic lines of '717' and '84 K', and between non-transgenic lines (CK) and transgenic plants. The real-time quantitative polymerase chain reaction (RT-qPCR) analysis confirmed the expression levels of the genes involved in the pathway of zeatin biosynthesis and brassinosteroid biosynthesis. The increase in expression levels of AHP and CYCD3 was related to multiple branches. Enhancing the expression of the ARK1 gene in poplar seedlings leads to multiple branches and transcriptomic changes.
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Affiliation(s)
- Xiaozhen Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Ministry of Education, Kunming, Yunnan 650224, People's Republic of China
| | - Zhiming Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, Yunnan 650224, People's Republic of China
| | - Wen Bian
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forest Administration, Southwest Forestry University, Kunming, Yunnan 650224, People's Republic of China
| | - Anan Duan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Ministry of Education, Kunming, Yunnan 650224, People's Republic of China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Ministry of Education, Kunming, Yunnan 650224, People's Republic of China
- Author for correspondence: Hanyao Zhang e-mail:
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12
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Schwarzkopf EJ, Motamayor JC, Cornejo OE. Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations. BMC Genomics 2020; 21:332. [PMID: 32349675 PMCID: PMC7191684 DOI: 10.1186/s12864-020-6746-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated. Results Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo. Conclusions We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.
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Affiliation(s)
| | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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13
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Wu H, Yao D, Chen Y, Yang W, Zhao W, Gao H, Tong C. De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections. G3 (BETHESDA, MD.) 2020; 10:455-466. [PMID: 31806765 PMCID: PMC7003099 DOI: 10.1534/g3.119.400913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/03/2019] [Indexed: 11/18/2022]
Abstract
Populus simonii is an important tree in the genus Populus, widely distributed in the Northern Hemisphere and having a long cultivation history. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Here, we report a chromosome-level genome assembly of P. simonii using PacBio long-read sequencing data aided by Illumina paired-end reads and related genetic linkage maps. The assembly is 441.38 Mb in length and contain 686 contigs with a contig N50 of 1.94 Mb. With the linkage maps, 336 contigs were successfully anchored into 19 pseudochromosomes, accounting for 90.2% of the assembled genome size. Genomic integrity assessment showed that 1,347 (97.9%) of the 1,375 genes conserved among all embryophytes can be found in the P. simonii assembly. Genomic repeat analysis revealed that 41.47% of the P. simonii genome is composed of repetitive elements, of which 40.17% contained interspersed repeats. A total of 45,459 genes were predicted from the P. simonii genome sequence and 39,833 (87.6%) of the genes were annotated with one or more related functions. Phylogenetic analysis indicated that P. simonii and Populus trichocarpa should be placed in different sections, contrary to the previous classification according to morphology. The genome assembly not only provides an important genetic resource for the comparative and functional genomics of different Populus species, but also furnishes one of the closest reference sequences for identifying genomic variants in an F1 hybrid population derived by crossing P. simonii with other Populus species.
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Affiliation(s)
- Hainan Wu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dan Yao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuhua Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenguo Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Zhao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hua Gao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Chunfa Tong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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14
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Xin H, Zhang T, Wu Y, Zhang W, Zhang P, Xi M, Jiang J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:253-264. [PMID: 31529535 DOI: 10.1111/tpj.14536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/25/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
The karyotype represents the basic genetic make-up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.
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Affiliation(s)
- Haoyang Xin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yufeng Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenli Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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15
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Lu N, Zhang M, Xiao Y, Han D, Liu Y, Zhang Y, Yi F, Zhu T, Ma W, Fan E, Qu G, Wang J. Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F 1 population of Catalpa bungei × Catalpa duclouxii Dode. BMC PLANT BIOLOGY 2019; 19:596. [PMID: 31888555 PMCID: PMC6937828 DOI: 10.1186/s12870-019-2207-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/17/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies. RESULTS Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis. CONCLUSIONS This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.
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Affiliation(s)
- Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Donghua Han
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 Jiangsu People’s Republic of China
| | - Ying Liu
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Erqin Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
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16
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Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B. The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). Genome Biol Evol 2019; 11:3353-3371. [PMID: 31702783 PMCID: PMC6907397 DOI: 10.1093/gbe/evz245] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the R. williamsianum genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in R. williamsianum. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.
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Affiliation(s)
- Valerie L Soza
- Department of Biology, University of Washington, Seattle, WA
| | - Dale Lindsley
- Department of Biology, University of Washington, Seattle, WA
- Retired
| | - Adam Waalkes
- Department of Biology, University of Washington, Seattle, WA
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | | | | | - Joshua N Burton
- Department of Genome Sciences, University of Washington, Seattle, WA
- Adaptive Biotechnologies, Seattle, WA
| | - Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR
| | - Akash Kumar
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Pediatrics, Stanford University, Palo Alto, CA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA
- Retired
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Benjamin Hall
- Department of Biology, University of Washington, Seattle, WA
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Zhebentyayeva TN, Sisco PH, Georgi LL, Jeffers SN, Perkins MT, James JB, Hebard FV, Saski C, Nelson CD, Abbott AG. Dissecting Resistance to Phytophthora cinnamomi in Interspecific Hybrid Chestnut Crosses Using Sequence-Based Genotyping and QTL Mapping. PHYTOPATHOLOGY 2019; 109:1594-1604. [PMID: 31287366 DOI: 10.1094/phyto-11-18-0425-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The soilborne oomycete Phytophthora cinnamomi-which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development. Introduction of resistant genotypes is the most practical solution for disease management in forests because treatment with fungicides and eradication of the pathogen are neither practical nor economically feasible in natural ecosystems. Using backcross families derived from crosses of American chestnuts with two resistant Chinese chestnut cultivars Mahogany and Nanking, we constructed linkage maps and identified quantitative trait loci (QTLs) for resistance to P. cinnamomi that had been introgressed from these Chinese chestnut cultivars. In total, 957 plants representing five cohorts of three hybrid crosses were genotyped by sequencing and phenotyped by standardized inoculation and visual examination over a 6-year period from 2011 to 2016. Eight parental linkage maps comprising 7,715 markers were constructed, and 17 QTLs were identified on four linkage groups (LGs): LG_A, LG_C, LG_E, and LG_K. The most consistent QTLs were detected on LG_E in seedlings from crosses with both 'Mahogany' and 'Nanking' and LG_K in seedlings from 'Mahogany' crosses. Two consistent large and medium effect QTLs located ∼10 cM apart were present in the middle and at the lower end of LG_E; other QTLs were considered to have small effects. These results imply that the genetic architecture of resistance to P. cinnamomi in Chinese chestnut × American chestnut hybrid progeny may resemble the P. sojae-soybean pathosystem, with a few dominant QTLs along with quantitatively inherited partial resistance conferred by multiple small-effect QTLs.
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Affiliation(s)
- Tetyana N Zhebentyayeva
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802
- Clemson University Genomics and Computational Biology Laboratory, Clemson, SC 29634
| | - Paul H Sisco
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Laura L Georgi
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - M Taylor Perkins
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | | | - Frederick V Hebard
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - C Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, U.S. Department of Agriculture Forest Service, Saucier, MS 39574
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
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Li Y, Dungey HS. Expected benefit of genomic selection over forward selection in conifer breeding and deployment. PLoS One 2018; 13:e0208232. [PMID: 30532178 PMCID: PMC6287808 DOI: 10.1371/journal.pone.0208232] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
Genomic selection is a proven technology in animal and plant breeding to accelerate genetic gain, but as yet is to be fully realised in forest tree breeding. This paper examines, through stochastic simulation, the potential benefits of genomic selection (GS) over forward selection (FS) in a typical conifer breeding program. Methods of speeding the deployment of selected material were also considered, including top-grafting onto mature seed orchard ortets, using additional replicates of clones in archives for crossing, and embryogenesis and clonal propagation. Genetic gain per generation was found to increase considerably when the size of the training population was larger (800 c.f. 3000 clones), or when the heritability was higher (0.2 c.f. 0.5). The largest genetic gain, of 24% was achieved where large training populations (3000 clones) and high heritability traits (0.5) were combined. The accuracy of genomic breeding values (GEBVs) increased with the increase in the number of clones in the training population, the heritability of the trait and the density of the SNP markers. Calculated accuracies of simulated GEBVs and genetic gain per unit of time suggested that 2000 clones in the training population is the minimum size for effective genomic selection for conifers. Compared with forward selection, genomic selection with 2000 clones in the training population, and a 60K SNP panel, an increase of 1.58 mm per year in diameter-at-breast-height (DBH) and 2.44 kg/m3 per year for wood density can be expected. After one generation (9-years), this would be equivalent to 14.23 mm and 21.97 kg/m3 for DBH and wood density respectively. Deploying clones of the selected individuals always resulted in higher additional genetic gain than deploying progeny/seedlings. Deploying genetic material selected from genomic selection with top-grafting for early coning appeared to be the best option. Application of genomic selection to conifer breeding programs, combined with deployment tools such as top-grafting and embryogenesis are powerful tools to speed the delivery of genetic gain to the forest.
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Affiliation(s)
- Yongjun Li
- Scion (New Zealand Forest Research Institute), Rotorua, New Zealand
- Agriculture Victoria, AgriBio Centre, DEDJTR, Bundoora, Victoria, Australia
- * E-mail:
| | - Heidi S. Dungey
- Scion (New Zealand Forest Research Institute), Rotorua, New Zealand
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Dungey HS, Dash JP, Pont D, Clinton PW, Watt MS, Telfer EJ. Phenotyping Whole Forests Will Help to Track Genetic Performance. TRENDS IN PLANT SCIENCE 2018; 23:854-864. [PMID: 30217472 DOI: 10.1016/j.tplants.2018.08.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Phenotyping is the accurate and precise physical description of organisms. Accurate and quantitative phenotyping underpins the delivery of benefits from genetic improvement programs in agriculture. In forest trees, phenotyping at an equivalent precision has been impossible because trees and forests are large, long-lived, and highly variable. These facts have restricted the delivery of genetic gains in forestry compared to other agricultural sectors. We describe a landscape-scale phenotyping platform that integrates remote sensing, spatial information systems, and genomics to facilitate the delivery of greater gains enabling forestry to catch up with other sectors. Combining remote sensing at a range of spatial and temporal scales with genomics will ultimately impact on tree breeding globally.
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Affiliation(s)
- Heidi S Dungey
- Scion, 49 Sala Street, Rotorua, 3020, New Zealand; www.scionresearch.com/about-us/about-scion/our-people/people/forest-science/heidi-dungey.
| | | | - David Pont
- Scion, 49 Sala Street, Rotorua, 3020, New Zealand
| | - Peter W Clinton
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
| | - Michael S Watt
- Scion, 10 Kyle Street, Riccarton, Christchurch 8011, New Zealand
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20
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Lin CW, Kuo JC, Liu HL, Cheng YS, Huang HL. A new method for detection of single nucleotide polymorphism in a female reproduction-associated gene, tmigd1, of Anas platyrhynchos using a strip biosensor with gold nanoparticles. Poult Sci 2018; 97:3456-3462. [DOI: 10.3382/ps/pey240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
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21
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Tao S, Wu J, Yao D, Chen Y, Yang W, Tong C. Identification of recombination events in outbred species with next-generation sequencing data. BMC Genomics 2018; 19:398. [PMID: 29801431 PMCID: PMC5970487 DOI: 10.1186/s12864-018-4791-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/14/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps. RESULTS We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F1 hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO . CONCLUSIONS The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.
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Affiliation(s)
- Shentong Tao
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China
| | - Jiyan Wu
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China
| | - Dan Yao
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China
| | - Yuhua Chen
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China
| | - Wenguo Yang
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China
| | - Chunfa Tong
- Co-Innovation Center for Sustainable Forestry in South China, College of Forestry, Nanjing Forestry University, No.159, Longpan Road, Xuanwu Qu, Nanjing, 210037, China.
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Yu H, You X, Li J, Zhang X, Zhang S, Jiang S, Lin X, Lin HR, Meng Z, Shi Q. A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping. SCIENCE CHINA-LIFE SCIENCES 2018. [DOI: 10.1007/s11427-017-9161-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 2018. [PMID: 29520650 DOI: 10.1007/s00412-018-0664-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dioecious species accounted for 6% of all plant species, including a number of crops and economically important species, such as poplar. However, sex determination and sex chromosome evolution have been studied only in few dioecious species. In poplar, the sex-determining locus was mapped to chromosome 19. Interestingly, this locus was mapped to either a peritelomeric or a centromeric region among different poplar species. We developed an oligonucleotide (oligo)-based chromosome painting probe based on the sequence of chromosome 19 from Populus trichocarpa. We performed chromosome painting in P. tomentosa and P. deltoides. Surprisingly, the distal end on the short arm of chromosome 19, which corresponds to the location of the sex-determining locus reported in several species, was not painted in both species. Thus, the DNA sequences associated with this region have not been anchored to the current chromosome 19 pseudomolecule, which was confirmed by painting of somatic metaphase chromosome 19 of P. trichocarpa. Interestingly, the unpainted distal ends of the two chromosome 19 did not pair at the pachytene stage in 22-24% of the meiotic cells in the two species, suggest that these regions from the sex chromosomes have structurally diverged from each other, resulting in the reduced pairing frequency. These results shed light on divergence of a pair of young sex chromosomes in poplar.
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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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25
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Liu F, Tong C, Tao S, Wu J, Chen Y, Yao D, Li H, Shi J. MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F 1 population of outbred species. BMC Bioinformatics 2017; 18:515. [PMID: 29169342 PMCID: PMC5701343 DOI: 10.1186/s12859-017-1908-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/01/2017] [Indexed: 01/02/2023] Open
Abstract
Background With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative trait loci (QTL) mapping cannot be directly conducted with traditional statistical methods or tools because the linkage phase and segregation pattern of molecular markers are not always fixed as in inbred lines. Results We implemented the traditional composite interval mapping (CIM) method to multivariate trait data in forest trees and developed the corresponding software, mvqtlcim. Our method not only incorporated the various segregations and linkage phases of molecular markers, but also applied Takeuchi’s information criterion (TIC) to discriminate the QTL segregation type among several possible alternatives. QTL mapping was performed in a hybrid F1 population of Populus deltoides and P. simonii, and 12 QTLs were detected for tree height over 6 time points. The software package allowed many options for parameters as well as parallel computing for permutation tests. The features of the software were demonstrated with the real data analysis and a large number of Monte Carlo simulations. Conclusions We provided a powerful tool for QTL mapping of multiple or longitudinal traits in an outbred F1 population, in which the traditional software for QTL mapping cannot be used. This tool will facilitate studying of QTL mapping and thus will accelerate molecular breeding programs especially in forest trees. The tool package is freely available from https://github.com/tongchf /mvqtlcim. Electronic supplementary material The online version of this article (10.1186/s12859-017-1908-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fenxiang Liu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.,College of Department of Computer Science and Engineering, Sanjiang University, Nanjing, 210012, China
| | - Chunfa Tong
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
| | - Shentong Tao
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiyan Wu
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuhua Chen
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Dan Yao
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jisen Shi
- The Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
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Zhigunov AV, Ulianich PS, Lebedeva MV, Chang PL, Nuzhdin SV, Potokina EK. Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology. BMC PLANT BIOLOGY 2017; 17:180. [PMID: 29143610 PMCID: PMC5688504 DOI: 10.1186/s12870-017-1127-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation. CONCLUSIONS The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.
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Affiliation(s)
- Anatoly V Zhigunov
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia
| | - Pavel S Ulianich
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia
- Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Marina V Lebedeva
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia
- Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Peter L Chang
- University of Southern California, Los Angeles, CA, 90089, USA
| | | | - Elena K Potokina
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.
- Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia.
- Saint Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russia.
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