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Dong L, Xie Y, Zhang Y, Wang R, Sun X. Genomic dissection of additive and non-additive genetic effects and genomic prediction in an open-pollinated family test of Japanese larch. BMC Genomics 2024; 25:11. [PMID: 38166605 PMCID: PMC10759612 DOI: 10.1186/s12864-023-09891-4] [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: 06/14/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Genomic dissection of genetic effects on desirable traits and the subsequent use of genomic selection hold great promise for accelerating the rate of genetic improvement of forest tree species. In this study, a total of 661 offspring trees from 66 open-pollinated families of Japanese larch (Larix kaempferi (Lam.) Carrière) were sampled at a test site. The contributions of additive and non-additive effects (dominance, imprinting and epistasis) were evaluated for nine valuable traits related to growth, wood physical and chemical properties, and competitive ability using three pedigree-based and four Genomics-based Best Linear Unbiased Predictions (GBLUP) models and used to determine the genetic model. The predictive ability (PA) of two genomic prediction methods, GBLUP and Reproducing Kernel Hilbert Spaces (RKHS), was compared. The traits could be classified into two types based on different quantitative genetic architectures: for type I, including wood chemical properties and Pilodyn penetration, additive effect is the main source of variation (38.20-67.46%); for type II, including growth, competitive ability and acoustic velocity, epistasis plays a significant role (50.76-91.26%). Dominance and imprinting showed low to moderate contributions (< 36.26%). GBLUP was more suitable for traits of type I (PAs = 0.37-0.39 vs. 0.14-0.25), and RKHS was more suitable for traits of type II (PAs = 0.23-0.37 vs. 0.07-0.23). Non-additive effects make no meaningful contribution to the enhancement of PA of GBLUP method for all traits. These findings enhance our current understanding of the architecture of quantitative traits and lay the foundation for the development of genomic selection strategies in Japanese larch.
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Affiliation(s)
- Leiming Dong
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, 100093, China
| | - Yunhui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yalin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ruizhen Wang
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex situ Conservation, Beijing Floriculture Engineering Technology Research Centre, Beijing Botanical Garden, Beijing, 100093, China
| | - Xiaomei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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Wu H, Zhao S, Wang X, Duan A, Zhang J. Mating pattern and pollen dispersal in an advanced generation seed orchard of Cunninghamia lanceolata (Lamb.) Hook. FRONTIERS IN PLANT SCIENCE 2022; 13:1042290. [PMID: 36388519 PMCID: PMC9646989 DOI: 10.3389/fpls.2022.1042290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Seed orchards represent the link between forest breeding and conifer production forests, and their mating patterns determine the genetic quality of seed orchard crops to a large extent. We genotyped the parental clones and their open pollination offspring in the third-generation seed orchard of Chinese fir using microsatellite markers and observed the synchronization of florescence in the seed orchard to understand the genetic diversity and mating structure of the seed orchard population. Genetic coancestry among parental clones was detected in the third generation seed orchard of Chinese fir, and the genetic diversity of the open-pollinated offspring was slightly higher than that of the parental clones. The external pollen contamination rate ranged from 10.1% to 33.7%, 80% of the offspring were produced by 44% of the parental clones in the orchard, and no evidence of selfing was found. We found that 68.1% of the effective pollination occurred within 50 m, and 19.9% of the effective pollination occurred in the nearest neighbors. We also found that successful mating requires about 30% of florescence overlap between males and females, and there was a significant positive correlation between male reproductive energy and male parental contribution. Our results provide a valuable reference for the management and design of advanced generation seed orchards.
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Affiliation(s)
- Hanbin Wu
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shirong Zhao
- State-owned Forestry Farm of Weimin, Shaowu, China
| | - Xihan Wang
- State-owned Forestry Farm of Weimin, Shaowu, China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Sun C, Xie YH, Li Z, Liu YJ, Sun XM, Li JJ, Quan WP, Zeng QY, Van de Peer Y, Zhang SG. The Larix kaempferi genome reveals new insights into wood properties. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1364-1373. [PMID: 35442564 DOI: 10.1111/jipb.13265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jing-Jing Li
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Wei-Peng Quan
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa
| | - Shou-Gong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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Lee K, Kim IS, Kang KS. Pedigree reconstruction and spatial analysis for genetic testing and selection in a Larix kaempferi (Lamb.) Carrière plantation. BMC PLANT BIOLOGY 2022; 22:152. [PMID: 35346034 PMCID: PMC8962119 DOI: 10.1186/s12870-022-03530-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Larix kaempferi is one of the major timber species in Northeast Asia. Demand for the reforestation of the species is rising in South Korea due to an increase in large timber production and utilization. However, progeny trials for the species have not been explored, making it challenging to foster advanced generations of tree improvement. In the present study, genetic testing and selection for diameter growth were conducted using pedigree reconstruction and phenotypic spatial distribution analysis in a plantation of L. kaempferi. The aim of the present study was to select the superior larch individuals using the pedigree reconstruction and phenotypic spatial distribution to substitute progeny trials. The plantation of seed orchard crops was established in 1990 and one-hundred and eighty-eight trees were selected as the study material. Genetic variation was investigated first to validate its adequacy as breeding material. Genetic testing was carried out using a model considering pedigree information and spatial autoregression of the phenotypes. RESULTS The expected heterozygosity of the mother trees and offspring were 0.672 and 0.681 presenting the corresponding level of genetic variation between two groups. The pedigree reconstruction using maternity analysis assigned one to six progenies to ninety-two candidate mothers. The accuracy of genetic testing was exceedingly increased with the animal model considering AR1 ⊗ AR1 structure compared to the animal model only. The estimated genetic variance of the former was 9.086 whereas that of the latter was 4.9E-5 for DBH. The predicted breeding values of the offspring for DBH were ranged from -5.937 cm to 5.655 cm and the estimated heritability of diameter growth was 0.344. CONCLUSIONS The genetic testing approach based on pedigree reconstruction and phenotypic spatial distribution analysis was considered a useful analytical scheme that could replace or supplement progeny trials.
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Affiliation(s)
- Kyungmi Lee
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - In-Sik Kim
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Kyu-Suk Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Three-dimensional reconstruction of Picea wilsonii Mast. pollen grains using automated electron microscopy. SCIENCE CHINA-LIFE SCIENCES 2019; 63:171-179. [PMID: 31625022 DOI: 10.1007/s11427-019-9820-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 08/16/2019] [Indexed: 01/07/2023]
Abstract
Three-dimensional electron microscopy (3D-EM) has attracted considerable attention because of its ability to provide detailed information with respect to developmental analysis. However, large-scale high-resolution 3D reconstruction of biological samples remains challenging. Herein, we present a 3D view of a Picea wilsonii Mast. pollen grain with 100 nm axial and 38.57 nm lateral resolution using AutoCUTS-SEM (automatic collector of ultrathin sections-scanning electron microscopy). We established a library of 3,127 100 nm thick serial sections of pollen grains for preservation and observation, demonstrating that the protocol can be used to analyze large-volume samples. After obtaining the SEM images, we reconstructed an entire pollen grain comprising 734 serial sections. The images produced by 3D reconstruction clearly revealed the main components of the P. wilsonii pollen grain, i.e., two sacci and pollen corpus, tube cell, generative cell, and two degenerated prothallial cells, and their internal organization. In addition, we performed a quantitative analysis of the different pollen grain cells, including sacci, and found that there were 202 connections within a saccus SEM image. Thus, for the first time, this study provided a global 3D view of the entire pollen grain, which will be useful for analyzing pollen development and growth.
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Dong M, He Q, Zhao J, Zhang Y, Yuan D, Zhang AJ. Genetic Mapping of Prince Rupprecht's Larch ( Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing. Genes (Basel) 2019; 10:genes10080583. [PMID: 31370324 PMCID: PMC6723236 DOI: 10.3390/genes10080583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/12/2019] [Accepted: 07/29/2019] [Indexed: 11/24/2022] Open
Abstract
A high-density genetic linkage map is essential for plant genetics and genomics research. However, due to the deficiency of genomic data and high-quality molecular markers, no genetic map has been published for Prince Rupprecht’s larch (Larix principis-rupprechtii Mayr), a conifer species with high ecological and commercial value in northern China. In this study, 145 F1 progeny individuals from an intraspecific cross between two elite clones of L. principis-rupprechtii and their parents were employed to construct the first genetic map in this important tree species using specific-locus amplified fragment sequencing (SLAF-seq). After preprocessing, the procedure yielded 300.20 Gb of raw data containing 1501.22 M pair-end reads. A total of 324,352 SNP markers were detected and 122,785 of them were polymorphic, with a polymorphism rate of 37.86%. Ultimately, 6099 SNPs were organized into a genetic map containing 12 linkage groups, consistent with the haploid chromosome number of larch and most other species in the Pinaceae family. The linkage map spanned 2415.58 cM and covered 99.6% of the L. principis-rupprechtii genome with an average of 0.4 cM between adjacent markers. To the best of our knowledge, this map is the first reference map for L. principis-rupprechtii, as well as the densest one obtained in larch species thus far. The genome-wide SNPs and the high-resolution genetic map will provide a foundation for future quantitative trait loci mapping, map-based cloning, marker-assisted selection, comparative genomics, and genome sequence assembly for larch trees.
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Affiliation(s)
- Mingliang Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Qingwei He
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jian Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Deshui Yuan
- National Key Seed Base of Larch, Weichang, Chengde 068450, China
| | - And Jinfeng Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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