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Chen ZQ, Klingberg A, Hallingbäck HR, Wu HX. Preselection of QTL markers enhances accuracy of genomic selection in Norway spruce. BMC Genomics 2023; 24:147. [PMID: 36973641 PMCID: PMC10041705 DOI: 10.1186/s12864-023-09250-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 - 13 associations were observed and the PVE of the strongest effects ranged from 1.2% to 2.0%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000-4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5%.
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Affiliation(s)
- Zhi-Qiang Chen
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.
| | | | | | - Harry X Wu
- Umeå Plant Science Centre, Department Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden.
- Black Mountain Laboratory, CSIRO National Collection Research Australia, Canberra, ACT, 2601, Australia.
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Mishima K, Hirakawa H, Iki T, Fukuda Y, Hirao T, Tamura A, Takahashi M. Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica). BMC PLANT BIOLOGY 2022; 22:470. [PMID: 36192701 PMCID: PMC9531402 DOI: 10.1186/s12870-022-03862-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Japanese larch (Larix kaempferi) is an economically important deciduous conifer species that grows in cool-temperate forests and is endemic to Japan. Kuril larch (L. gmelinii var. japonica) is a variety of Dahurian larch that is naturally distributed in the Kuril Islands and Sakhalin. The hybrid larch (L. gmelinii var. japonica × L. kaempferi) exhibits heterosis, which manifests as rapid juvenile growth and high resistance to vole grazing. Since these superior characteristics have been valued by forestry managers, the hybrid larch is one of the most important plantation species in Hokkaido. To accelerate molecular breeding in these species, we collected and compared full-length cDNA isoforms (Iso-Seq) and RNA-Seq short-read, and merged them to construct candidate gene as reference for both Larix species. To validate the results, candidate protein-coding genes (ORFs) related to some flowering signal-related genes were screened from the reference sequences, and the phylogenetic relationship with closely related species was elucidated. RESULTS Using the isoform sequencing of PacBio RS ll and the de novo assembly of RNA-Seq short-read sequences, we identified 50,690 and 38,684 ORFs in Japanese larch and Kuril larch, respectively. BUSCO completeness values were 90.5% and 92.1% in the Japanese and Kuril larches, respectively. After comparing the collected ORFs from the two larch species, a total of 19,813 clusters, comprising 22,571 Japanese larch ORFs and 22,667 Kuril larch ORFs, were contained in the intersection of the Venn diagram. In addition, we screened several ORFs related to flowering signals (SUPPRESSER OF OVEREXPRESSION OF CO1: SOC1, LEAFY: LFY, FLOWERING Locus T: FT, CONSTANCE: CO) from both reference sequences, and very similar found in other species. CONCLUSIONS The collected ORFs will be useful as reference sequences for molecular breeding of Japanese and Kuril larches, and also for clarifying the evolution of the conifer genome and investigating functional genomics.
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Affiliation(s)
- Kentaro Mishima
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 95 Osaki, Takizawa, Iwate, 020-0621, Japan.
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Taiichi Iki
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 95 Osaki, Takizawa, Iwate, 020-0621, Japan
| | - Yoko Fukuda
- Hokkaido Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 561-1 Bunkyodaimidorimachi, Ebetsu, Hokkaido, 069-0836, Japan
| | - Tomonori Hirao
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Akira Tamura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
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Chen ZQ, Zan Y, Zhou L, Karlsson B, Tuominen H, García-Gil MR, Wu HX. Genetic architecture behind developmental and seasonal control of tree growth and wood properties in Norway spruce. FRONTIERS IN PLANT SCIENCE 2022; 13:927673. [PMID: 36017254 PMCID: PMC9396349 DOI: 10.3389/fpls.2022.927673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/12/2022] [Indexed: 06/01/2023]
Abstract
Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.
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Affiliation(s)
- Zhi-Qiang Chen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Yanjun Zan
- Department Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Linghua Zhou
- Department Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Hannele Tuominen
- Department Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Maria Rosario García-Gil
- Department Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Harry X. Wu
- Department Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO) National Collection Research Australia, Black Mountain Laboratory, Canberra, ACT, Australia
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Wood Formation under Changing Environment: Omics Approaches to Elucidate the Mechanisms Driving the Early-to-Latewood Transition in Conifers. FORESTS 2022. [DOI: 10.3390/f13040608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The global change scenarios highlight the urgency of clarifying the mechanisms driving the determination of wood traits in forest trees. Coniferous xylem is characterized by the alternation between earlywood (EW) and latewood (LW), on which proportions the wood density depend, one of the most important mechanical xylem qualities. However, the molecular mechanisms triggering the transition between the production of cells with the typical features of EW to the LW are still far from being completely elucidated. The increasing availability of omics resources for conifers, e.g., genomes and transcriptomes, would lay the basis for the comprehension of wood formation dynamics, boosting both breeding and gene-editing approaches. This review is intended to introduce the importance of wood formation dynamics and xylem traits of conifers in a changing environment. Then, an up-to-date overview of the omics resources available for conifers was reported, focusing on both genomes and transcriptomes. Later, an analysis of wood formation studies using omics approaches was conducted, with the aim of elucidating the main metabolic pathways involved in EW and LW determination. Finally, the future perspectives and the urgent needs on this research topic were highlighted.
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Genome Wide Association Study Identifies Candidate Genes Related to the Earlywood Tracheid Properties in Picea crassifolia Kom. FORESTS 2022. [DOI: 10.3390/f13020332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Picea crassifolia Kom. is one of the timber and ecological conifers in China and its wood tracheid traits directly affect wood formation and adaptability under harsh environment. Molecular studies on P. crassifolia remain inadequate because relatively few genes have been associated with these traits. To identify markers and candidate genes that can potentially be used for genetic improvement of wood tracheid traits, we examined 106 clones of P. crassifolia, and investigated phenotypic data for 14 wood tracheid traits before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the studied traits. We developed 4,058,883 SLAF-tags and 12,275,765 SNP loci, and our analyses identified a total of 96 SNP loci that showed significant correlations with three earlywood tracheid traits using a mixed linear model (MLM). Next, candidate genes were screened in the 100 kb zone (50 kb upstream, 50 kb downstream) of each of the SNP loci, whereby 67 candidate genes were obtained in earlywood tracheid traits, including 34 genes of known function and 33 genes of unknown function. We provide the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in wood traits improvement and candidate genes for the development of earlywood tracheid in P. crassifolia.
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De La Torre AR, Sekhwal MK, Puiu D, Salzberg SL, Scott AD, Allen B, Neale DB, Chin ARO, Buckley TN. Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:7-22. [PMID: 34800071 PMCID: PMC10773529 DOI: 10.1111/tpj.15592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate genome-wide association study methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western USA, coast redwood and giant sequoia, using 10 drought-related physiological and anatomical traits and genome-wide sequence-capture single nucleotide polymorphisms. Population-level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter, and total area of transporting fibers in both species. Our study identified new 78 new marker × trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress, and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA
| | - Manoj K. Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Computer Science and Biostatistics & Center for Computational Biology, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA
| | - Steven L. Salzberg
- Department of Biomedical Engineering, Computer Science and Biostatistics & Center for Computational Biology, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA
| | - Alison D. Scott
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Brian Allen
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - David B. Neale
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Alana R. O. Chin
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Thomas N. Buckley
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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