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Wu X, Simpson SA, Youngblood RC, Liu XF, Scheffler BE, Rinehart TA, Alexander LW, Hulse-Kemp AM. Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea ( Hydrangea macrophylla) and insights into Asterid evolution. HORTICULTURE RESEARCH 2023; 10:uhad217. [PMID: 38130599 PMCID: PMC10734616 DOI: 10.1093/hr/uhad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 12/23/2023]
Abstract
The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.
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Affiliation(s)
- Xingbo Wu
- Department of Environmental Horticulture, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, United States
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, United States
| | - Xiaofen F Liu
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Timothy A Rinehart
- Crop Production and Protection, USDA-ARS, Beltsville, MD 20705, United States
| | - Lisa W Alexander
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, USDA-ARS, McMinnville, TN 37110, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, United States
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Schulz D, Linde M, Debener T. Robust markers associated with floral traits in roses are suitable for marker-assisted selection across gene pools. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:90. [PMID: 38077450 PMCID: PMC10709285 DOI: 10.1007/s11032-023-01438-5] [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: 09/14/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023]
Abstract
We investigated the potential of markers associated with floral traits for parental selection in a cut rose breeding program. We analysed six Kompetitive Allele Specific PCR (KASP) markers for three important floral traits, petal length, petal number and scent, derived from experiments in a garden rose population. The six markers were applied to genotype a collection of 384 parental genotypes used for commercial cut rose breeding. We phenotyped a selection of progeny derived from pairs of parents having either high or low dosages of (contrasting) marker alleles associated with these traits. Significant differences were found between the contrasting progeny groups for each of the traits, although parents with the optimal allele dosage combinations could not always be used for the crosses. This not only supports the robustness of these marker‒trait associations but also demonstrates their potential for commercial rose breeding. It also demonstrates the use of marker information generated in garden rose populations for cut rose breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01438-5.
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Affiliation(s)
- Dietmar Schulz
- Institute of Plant Genetics, Molecular Plant Breeding Section, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
- Bundesamt Für Verbraucherschutz Und Lebensmittelsicherheit, Referat 231/Abteilung 2, Bundesallee 51, 38116 Brunswick, Germany
| | - Marcus Linde
- Institute of Plant Genetics, Molecular Plant Breeding Section, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Molecular Plant Breeding Section, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
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Lei X, Li H, Li P, Zhang H, Han Z, Yang B, Duan Y, Njeri NS, Yang D, Zheng J, Ma Y, Zhu X, Fang W. Genome-Wide Association Studies of Biluochun Tea Plant Populations in Dongting Mountain and Comprehensive Identification of Candidate Genes Associated with Core Agronomic Traits by Four Analysis Models. PLANTS (BASEL, SWITZERLAND) 2023; 12:3719. [PMID: 37960075 PMCID: PMC10650078 DOI: 10.3390/plants12213719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The elite germplasm resources are key to the beautiful appearance and pleasant flavor of Biluochun tea. We collected and measured the agronomic traits of 95 tea plants to reveal the trait diversity and breeding value of Biluochun tea plant populations. The results revealed that the agronomic traits of Biluochun tea plant populations were diverse and had high breeding value. Additionally, we resequenced these tea plant populations to reveal genetic diversity, population structure, and selection pressure. The Biluochun tea plant populations contained two groups and were least affected by natural selection based on the results of population structure and selection pressure. More importantly, four non-synonymous single nucleotide polymorphisms (nsSNPs) and candidate genes associated with (-)-gallocatechin gallate (GCG), (-)-gallocatechin (GC), and caffeine (CAF) were detected using at least two GWAS models. The results will promote the development and application of molecular markers and the utilization of elite germplasm from Biluochun populations.
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Affiliation(s)
- Xiaogang Lei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Haoyu Li
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Pingping Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Huan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Bin Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Ndombi Salome Njeri
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Daqiang Yang
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Junhua Zheng
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
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Bhattarai K, Sharma S, Verma S, Peres NA, Xiao S, Clark DG, Deng Z. Construction of a genome-wide genetic linkage map and identification of quantitative trait loci for powdery mildew resistance in Gerbera daisy. FRONTIERS IN PLANT SCIENCE 2023; 13:1072717. [PMID: 36684731 PMCID: PMC9853552 DOI: 10.3389/fpls.2022.1072717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Powdery mildew (PM) is a common fungal disease in many important crops. The PM caused by Podosphaera xanthii has been the most challenging problem in commercial Gerbera (Gerbera hybrida) production globally, often leading to severe losses of crop yield and quality. A small number of PM-resistant breeding lines and cultivars have been reported in Gerbera, but the underlying genetics for PM resistance in Gerbera is largely unknown. Scarcity of genomic resources such as genetic linkage maps and molecular markers has severely hindered the effort to understand the genetic basis and locate loci controlling PM resistance in Gerbera. This study aimed to construct a genome-wide genetic linkage map, identify quantitative trait loci (QTL), and molecular markers for PM resistance in Gerbera. A segregating mapping population was developed by crossing PM-resistant and -susceptible Gerbera breeding lines, genotyped by sequencing, and phenotyped for PM resistance. A genome-wide genetic linkage map constructed with 791 single polymorphic site (SNP) markers spans 1912.30 cM across 27 linkage groups (LG) and reaches a density of 1 marker per 2.42 cM. One major consistent QTL was discovered in LG16, explaining more than 16.6% of the phenotypic variance for PM resistance. The QTL was tagged with two flanking SNP markers. The availability of this genetic linkage map will be very useful for locating and tagging QTLs for other important traits in Gerbera, and the newly discovered QTL and SNP markers will enable development of molecular markers for improving Gerbera for resistance to PM.
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Affiliation(s)
- Krishna Bhattarai
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences (IFAS), Wimauma, FL, United States
| | - Sadikshya Sharma
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Sujeet Verma
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Natalia A. Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma, FL, United States
| | - Shunyuan Xiao
- University of Maryland, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, United States
| | - David G. Clark
- Department of Environmental Horticulture, University of Florida, IFAS, Gainesville, FL, United States
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences (IFAS), Wimauma, FL, United States
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Gao Z, Liang Y, Wang Y, Xiao Y, Chen J, Yang X, Shi T. Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. FRONTIERS IN PLANT SCIENCE 2022; 13:973347. [PMID: 36212363 PMCID: PMC9539442 DOI: 10.3389/fpls.2022.973347] [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: 06/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuting Liang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Yuhan Wang
- Wuhan Institute of Design and Sciences, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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Qi X, Chen S, Wang H, Feng J, Chen H, Qin Z, Deng Y. Comparative physiology and transcriptome analysis reveals that chloroplast development influences silver-white leaf color formation in Hydrangea macrophylla var. maculata. BMC PLANT BIOLOGY 2022; 22:345. [PMID: 35842592 PMCID: PMC9287875 DOI: 10.1186/s12870-022-03727-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Hydrangea macrophylla var. Maculata 'Yinbianxiuqiu' (YB) is an excellent plant species with beautiful flowers and leaves with silvery white edges. However, there are few reports on its leaf color characteristics and color formation mechanism. RESULTS The present study compared the phenotypic, physiological and transcriptomic differences between YB and a full-green leaf mutant (YM) obtained from YB. The results showed that YB and YM had similar genetic backgrounds, but photosynthesis was reduced in YB. The contents of pigments were significantly decreased at the edges of YB leaves compared to YM leaves. The ultrastructure of chloroplasts in the YB leaves was irregular. Transcriptome profiling identified 7,023 differentially expressed genes between YB and YM. The expression levels of genes involved in photosynthesis, chloroplast development and division were different between YB and YM. Quantitative real-time PCR showed that the expression trends were generally consistent with the transcriptome data. CONCLUSIONS Taken together, the formation of the silvery white leaf color of H. macrophylla var. maculata was primarily due to the abnormal development of chloroplasts. This study facilitates the molecular function analysis of key genes involved in chloroplast development and provides new insights into the molecular mechanisms involved in leaf coloration in H. macrophylla.
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Affiliation(s)
- Xiangyu Qi
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Shuangshuang Chen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Huadi Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Jing Feng
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Huijie Chen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Ziyi Qin
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Yanming Deng
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China.
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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Lu X, Lü P, Liu H, Chen H, Pan X, Liu P, Feng L, Zhong S, Zhou B. Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:819188. [PMID: 35283888 PMCID: PMC8905319 DOI: 10.3389/fpls.2022.819188] [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: 11/21/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Litchi is an important Sapindaceae fruit tree. Flowering in litchi is triggered by low temperatures in autumn and winter. It can be divided into early-, medium-, and late-flowering phenotypes according to the time for floral induction. Early-flowering varieties need low chilling accumulation level for floral induction, whereas the late-flowering varieties require high chilling accumulation level. In the present study, RNA-Seq of 87 accessions was performed and transcriptome-based genome-wide association studies (GWAS) was used to identify candidate genes involved in chilling accumulation underlying the time for floral induction. A total of 98,155 high-quality single-nucleotide polymorphism (SNP) sites were obtained. A total of 1,411 significantly associated SNPs and 1,115 associated genes (AGs) were identified, of which 31 were flowering-related, 23 were hormone synthesis-related, and 27 were hormone signal transduction-related. Association analysis between the gene expression of the AGs and the flowering phenotypic data was carried out, and differentially expressed genes (DEGs) in a temperature-controlled experiment were obtained. As a result, 15 flowering-related candidate AGs (CAGs), 13 hormone synthesis-related CAGs, and 11 hormone signal transduction-related CAGs were further screened. The expression levels of the CAGs in the early-flowering accessions were different from those in the late-flowering ones, and also between the flowering trees and non-flowering trees. In a gradient chilling treatment, flowering rates of the trees and the CAGs expression were affected by the treatment. Our present work for the first time provided candidate genes for genetic regulation of flowering in litchi using transcriptome-based GWAS.
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Affiliation(s)
- Xingyu Lu
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Life and Health Science, Kaili University, Kaili, China
| | - Peitao Lü
- College of Horticulture, Fujian Agriculture and Forestry University-University of California Riverside (FAFU-UCR) Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hao Liu
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Houbin Chen
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xifen Pan
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Pengxu Liu
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Lei Feng
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Biyan Zhou
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
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Schulz D, Linde M, Debener T. Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050897. [PMID: 33946713 PMCID: PMC8145204 DOI: 10.3390/plants10050897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The detection of QTL by association genetics depends on the genetic architecture of the trait under study, the size and structure of the investigated population and the availability of phenotypic and marker data of sufficient quality and quantity. In roses, we previously demonstrated that major QTL could already be detected in small association panels. In this study, we analyzed petal number, petal size and fragrance in a small panel of 95 mostly tetraploid garden rose genotypes. After genotyping the panel with the 68 K Axiom WagRhSNP chip we detected major QTL for all three traits. Each trait was significantly influenced by several genomic regions. Some of the QTL span genomic regions that comprise several candidate genes. Selected markers from some of these regions were converted into KASP markers and were validated in independent populations of up to 282 garden rose genotypes. These markers demonstrate the robustness of the detected effects independent of the set of genotypes analyzed. Furthermore, the markers can serve as tools for marker-assisted breeding in garden roses. Over an extended timeframe, they may be used as a starting point for the isolation of the genes underlying the QTL.
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Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7020025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.
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Wu B, Zhong Y, Wu Q, Chen F, Zhong G, Cui Y. Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:563452. [PMID: 33013982 PMCID: PMC7509436 DOI: 10.3389/fpls.2020.563452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/24/2020] [Indexed: 05/16/2023]
Abstract
High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.
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Affiliation(s)
- Bo Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
| | - Yun Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
| | - Qianqian Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
| | - Fangyong Chen
- Citrus Research Institute of Zhejiang, Huangyan, China
- *Correspondence: Fangyong Chen, ; Guangyan Zhong,
| | - Guangyan Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
- *Correspondence: Fangyong Chen, ; Guangyan Zhong,
| | - Yiping Cui
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, & Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
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