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Qiao Q, Cao Q, Zhang R, Wu M, Zheng Y, Xue L, Lei J, Sun H, Liston A, Zhang T. Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1552-1565. [PMID: 38184782 PMCID: PMC11123429 DOI: 10.1111/pbi.14286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
The strawberry genus, Fragaria, exhibits a wide range of sexual systems and natural ploidy variation. Nearly, all polyploid strawberry species exhibit separate sexes (dioecy). Research has identified the sex-determining sequences as roughly conserved but with repeatedly changed genomic locations across octoploid strawberries. However, it remains unclear whether tetraploid wild strawberries evolved dioecy independently or shared a common origin with octoploid strawberries. In this study, we investigated the sex determinants of F. moupinensis, a dioecious plant with heterogametic females (ZW). Utilizing a combination of haplotype-resolved genome sequencing of the female F. moupinensis, k-mer-based and coverage-based genome-wide association studies (GWAS), and transcriptomic analysis, we discovered a non-recombining, approximately 33.6 kb W-specific region on chromosome 2a. Within this region, only one candidate sex-determining gene (FmoAFT) was identified. Furthermore, an extensive resequencing of the entire Fragaria genus indicated that the W-specific region displays conservative female specificity across all tetraploid species. This observation suggests that dioecy evolved independently in tetraploid and octoploid strawberries. Moreover, employing virus-induced gene silencing (VIGS), we knocked down the expression of the FmoAFT homologue transcript in cultivated strawberries, revealing its potential role in promoting female functions during early carpel development. We also applied DNA affinity purification sequencing (DAP-seq) and yeast one-hybrid assays to identify potential direct targets of FmoAFT. These insights shed new light on the genetic basis and evolutionary history of sex determination in strawberries, thereby facilitating the formulation of strategies to manipulate sex determination in breeding programs.
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Affiliation(s)
- Qin Qiao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Qiang Cao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Rengang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Mingzhao Wu
- School of AgricultureYunnan UniversityKunmingChina
| | | | - Li Xue
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Jiajun Lei
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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Charlesworth D, Harkess A. Why should we study plant sex chromosomes? THE PLANT CELL 2024; 36:1242-1256. [PMID: 38163640 PMCID: PMC11062472 DOI: 10.1093/plcell/koad278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/10/2023] [Indexed: 01/03/2024]
Abstract
Understanding plant sex chromosomes involves studying interactions between developmental and physiological genetics, genome evolution, and evolutionary ecology. We focus on areas of overlap between these. Ideas about how species with separate sexes (dioecious species, in plant terminology) can evolve are even more relevant to plants than to most animal taxa because dioecy has evolved many times from ancestral functionally hermaphroditic populations, often recently. One aim of studying plant sex chromosomes is to discover how separate males and females evolved from ancestors with no such genetic sex-determining polymorphism, and the diversity in the genetic control of maleness vs femaleness. Different systems share some interesting features, and their differences help to understand why completely sex-linked regions may evolve. In some dioecious plants, the sex-determining genome regions are physically small. In others, regions without crossing over have evolved sometimes extensive regions with properties very similar to those of the familiar animal sex chromosomes. The differences also affect the evolutionary changes possible when the environment (or pollination environment, for angiosperms) changes, as dioecy is an ecologically risky strategy for sessile organisms. Dioecious plants have repeatedly reverted to cosexuality, and hermaphroditic strains of fruit crops such as papaya and grapes are desired by plant breeders. Sex-linked regions are predicted to become enriched in genes with sex differences in expression, especially when higher expression benefits one sex function but harms the other. Such trade-offs may be important for understanding other plant developmental and physiological processes and have direct applications in plant breeding.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Fan Z, Whitaker VM. Genomic signatures of strawberry domestication and diversification. THE PLANT CELL 2024; 36:1622-1636. [PMID: 38113879 PMCID: PMC11062436 DOI: 10.1093/plcell/koad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa) has a brief history of less than 300 yr, beginning with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we explored the genomic signatures of early domestication and subsequent diversification for different climates using whole-genome sequences of 289 wild, heirloom, and modern varieties from two major breeding programs in the United States. Four nonadmixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0% to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out of 28 chromosomes. Overlapping divergent selective sweeps in natural and domesticated populations revealed 16 convergent genomic signatures that may be important for climatic adaptation. Despite 20 breeding cycles since initial hybridization, more than half of loci underlying yield and fruit size are still not under artificial selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.
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Affiliation(s)
- Zhen Fan
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
| | - Vance M Whitaker
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL 33597, USA
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Filipović I, Marshall JM, Rašić G. Finding divergent sequences of homomorphic sex chromosomes via diploidized nanopore-based assembly from a single male. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582759. [PMID: 38464271 PMCID: PMC10925256 DOI: 10.1101/2024.02.29.582759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Although homomorphic sex chromosomes can have non-recombining regions with elevated sequence divergence between its complements, such divergence signals can be difficult to detect bioinformatically. If found in genomes of e.g. insect pests, these sequences could be targeted by the engineered genetic sexing and control systems. Here, we report an approach that can leverage long-read nanopore sequencing of a single XY male to identify divergent regions of homomorphic sex chromosomes. Long-read data are used for de novo genome assembly that is diploidized in a way that maximizes sex-specific differences between its haploid complements. We show that the correct assembly phasing is supported by the mapping of nanopore reads from the male's haploid Y-bearing sperm cells. The approach revealed a highly divergent region (HDR) near the centromere of the homomorphic sex chromosome of Aedes aegypti, the most important arboviral vector, for which there is a great interest in creating new genetic control tools. HDR is located ~5Mb downstream of the known male-determining locus on chromosome 1 and is significantly enriched for ovary-biased genes. While recombination in HDR ceased relatively recently (~1.4 MYA), HDR gametologs have divergent exons and introns of protein coding genes, and most lncRNA genes became X-specific. Megabases of previously invisible sex-linked sequences provide new putative targets for engineering the genetic systems to control this deadly mosquito. Broadly, our approach expands the toolbox for studying cryptic structure of sex chromosomes.
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Affiliation(s)
- Igor Filipović
- Mosquito Genomics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
- The University of Queensland, School of Biological Sciences, St Lucia, QLD, Australia
| | - John M Marshall
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gordana Rašić
- Mosquito Genomics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
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Clare SJ, King RM, Tawril AL, Havill JS, Muehlbauer GJ, Carey SB, Harkess A, Bassil N, Altendorf KR. An affordable and convenient diagnostic marker to identify male and female hop plants. G3 (BETHESDA, MD.) 2023; 14:jkad216. [PMID: 37963231 PMCID: PMC10755173 DOI: 10.1093/g3journal/jkad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/11/2023] [Indexed: 11/16/2023]
Abstract
Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.
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Affiliation(s)
- Shaun J Clare
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Ryan M King
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Anna L Tawril
- Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA
| | - Joshua S Havill
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St.Paul, MN 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St.Paul, MN 55108, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Nahla Bassil
- National Clonal Germplasm Repository, USDA-ARS, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Kayla R Altendorf
- Forage Seed and Cereal Research Unit, USDA-ARS, 24106 N Bunn Road, Prosser, WA 99350, USA
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Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int J Mol Sci 2023; 24:16935. [PMID: 38069258 PMCID: PMC10706760 DOI: 10.3390/ijms242316935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.
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Affiliation(s)
- Keliang Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiajing Xiao
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
| | - Renyi Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Mao J, Wang Y, Wang B, Li J, Zhang C, Zhang W, Li X, Li J, Zhang J, Li H, Zhang Z. High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry. HORTICULTURE RESEARCH 2023; 10:uhad002. [PMID: 37077373 PMCID: PMC10108017 DOI: 10.1093/hr/uhad002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/03/2023] [Indexed: 05/03/2023]
Abstract
Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, "Yanli", using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The "Yanli" genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ~ 10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.
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Affiliation(s)
| | | | - Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jiqi Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Chao Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Wenshuo Zhang
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Xue Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jie Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Junxiang Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang 110866, China
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He L, Hörandl E. Does polyploidy inhibit sex chromosome evolution in angiosperms? FRONTIERS IN PLANT SCIENCE 2022; 13:976765. [PMID: 36212292 PMCID: PMC9541106 DOI: 10.3389/fpls.2022.976765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Dioecy is rare in flowering plants (5-6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany
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