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Liu D, Ye Y, Tang R, Gong Y, Chen S, Zhang C, Mei P, Chen J, Chen L, Ma C. High-density genetic map construction and QTL mapping of a zigzag-shaped stem trait in tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2024; 24:382. [PMID: 38724900 PMCID: PMC11080114 DOI: 10.1186/s12870-024-05082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic variation explained (PVE) value of 13.62%. Within this QTL, six candidate genes were pinpointed. To better understand their roles, we analyzed gene expression in various tissues and individuals with erect and zigzag-shaped stems. The results implicated CsXTH (CSS0035625) and CsCIPK14 (CSS0044366) as potential key contributors to the zigzag-shaped stem formation. These discoveries lay a robust foundation for future functional genetic mapping and tea plant genetic enhancement.
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Affiliation(s)
- Dingding Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yuanyuan Ye
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Rongjin Tang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Yang Gong
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Si Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Chenyu Zhang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Piao Mei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Jiedan Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Liang Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Chunlei Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
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Joshi JR, Paudel D, Eddy E, Charkowski AO, Heuberger AL. Plant necrotrophic bacterial disease resistance phenotypes, QTL, and metabolites identified through integrated genetic mapping and metabolomics in Solanum species. FRONTIERS IN PLANT SCIENCE 2024; 15:1336513. [PMID: 38504885 PMCID: PMC10949924 DOI: 10.3389/fpls.2024.1336513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
Most food crops are susceptible to necrotrophic bacteria that cause rotting and wilting diseases in fleshy organs and foods. All varieties of cultivated potato (Solanum tuberosum L.) are susceptible to diseases caused by Pectobacterium species, but resistance has been demonstrated in wild potato relatives including S. chacoense. Previous studies demonstrated that resistance is in part mediated by antivirulence activity of phytochemicals in stems and tubers. Little is known about the genetic basis of antivirulence traits, and the potential for inheritance and introgression into cultivated potato is unclear. Here, the metabolites and genetic loci associated with antivirulence traits in S. chacoense were elucidated by screening a sequenced S. tuberosum x S. chacoense recombinant inbred line (RIL) population for antivirulence traits of its metabolite extracts. Metabolite extracts from the RILs exhibited a quantitative distribution for two antivirulence traits that were positively correlated: quorum sensing inhibition and exo-protease inhibition, with some evidence of transgressive segregation, supporting the role of multiple loci and metabolites regulating these resistance-associated systems. Metabolomics was performed on the highly resistant and susceptible RILs that revealed 30 metabolites associated with resistance, including several alkaloids and terpenes. Specifically, several prenylated metabolites were more abundant in resistant RILs. We constructed a high-density linkage map with 795 SNPs mapped to 12 linkage groups, spanning a length of 1,507 cM and a density of 1 marker per 1.89 cM. Genetic mapping of the antivirulence and metabolite data identified five quantitative trait loci (QTLs) related to quorum sensing inhibition that explained 8-28% of the phenotypic variation and two QTLs for protease activity inhibition that explained 14-19% of the phenotypic variation. Several candidate genes including alkaloid, and secondary metabolite biosynthesis that are related to disease resistance were identified within these QTLs. Taken together, these data support that quorum sensing inhibition and exo-protease inhibition assays may serve as breeding targets to improve resistance to nectrotrophic bacterial pathogens in potato and other plants. The identified candidate genes and metabolites can be utilized in marker assisted selection and genomic selection to improve soft- rot and blackleg disease resistance.
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Affiliation(s)
- Janak R. Joshi
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, United States
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Dev Paudel
- Department of Environmental Horticulture, University of Florida Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Ethan Eddy
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Amy O. Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Adam L. Heuberger
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
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Gao AW, Alam GE, Zhu Y, Li W, Katsyuba E, Sulc J, Li TY, Li X, Overmyer KA, Lalou A, Mouchiroud L, Sleiman MB, Cornaglia M, Morel JD, Houtkooper RH, Coon JJ, Auwerx J. High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575638. [PMID: 38293129 PMCID: PMC10827074 DOI: 10.1101/2024.01.15.575638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Lifespan is influenced by complex interactions between genetic and environmental factors. Studying those factors in model organisms of a single genetic background limits their translational value for humans. Here, we mapped lifespan determinants in 85 genetically diverse C. elegans recombinant intercross advanced inbred lines (RIAILs). We assessed molecular profiles - transcriptome, proteome, and lipidome - and life-history traits, including lifespan, development, growth dynamics, and reproduction. RIAILs exhibited large variations in lifespan, which positively correlated with developmental time. Among the top candidates obtained from multi-omics data integration and QTL mapping, we validated known and novel longevity modulators, including rict-1, gfm-1 and mltn-1. We translated their relevance to humans using UK Biobank data and showed that variants in RICTOR and GFM1 are associated with an elevated risk of age-related heart disease, dementia, diabetes, kidney, and liver diseases. We organized our dataset as a resource (https://lisp-lms.shinyapps.io/RIAILs/) that allows interactive explorations for new longevity targets.
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Affiliation(s)
- Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Weisha Li
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Elena Katsyuba
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Jonathan Sulc
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Terytty Y. Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Present address: State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Metabolic Remodeling and Health, Laboratory of Longevity and Metabolic Adaptations, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
| | - Amelia Lalou
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Laurent Mouchiroud
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Cornaglia
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Waizumi R, Hirayama C, Tomita S, Iizuka T, Kuwazaki S, Jouraku A, Tsubota T, Yokoi K, Yamamoto K, Sezutsu H. A major endogenous glycoside hydrolase mediating quercetin uptake in Bombyx mori. PLoS Genet 2024; 20:e1011118. [PMID: 38232119 PMCID: PMC10824415 DOI: 10.1371/journal.pgen.1011118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/29/2024] [Accepted: 12/28/2023] [Indexed: 01/19/2024] Open
Abstract
Quercetin is a common plant flavonoid which is involved in herbivore-plant interactions. Mulberry silkworms (domestic silkworm, Bombyx mori, and wild silkworm, Bombyx mandarina) take up quercetin from mulberry leaves and accumulate the metabolites in the cocoon, thereby improving its protective properties. Here we identified a glycoside hydrolase, named glycoside hydrolase family 1 group G 5 (GH1G5), which is expressed in the midgut and is involved in quercetin metabolism in the domestic silkworm. Our results suggest that this enzyme mediates quercetin uptake by deglycosylating the three primary quercetin glycosides present in mulberry leaf: rutin, quercetin-3-O-malonylglucoside, and quercetin-3-O-glucoside. Despite being located in an unstable genomic region that has undergone frequent structural changes in the evolution of Lepidoptera, GH1G5 has retained its hydrolytic activity, suggesting quercetin uptake has adaptive significance for mulberry silkworms. GH1G5 is also important in breeding: defective mutations which result in discoloration of the cocoon and increased silk yield are homozygously conserved in 27 of the 32 Japanese white-cocoon domestic silkworm strains and 12 of the 30 Chinese ones we investigated.
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Affiliation(s)
- Ryusei Waizumi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Chikara Hirayama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shuichiro Tomita
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Tetsuya Iizuka
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Seigo Kuwazaki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takuya Tsubota
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Kakeru Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Kimiko Yamamoto
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hideki Sezutsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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Norman M, Chen C, Miah H, Patpour M, Sørensen C, Hovmøller M, Forrest K, Kumar S, Prasad P, Gangwar OP, Bhardwaj S, Bariana H, Periyannan S, Bansal U. Sr65: a widely effective gene for stem rust resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:1. [PMID: 38071267 DOI: 10.1007/s00122-023-04507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Sr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat from stem rust in Australia, India, Africa and Europe. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatened global wheat production with the appearance of widely virulent races that included TTKSK and TTRTF. Indian landrace Hango-2 showed resistance to Pgt races in India and Australia. Screening of a Hango-2/Avocet 'S' (AvS) recombinant inbred line population identified two stem rust resistance genes, a novel gene (temporarily named as SrH2) from Hango-2 and Sr26 from AvS. A mapping population segregating for SrH2 alone was developed from two recombinant lines. SrH2 was mapped on the short arm of chromosome 1A, where it was flanked by KASP markers KASP_7944 (proximal) and KASP_12147 (distal). SrH2 was delimited to an interval of 1.8-2.3 Mb on chromosome arm 1AS. The failure to detect candidate genes through MutRenSeq and comparative genomic analysis with the pan-genome dataset indicated the necessity to generate a Hango-2 specific assembly for detecting the gene sequence linked with SrH2 resistance. MutRenSeq however enabled identification of SrH2-linked KASP marker sunCS_265. Markers KASP_12147 and sunCS_265 showed 92% and 85% polymorphism among an Australian cereal cultivar diversity panel and can be used for marker-assisted selection of SrH2 in breeding programs. The effectiveness of SrH2 against Pgt races from Europe, Africa, India, and Australia makes it a valuable resource for breeding stem rust-resistant wheat cultivars. Since no wheat-derived gene was previously located in chromosome arm 1AS, SrH2 represents a new locus and named as SR65.
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Affiliation(s)
- Michael Norman
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Hanif Miah
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Subodh Kumar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Om Prakash Gangwar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash Bhardwaj
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW, 2753, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia.
- School of Agriculture and Environmental Science, Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba, QLD, 4350, Australia.
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
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Mackenzie A, Norman M, Gessese M, Chen C, Sørensen C, Hovmøller M, Ma L, Forrest K, Hickey L, Bariana H, Bansal U, Periyannan S. Wheat stripe rust resistance locus YR63 is a hot spot for evolution of defence genes - a pangenome discovery. BMC PLANT BIOLOGY 2023; 23:590. [PMID: 38008766 PMCID: PMC10680240 DOI: 10.1186/s12870-023-04576-2] [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: 06/19/2023] [Accepted: 11/01/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63 from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection. RESULTS YR63 exhibits resistance to a broad spectrum of Pst races from Australia, Africa, Asia, Europe, Middle East and South America. It was mapped to the short arm of chromosome 7B, between two single nucleotide polymorphic (SNP) markers sunCS_YR63 and sunCS_67, positioned at 0.8 and 3.7 Mb, respectively, in the Chinese Spring genome assembly v2.1. We characterised YR63 locus using an integrated approach engaging targeted genotyping-by-sequencing (tGBS), mutagenesis, resistance gene enrichment and sequencing (MutRenSeq), RNA sequencing (RNASeq) and comparative genomic analysis with tetraploid (Zavitan and Svevo) and hexaploid (Chinese Spring) wheat genome references and 10+ hexaploid wheat genomes. YR63 is positioned at a hot spot enriched with multiple nucleotide-binding and leucine rich repeat (NLR) and kinase domain encoding genes, known widely for defence against pests and diseases in plants and animals. Detection of YR63 within these gene clusters is not possible through short-read sequencing due to high homology between members. However, using the sequence of a NLR member we were successful in detecting a closely linked SNP marker for YR63 and validated on a panel of Australian bread wheat, durum and triticale cultivars. CONCLUSIONS This study highlights YR63 as a valuable source for resistance against Pst in Australia and elsewhere. The closely linked SNP marker will facilitate rapid introgression of YR63 into elite cultivars through marker-assisted selection. The bottleneck of this study reinforces the necessity for a long-read sequencing such as PacBio or Oxford Nanopore based techniques for accurate detection of the underlying resistance gene when it is part of a large gene cluster.
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Affiliation(s)
- Amy Mackenzie
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Michael Norman
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia
| | - Mesfin Gessese
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia
- Present address:, Wolaita sodo University, Sodo, Ethiopia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Lina Ma
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd, Bundoora, Victoria, 3083, Australia
| | - Lee Hickey
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia
| | - Harbans Bariana
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, New South Wales, 2753, Australia
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, New South Wales, 2570, Australia.
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, Australian Capital Territory, 2601, Australia.
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.
- School of Agriculture and Environmental Science & Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia.
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Baltzegar JF, Gould F. Development of the first high-density linkage map in the maize weevil, Sitophilus zeamais. PeerJ 2023; 11:e15414. [PMID: 37337584 PMCID: PMC10276983 DOI: 10.7717/peerj.15414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/24/2023] [Indexed: 06/21/2023] Open
Abstract
The maize weevil, Sitophilus zeamais, is a worldwide pest that disproportionately affects subsistence farmers in developing countries. Damage from this pest threatens food security in these communities as widely available and effective control methods are lacking. With advances over the last decade in the development of genetic pest management techniques, addressing pest issues at the ecosystem level as opposed to the farm level may be a possibility. However, pest species selected for genetic management techniques require a well-characterized genome and few genomic tools have been developed for S. zeamais. Here, we have measured the genome size and developed the first genetic linkage map for this species. The genome size was determined using flow cytometry as 682 Mb and 674 Mb for females and males, respectively. The linkage map contains 11 linkage groups, which correspond to the 10 autosomes and 1 X-chromosome found in the species and it contains 1,121 SNPs. This linkage map will be useful for assembling a complete genome for S. zeamais.
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Affiliation(s)
| | - Fred Gould
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC, United States
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States
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Waizumi R, Tsubota T, Jouraku A, Kuwazaki S, Yokoi K, Iizuka T, Yamamoto K, Sezutsu H. Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01. G3 (BETHESDA, MD.) 2023; 13:jkad044. [PMID: 36814357 PMCID: PMC10085791 DOI: 10.1093/g3journal/jkad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/23/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
The silkworm (Bombyx mori) is an important lepidopteran model insect and an industrial domestic animal traditionally used for silk production. Here, we report the genome assembly of an improved Japanese strain Nichi01, in which the cocoon yield is comparable to that of commercial silkworm strains. The integration of PacBio Sequel II long-read and ddRAD-seq-based high-density genetic linkage map achieved the highest quality genome assembly of silkworms to date; 22 of the 28 pseudomolecules contained telomeric repeats at both ends, and only four gaps were present in the assembly. A total of 452 Mbp of the assembly with an N50 of 16.614 Mbp covered 99.3% of the complete orthologs of the lepidopteran core genes. Although the genome sequence of Nichi01 and that of the previously reported low-yielding tropical strain p50T assured their accuracy in most regions, we corrected several regions, misassembled in p50T, in our assembly. A total of 18,397 proteins were predicted using over 95 Gb of mRNA-seq derived from 10 different organs, covering 96.9% of the complete orthologs of the lepidopteran core genes. The final assembly and annotation files are available in KAIKObase (https://kaikobase.dna.affrc.go.jp/index.html) along with a genome browser and BLAST searching service, which would facilitate further studies and the breeding of silkworms and other insects.
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Affiliation(s)
- Ryusei Waizumi
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Takuya Tsubota
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Akiya Jouraku
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Seigo Kuwazaki
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kakeru Yokoi
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Tetsuya Iizuka
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kimiko Yamamoto
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hideki Sezutsu
- Silkworm Research Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
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9
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Waldbieser GC, Liu S, Yuan Z, Older CE, Gao D, Shi C, Bosworth BG, Li N, Bao L, Kirby MA, Jin Y, Wood ML, Scheffler B, Simpson S, Youngblood RC, Duke MV, Ballard L, Phillippy A, Koren S, Liu Z. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biol 2023; 21:67. [PMID: 37013528 PMCID: PMC10071708 DOI: 10.1186/s12915-023-01556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences. RESULTS We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F1 hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species. CONCLUSIONS We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.
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Affiliation(s)
- Geoffrey C Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Shikai Liu
- MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China, Qingdao, 266003, China
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Caitlin E Older
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA
| | - Chenyu Shi
- MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Brian G Bosworth
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Mona A Kirby
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Monica L Wood
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Brian Scheffler
- US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Sheron Simpson
- US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Mary V Duke
- US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Linda Ballard
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Adam Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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10
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Karlström A, Papp-Rupar M, Passey TAJ, Deakin G, Xu X. Quantitative trait loci associated with apple endophytes during pathogen infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1054914. [PMID: 37056502 PMCID: PMC10086318 DOI: 10.3389/fpls.2023.1054914] [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: 09/27/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
The plant phyllosphere is colonized by microbial communities that can influence the fitness and growth of their host, including the host's resilience to plant pathogens.There are multiple factors involved in shaping the assemblages of bacterial and fungal endophytes within the phyllosphere, including host genetics and environment. In this work, the role of host genetics in plant-microbiome assembly was studied in a full-sibling family of apple (Malus x domestica) trees infected with the fungal pathogen Neonectria ditissima. A Quantitative Trait Loci (QTL) analysis showed that there are multiple loci which influence the abundance of individual endophytic taxa, with the majority of QTL having a moderate to large effect (20-40%) on endophyte abundance. QTL regions on LG 1, 3, 4, 5, 10, 12, 13, 14 and 15 were shown to affect multiple taxa. Only a small proportion of the variation in overall taxonomic composition was affected by host genotype, with significant QTL hits for principal components explaining <8% and <7.4% of the total variance in bacterial and fungal composition, respectively. Four of the identified QTL colocalised with previously identified regions associated with tolerance to Neonectria ditissima. These results suggest that there is a genetic basis shaping apple endophyte composition and that microbe-host associations in apple could be tailored through breeding.
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11
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XY sex determination in a cnidarian. BMC Biol 2023; 21:32. [PMID: 36782149 PMCID: PMC9926710 DOI: 10.1186/s12915-023-01532-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Sex determination occurs across animal species, but most of our knowledge about its mechanisms comes from only a handful of bilaterian taxa. This limits our ability to infer the evolutionary history of sex determination within animals. RESULTS In this study, we generated a linkage map of the genome of the colonial cnidarian Hydractinia symbiolongicarpus and used it to demonstrate that this species has an XX/XY sex determination system. We demonstrate that the X and Y chromosomes have pseudoautosomal and non-recombining regions. We then use the linkage map and a method based on the depth of sequencing coverage to identify genes encoded in the non-recombining region and show that many of them have male gonad-specific expression. In addition, we demonstrate that recombination rates are enhanced in the female genome and that the haploid chromosome number in Hydractinia is n = 15. CONCLUSIONS These findings establish Hydractinia as a tractable non-bilaterian model system for the study of sex determination and the evolution of sex chromosomes.
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12
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Hasing T, Bombarely A. Genomic Approaches for the Study of Flower Development in Floriculture Crops. Methods Mol Biol 2023; 2686:453-494. [PMID: 37540373 DOI: 10.1007/978-1-0716-3299-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The advances in genomics and bioinformatics have made possible the study in non-model plants of phenotypes associated to flower development. Floriculture crops are an interesting source of traits associated to flower development such as the transition between zygomorphic and actinomorphic flowers or the production of flowers with double and triple corollas. In this chapter, we summarize the material and methods for the use of floriculture crops to study flower development using genomic tools, from the sequencing and assembly of a reference genome to QTL and RNA-Seq analysis to search candidate genes associated to specific traits.
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Affiliation(s)
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (UPV-CSIC), Valencia, Spain.
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13
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Takahashi Y, Sakai H, Ariga H, Teramoto S, Shimada TL, Eun H, Muto C, Naito K, Tomooka N. Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness. FRONTIERS IN PLANT SCIENCE 2023; 14:1119625. [PMID: 37139108 PMCID: PMC10149957 DOI: 10.3389/fpls.2023.1119625] [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: 12/09/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
To increase food production under the challenges presented by global climate change, the concept of de novo domestication-utilizing stress-tolerant wild species as new crops-has recently gained considerable attention. We had previously identified mutants with desired domestication traits in a mutagenized population of the legume Vigna stipulacea Kuntze (minni payaru) as a pilot for de novo domestication. Given that there are multiple stress-tolerant wild legume species, it is important to establish efficient domestication processes using reverse genetics and identify the genes responsible for domestication traits. In this study, we identified VsPSAT1 as the candidate gene responsible for decreased hard-seededness, using a Vigna stipulacea isi2 mutant that takes up water from the lens groove. Scanning electron microscopy and computed tomography revealed that the isi2 mutant has lesser honeycomb-like wax sealing the lens groove than the wild-type, and takes up water from the lens groove. We also identified the pleiotropic effects of the isi2 mutant: accelerating leaf senescence, increasing seed size, and decreasing numbers of seeds per pod. While doing so, we produced a V. stipulacea whole-genome assembly of 441 Mbp in 11 chromosomes and 30,963 annotated protein-coding sequences. This study highlights the importance of wild legumes, especially those of the genus Vigna with pre-existing tolerance to biotic and abiotic stresses, for global food security during climate change.
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Affiliation(s)
- Yu Takahashi
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
- *Correspondence: Yu Takahashi,
| | - Hiroaki Sakai
- Research Center of Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hirotaka Ariga
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takashi L. Shimada
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
- Plant Molecular Science Center, Chiba University, Inage-ku, Japan
| | - Heesoo Eun
- Research Center of Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chiaki Muto
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ken Naito
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Norihiko Tomooka
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
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14
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Taniguti CH, Taniguti LM, Amadeu RR, Lau J, Gesteira GDS, Oliveira TDP, Ferreira GC, Pereira GDS, Byrne D, Mollinari M, Riera-Lizarazu O, Garcia AAF. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. Gigascience 2022; 12:giad092. [PMID: 37889010 PMCID: PMC10603770 DOI: 10.1093/gigascience/giad092] [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: 11/29/2022] [Revised: 06/27/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. RESULTS We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent). CONCLUSIONS We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
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Affiliation(s)
- Cristiane Hayumi Taniguti
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Lucas Mitsuo Taniguti
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Mendelics Genomic Analysis, São Paulo 02511-000, Brazil
| | | | - Jeekin Lau
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Gabriel de Siqueira Gesteira
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Bioinformatics Research Center, Department of Horticultural Sciences, North Carolina State University, Raleigh, NC 27695-7566, USA
| | | | | | | | - David Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Marcelo Mollinari
- Bioinformatics Research Center, Department of Horticultural Sciences, North Carolina State University, Raleigh, NC 27695-7566, USA
| | - Oscar Riera-Lizarazu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
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15
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Lytkin K, Nosulchak V, Agakhanov M, Matveikina E, Lushchay E, Karzhaev D, Raines E, Vasylyk I, Rybachenko N, Grigoreva E, Volkov V, Volynkin V, Gentzbittel L, Potokina E. Development of a High-Density Genetic Map for Muscadine Grape Using a Mapping Population from Selfing of the Perfect-Flowered Vine 'Dixie'. PLANTS (BASEL, SWITZERLAND) 2022; 11:3231. [PMID: 36501271 PMCID: PMC9738875 DOI: 10.3390/plants11233231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Intraspecific diversity of the immune grape Muscadinia rotundifolia Michaux. can serve as a rich source of valuable resistance loci to the most widespread pathogens and pests of grapevine. While only one Run1/Rpg1 resistance locus has been introgressed from M. rotundifolia to the Vitis vinifera gene pool, a number of other genes conferring resistance to powdery mildew and downy mildew have been identified in various Muscadinia cultivars. A larger introduction of Muscadinia varieties to the European continent would greatly facilitate experiments of interspecific crosses as well as stimulate biotechnological efforts to overcome the main barrier to F1 fertility caused by the differences in chromosome number. For the successful introduction of Muscadinia into the new European environment, it is necessary to overcome the difficulties associated with the physiological characteristics of the species, such as insufficient cold tolerance and very late fruit ripening. To facilitate the further discovery of valuable loci in Muscadinia and their transfer to grapevine breeding programs, we constructed a high-density linkage map using an S1 mapping population obtained from the self-pollination of M. rotundifolia cv. Dixie maintained on the southern coast of Crimea. Using ddRADseq, 3730 SNPs were ordered across 20 linkage groups spanning 2753.6 cM of the total map length. No segregation in resistance to diseases and pests was observed among the 'Dixie' S1 population, suggesting the presence of homozygous non-segregating resistant loci in the genetic background of 'Dixie'. Markers with high segregation distortion showed a bias towards chromosomal intervals on linkage groups 10 and 20, where loci affecting the survival of 'Dixie' S1 progeny may be localized. QTLs with significant additive and dominance effects were discovered on LG14 and LG18, affecting the morphological traits associated with the vigor of growth and adaptability of young Muscadinia vines in the conditions of Crimea.
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Affiliation(s)
- Kirill Lytkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vasily Nosulchak
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Magamedgusein Agakhanov
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia
| | - Elena Matveikina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Evgenii Raines
- Information Technologies and Programming Faculty, ITMO University, St. Petersburg 197101, Russia
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Nataliya Rybachenko
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
| | - Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
| | | | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, Yalta 298600, Russia
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, St. Petersburg 194021, Russia
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16
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Gomes-Messias LM, Vianello RP, Marinho GR, Rodrigues LA, Coelho AG, Pereira HS, Melo LC, de Souza TLPO. Genetic mapping of the Andean anthracnose resistance gene present in the common bean cultivar BRSMG Realce. FRONTIERS IN PLANT SCIENCE 2022; 13:1033687. [PMID: 36507385 PMCID: PMC9728541 DOI: 10.3389/fpls.2022.1033687] [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: 08/31/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
The rajado seeded Andean bean (Phaseolus vulgaris L.) cultivar BRSMG Realce (striped seed coat) developed by Embrapa expressed a high level of anthracnose resistance, caused by Colletotrichum lindemuthianum, in field and greenhouse screenings. The main goal of this study was to evaluate the inheritance of anthracnose resistance in BRSMG Realce, map the resistance locus or major gene cluster previously named as Co-Realce, identify resistance-related positional genes, and analyze potential markers linked to the resistance allele. F2 plants derived from the cross BRSMG Realce × BRS FC104 (Mesoamerican) and from the cross BRSMG Realce × BRS Notável (Mesoamerican) were inoculated with the C. lindemuthianum races 475 and 81, respectively. The BRSMG Realce × BRS FC104 F2 population was also genotyped using the DArTseq technology. Crosses between BRSMG Realce and BAT 93 (Mesoamerican) were also conducted and resulting F2 plants were inoculated with the C. lindemuthianum races 65 and 1609, individually. The results shown that anthracnose resistance in BRSMG Realce is controlled by a single locus with complete dominance. A genetic map including 1,118 SNP markers was built and shown 78% of the markers mapped at a distances less than 5.0 cM, with a total genetic length of 4,473.4 cM. A major locus (Co-Realce) explaining 54.6% of the phenotypic variation of symptoms caused by the race 475 was identified in Pv04, flanked by the markers snp1327 and snp12782 and 4.48 cM apart each other. These SNPs are useful for marker-assisted selection, due to an estimated selection efficiency of 99.2%. The identified resistance allele segregates independently of the resistance allele Co-33 (Pv04) present in BAT 93. The mapped genomic region with 704,867 bp comprising 63 putative genes, 44 of which were related to the pathogen-host interaction. Based on all these results and evidence, anthracnose resistance in BRSMG Realce should be considered as monogenic, useful for breeding purpose. It is proposed that locus Co-Realce is unique and be provisionally designated as CoPv04R until be officially nominated in accordance with the rules established by the Bean Improvement Cooperative Genetics Committee.
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17
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Tan HQ, Palyam S, Gouda J, Kumar PP, Chellian SK. Identification of two QTLs, BPH41 and BPH42, and their respective gene candidates for brown planthopper resistance in rice. Sci Rep 2022; 12:18538. [PMID: 36323756 PMCID: PMC9630283 DOI: 10.1038/s41598-022-21973-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
The brown planthopper (BPH) is the leading cause of insect damage to rice plants and BPH infestations have caused profound losses in rice production since the 1970's. There is an urgent need to discover new BPH resistance genes to ensure the successful production of rice. Here, a new BPH resistance source provided by SeedWorks International Pvt. Ltd., SWD10, was used for this purpose. QTL mapping using 232 F2 progenies and 216 polymorphic markers revealed two dominant BPH resistance QTLs, BPH41 and BPH42, located on chromosome 4. BPH resistance mechanism test revealed that antibiosis and antixenosis mechanisms both play a role in BPH resistance conferred by these two QTLs. The QTLs were delimited between markers SWRm_01617 and SWRm_01522 for BPH41, and SWRm_01695 and SWRm_00328 for BPH42. Additionally, using RNA-seq data of lines containing the resistant QTLs, we shortlisted four and three gene candidates for BPH41 and BPH42, respectively. Differential gene expression analysis of lines containing the QTLs suggested that SWD10 BPH resistance is contributed by the plant's innate immunity and the candidate genes may be part of the rice innate immunity pathway. Currently, the newly identified QTLs are being utilized for breeding BPH resistant rice varieties and hybrids.
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Affiliation(s)
- Han Qi Tan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Straits Biotech Pte. Ltd., Singapore, Singapore
| | | | | | - Prakash P Kumar
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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18
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Abeyratne CR, Macaya-Sanz D, Zhou R, Barry KW, Daum C, Haiby K, Lipzen A, Stanton B, Yoshinaga Y, Zane M, Tuskan GA, DiFazio SP. High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3 (BETHESDA, MD.) 2022; 13:6762080. [PMID: 36250890 PMCID: PMC9836356 DOI: 10.1093/g3journal/jkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
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Affiliation(s)
| | - David Macaya-Sanz
- Department of Forest Ecology & Genetics, CIFOR-INIA, CSIC, Madrid 28040, Spain
| | - Ran Zhou
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Anna Lipzen
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Gerald A Tuskan
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Stephen P DiFazio
- Corresponding author: Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
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19
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Cauret CMS, Mortimer SME, Roberti MC, Ashman TL, Liston A. Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 (BETHESDA, MD.) 2022; 12:6603112. [PMID: 35666193 PMCID: PMC9339316 DOI: 10.1093/g3journal/jkac139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/19/2022] [Indexed: 01/07/2023]
Abstract
When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
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Affiliation(s)
- Caroline M S Cauret
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sebastian M E Mortimer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marcelina C Roberti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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20
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Comparative transcriptome analysis of synthetic and common wheat in response to salt stress. Sci Rep 2022; 12:11534. [PMID: 35798819 PMCID: PMC9262916 DOI: 10.1038/s41598-022-15733-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
Salt stress reduces wheat yield. Therefore, improvement for enhanced salt stress tolerance is necessary for stable production. To understand the molecular mechanism of salt tolerance in common wheat and synthetic hexaploid (SH) wheat, RNA sequencing was performed on the roots of three wheat lines salt-tolerant SH wheat, salt-tolerant common wheat, and salt-sensitive common wheat. Differentially expressed genes (DEGs) in response to salt stress were characterized using gene ontology enrichment analysis. Salt tolerance in common wheat has been suggested to be mainly regulated by the activation of transporters. In contrast, salt tolerance in SH wheat is enhanced through up-regulation of the reactive oxygen species signaling pathway, other unknown pathways, and different ERF transcription factors. These results indicate that salt tolerance is differentially controlled between common wheat and SH wheat. Furthermore, QTL analysis was performed using the F2 population derived from SH and salt-sensitive wheat. No statistically significant QTL was detected, suggesting that numerous QTLs with negligible contributions are involved in salt tolerance in SH wheat. We also identified DEGs specific to each line near one probable QTL. These findings show that SH wheat possesses salt tolerance mechanisms lacking in common wheat and may be potential breeding material for salt tolerance.
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21
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Pincot DDA, Feldmann MJ, Hardigan MA, Vachev MV, Henry PM, Gordon TR, Bjornson M, Rodriguez A, Cobo N, Famula RA, Cole GS, Coaker GL, Knapp SJ. Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2121-2145. [PMID: 35583656 PMCID: PMC9205853 DOI: 10.1007/s00122-022-04102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 05/05/2023]
Abstract
Several Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant to Fusarium oxysporum f. sp. fragariae, a devastating soil-borne pathogen of strawberry. Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria [Formula: see text] ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.
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Affiliation(s)
- Dominique D. A. Pincot
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Mitchell J. Feldmann
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Michael A. Hardigan
- Horticultural Crops Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR 97331 USA
| | - Mishi V. Vachev
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Peter M. Henry
- United States Department of Agriculture Agricultural Research Service, 1636 East Alisal Street, Salinas, CA 93905 USA
| | - Thomas R. Gordon
- Department of Plant Pathology, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Marta Bjornson
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Alan Rodriguez
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Nicolas Cobo
- Departamento de Producción, Agropecuaria Universidad de La Frontera, Temuco, Chile
| | - Randi A. Famula
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Glenn S. Cole
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Gitta L. Coaker
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Steven J. Knapp
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
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22
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Molecular mapping of CLCuD resistance introgressed from synthetic cotton polyploid in upland cotton. J Genet 2022. [DOI: 10.1007/s12041-022-01365-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Giordani W, Gama HC, Chiorato AF, Marques JPR, Huo H, Benchimol-Reis LL, Camargo LEA, Garcia AAF, Vieira MLC. Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection. THE PLANT GENOME 2022; 15:e20161. [PMID: 34806826 DOI: 10.1002/tpg2.20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.
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Affiliation(s)
- Willian Giordani
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Henrique Castro Gama
- "Luiz de Queiroz" College of Agriculture, Univ. of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | | | | | - Heqiang Huo
- Mid-Florida Research and Education Center, Univ. of Florida, Apopka, FL, 32703, USA
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24
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High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
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25
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Nishimura K, Motoki K, Yamazaki A, Takisawa R, Yasui Y, Kawai T, Ushijima K, Nakano R, Nakazaki T. MIG-seq is an effective method for high-throughput genotyping in wheat ( Triticum spp.). DNA Res 2022; 29:6567359. [PMID: 35412600 PMCID: PMC9035812 DOI: 10.1093/dnares/dsac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/08/2022] [Indexed: 12/04/2022] Open
Abstract
MIG-seq (Multiplexed inter-simple sequence repeats genotyping by sequencing) has been developed as a low cost genotyping technology, although the number of polymorphisms obtained is assumed to be minimal, resulting in the low application of this technique to analyses of agricultural plants. We applied MIG-seq to 12 plant species that include various crops and investigated the relationship between genome size and the number of bases that can be stably sequenced. The genome size and the number of loci, which can be sequenced by MIG-seq, are positively correlated. This is due to the linkage between genome size and the number of simple sequence repeats (SSRs) through the genome. The applicability of MIG-seq to population structure analysis, linkage mapping, and quantitative trait loci (QTL) analysis in wheat, which has a relatively large genome, was further evaluated. The results of population structure analysis for tetraploid wheat showed the differences among collection sites and subspecies, which agreed with previous findings. Additionally, in wheat biparental mapping populations, over 3,000 SNPs/indels with low deficiency were detected using MIG-seq, and the QTL analysis was able to detect recognized flowering-related genes. These results revealed the effectiveness of MIG-seq for genomic analysis of agricultural plants with large genomes, including wheat.
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Affiliation(s)
- Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, Kizugawa City, Kyoto Prefecture 619-0218, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, Kizugawa City, Kyoto Prefecture 619-0218, Japan
| | - Akira Yamazaki
- Graduate School of Agriculture, Kyoto University, Kizugawa City, Kyoto Prefecture 619-0218, Japan
- Faculty of Agriculture, Kindai University, Nara City, Nara Prefecture 631-8505, Japan
| | - Rihito Takisawa
- Faculty of Agriculture, Ryukoku University, Otsu City, Shiga Prefecture 520-2194, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kizugawa City, Kyoto Prefecture 619-0218, Japan
| | - Takashi Kawai
- Graduate School of Environmental and Life Science, Okayama University, Okayama City, Okayama Prefecture 700-8530, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama City, Okayama Prefecture 700-8530, Japan
| | - Ryohei Nakano
- Graduate School of Agriculture, Kyoto University, Kizugawa City, Kyoto Prefecture 619-0218, Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, Kizugawa City, Kyoto Prefecture 619-0218, Japan
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26
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Petrasch S, Mesquida-Pesci SD, Pincot DDA, Feldmann MJ, López CM, Famula R, Hardigan MA, Cole GS, Knapp SJ, Blanco-Ulate B. Genomic prediction of strawberry resistance to postharvest fruit decay caused by the fungal pathogen Botrytis cinerea. G3 (BETHESDA, MD.) 2022; 12:6427547. [PMID: 34791166 PMCID: PMC8728004 DOI: 10.1093/g3journal/jkab378] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/08/2021] [Indexed: 12/18/2022]
Abstract
Gray mold, a disease of strawberry (Fragaria × ananassa) caused by the ubiquitous necrotroph Botrytis cinerea, renders fruit unmarketable and causes economic losses in the postharvest supply chain. To explore the feasibility of selecting for increased resistance to gray mold, we undertook genetic and genomic prediction studies in strawberry populations segregating for fruit quality and shelf life traits hypothesized to pleiotropically affect susceptibility. As predicted, resistance to gray mold was heritable but quantitative and genetically complex. While every individual was susceptible, the speed of symptom progression and severity differed. Narrow-sense heritability ranged from 0.38 to 0.71 for lesion diameter (LD) and 0.39 to 0.44 for speed of emergence of external mycelium (EM). Even though significant additive genetic variation was observed for LD and EM, the phenotypic ranges were comparatively narrow and genome-wide analyses did not identify any large-effect loci. Genomic selection (GS) accuracy ranged from 0.28 to 0.59 for LD and 0.37 to 0.47 for EM. Additive genetic correlations between fruit quality and gray mold resistance traits were consistent with prevailing hypotheses: LD decreased as titratable acidity increased, whereas EM increased as soluble solid content decreased and firmness increased. We concluded that phenotypic and GS could be effective for reducing LD and increasing EM, especially in long shelf life populations, but that a significant fraction of the genetic variation for resistance to gray mold was caused by the pleiotropic effects of fruit quality traits that differ among market and shelf life classes.
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Affiliation(s)
- Stefan Petrasch
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | | | - Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Cindy M López
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Randi Famula
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Barbara Blanco-Ulate
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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27
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McCarty AJ, Allen SK, Plough LV. Genome-wide analysis of acute low salinity tolerance in the eastern oyster Crassostrea virginica and potential of genomic selection for trait improvement. G3 (BETHESDA, MD.) 2022; 12:6409860. [PMID: 34849774 PMCID: PMC8727987 DOI: 10.1093/g3journal/jkab368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/11/2021] [Indexed: 11/12/2022]
Abstract
As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single-nucleotide polymorphism (SNP) data for four F2 families to investigate the genomic regions associated with survival in extreme low salinity (<3). SNP data were also used to assess the feasibility of genomic selection (GS) for improving this trait. Quantitative trait locus (QTL) mapping and combined linkage disequilibrium analysis revealed significant QTL on eastern oyster chromosomes 1 and 7 underlying both survival and day to death in a 36-day experimental challenge. Significant QTL were located in genes related to DNA/RNA function and repair, ion binding and membrane transport, and general response to stress. GS was investigated using Bayesian linear regression models and prediction accuracies ranged from 0.48 to 0.57. Genomic prediction accuracies were largest using the BayesB prior and prediction accuracies did not substantially decrease when SNPs located within the QTL region on Chr1 were removed, suggesting that this trait is controlled by many genes of small effect. Our results suggest that GS will likely be a viable option for improvement of survival in extreme low salinity.
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Affiliation(s)
- Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Standish K Allen
- Virginia Institute of Marine Science, Aquaculture Genetics and Breeding Technology Center, Gloucester Point, VA 23062, USA
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
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28
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Samayoa LF, Olukolu BA, Yang CJ, Chen Q, Stetter MG, York AM, Sanchez-Gonzalez JDJ, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Yang J, Ross-Ibarra J, Buckler ES, Doebley JF, Holland JB. Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte. PLoS Genet 2021; 17:e1009797. [PMID: 34928949 PMCID: PMC8722731 DOI: 10.1371/journal.pgen.1009797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/03/2022] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte. Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. Mating of close relatives increases the probability that an individual inherits two non-functioning mutations at the same gene, resulting in lower fitness of such matings. We do not know the extent to which inbreeding depression is due to mutations with large-effects versus small-effect polygenic variants. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits and we found that this was consistent with higher predicted ‘genetic load’ in maize based solely on the evolutionary conservation of the sequence variants observed in the population. We also mapped genome positions associated with inbreeding depression, identifying more and larger-effect genetic variants in teosinte than maize. These results suggest that during domestication, some of the rare large-effect variants in teosinte were bred out, but many genetic variants of small effects on inbreeding depression increased in frequency maize.
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Affiliation(s)
- Luis Fernando Samayoa
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Qiuyue Chen
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Markus G. Stetter
- Institute for Plant Sciences and Center of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Alessandra M. York
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | | | - Jeffrey C. Glaubitz
- Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Peter J. Bradbury
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - Maria Cinta Romay
- Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, California, United States of America
| | - Edward S. Buckler
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - John F. Doebley
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - James B. Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- United States Department of Agriculture–Agriculture Research Service, Raleigh, North Carolina, United States of America
- * E-mail:
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29
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Nürnberger B, Baird SJE, Čížková D, Bryjová A, Mudd AB, Blaxter ML, Szymura JM. A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata). G3 (BETHESDA, MD.) 2021; 11:6353606. [PMID: 34849761 PMCID: PMC8664441 DOI: 10.1093/g3journal/jkab286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022]
Abstract
Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7–10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.
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Affiliation(s)
- Beate Nürnberger
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Stuart J E Baird
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Dagmar Čížková
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Anna Bryjová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, 94720 CA, USA
| | - Mark L Blaxter
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jacek M Szymura
- Department of Comparative Anatomy, Jagiellonian University, 30-387 Kraków, Poland
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30
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Amadeu RR, Muñoz PR, Zheng C, Endelman JB. QTL mapping in outbred tetraploid (and diploid) diallel populations. Genetics 2021; 219:iyab124. [PMID: 34740237 PMCID: PMC8570786 DOI: 10.1093/genetics/iyab124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/24/2021] [Indexed: 11/14/2022] Open
Abstract
Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multiallelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and nonadditive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with three tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher-order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.
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Affiliation(s)
- Rodrigo R Amadeu
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Patricio R Muñoz
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Chaozhi Zheng
- Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
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García-Fernández C, Campa A, Ferreira JJ. Dissecting the genetic control of seed coat color in a RIL population of common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3687-3698. [PMID: 34328529 DOI: 10.1007/s00122-021-03922-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Three genes associated with the seed coat color in a TU/Musica RIL population were located on a genetic map, and two candidate genes proposed to control black seed coat in the TU genotype were characterized. Seed coat color is an important characteristic of common bean (Phaseolus vulgaris L.) associated with the marketability of dry bean cultivars, quality and nutritional characteristics of seed, as well as response to pathogens. In this study, the genetic control of seed coat color in a recombinant inbred line population (175 lines) obtained from the cross 'TU' × 'Musica' was investigated. Phenotypic segregation fitted 1:1 for white vs. nonwhite, and 3:1 for brown versus black, indicating the involvement of three independent genes, one controlling white color and two (with epistatic interaction) controlling black color. Using a genetic map built with 842 SNPs, the gene responsible for the white seed coat was mapped on the linkage group Pv07, in the position previously described for the P gene. For the black seed coat phenotype, two genes were mapped to the beginning of chromosomes Pv06 and Pv08, in the positions estimated for the V gene and the complex C locus, respectively, by classical studies. The involvement of these two genomic regions was verified through two crosses between three selected RILs exhibiting complementary and dominant inheritance, in which the TU alleles for both genes resulted in a black phenotype. Two genes involved in the anthocyanin biosynthesis pathway were proposed as candidate genes: Phvul.006G018800 encoding a flavonoid 3'5'hydroxylase and Phvul.008G038400 encoding MYB113 transcription factor. These findings add knowledge to the complex network of genes controlling seed coat color in common bean as well as providing genetic markers to be used in future genetic analysis or plant breeding.
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Affiliation(s)
- Carmen García-Fernández
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain.
| | - Ana Campa
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
| | - Juan Jose Ferreira
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
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32
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Souza VFD, Pereira GDS, Pastina MM, Parrella RADC, Simeone MLF, Barros BDA, Noda RW, da Costa e Silva L, Magalhães JVD, Schaffert RE, Garcia AAF, Damasceno CMB. QTL mapping for bioenergy traits in sweet sorghum recombinant inbred lines. G3 GENES|GENOMES|GENETICS 2021; 11:6370150. [PMID: 34519766 PMCID: PMC8527507 DOI: 10.1093/g3journal/jkab314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022]
Abstract
Abstract
During the past decade, sweet sorghum (Sorghum bicolor Moench L.) has shown great potential for bioenergy production, especially biofuels. In this study, 223 recombinant inbred lines (RILs) derived from a cross between two sweet sorghum lines (Brandes × Wray) were evaluated in three trials. Single-nucleotide polymorphisms (SNPs) derived from genotyping by sequencing of 272 RILs were used to build a high-density genetic map comprising 3,767 SNPs spanning 1,368.83 cM. Multitrait multiple interval mapping (MT-MIM) was carried out to map quantitative trait loci (QTL) for eight bioenergy traits. A total of 33 QTLs were identified for flowering time, plant height, total soluble solids and sucrose (five QTLs each), fibers (four QTLs), and fresh biomass yield, juice extraction yield, and reducing sugars (three QTLs each). QTL hotspots were found on chromosomes 1, 3, 6, 9, and 10, in addition to other QTLs detected on chromosomes 4 and 8. We observed that 14 out of the 33 mapped QTLs were found in all three trials. Upon further development and validation in other crosses, the results provided by the present study have a great potential to be used in marker-assisted selection in sorghum breeding programs for biofuel production.
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Affiliation(s)
| | - Guilherme da Silva Pereira
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | | | | | | | | | | | | | - Antonio Augusto Franco Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
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Cropano C, Manzanares C, Yates S, Copetti D, Do Canto J, Lübberstedt T, Koch M, Studer B. Identification of Candidate Genes for Self-Compatibility in Perennial Ryegrass ( Lolium perenne L.). FRONTIERS IN PLANT SCIENCE 2021; 12:707901. [PMID: 34721449 PMCID: PMC8554087 DOI: 10.3389/fpls.2021.707901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/30/2021] [Indexed: 05/10/2023]
Abstract
Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in ~40% of plant species. Two multiallelic loci, called S and Z, control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass (Lolium perenne L.) was previously mapped on linkage group (LG) 5 in an F2 population segregating for SC. Using a subset of the same population (n = 68), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 centimorgan (cM) using additional 2,056 plants and 23 novel sequence-based markers. Using Italian ryegrass (Lolium multiflorum Lam.) genome assembly as a reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our study is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm.
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Affiliation(s)
- Claudio Cropano
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Deutsche Saatveredelung AG, Lippstadt, Germany
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Javier Do Canto
- Instituto Nacional de Investigación Agropecuaria, Tacuarembó, Uruguay
| | | | | | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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34
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Michael VN, Fu Y, Shrestha S, Meru G. A Novel QTL for Resistance to Phytophthora Crown Rot in Squash. PLANTS 2021; 10:plants10102115. [PMID: 34685924 PMCID: PMC8537320 DOI: 10.3390/plants10102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022]
Abstract
Phytophthora capsici Leonian causes significant yield losses in commercial squash (Cucurbita pepo) production worldwide. The deployment of resistant cultivars can complement integrated management practices for P. capsici, but resistant cultivars are currently unavailable for growers. Moderate resistance to Phytophthora crown rot in a selection of accession PI 181761 (C. pepo) (designated line #181761-36P) is controlled by three dominant genes (R4, R5 and R6). Introgression of these loci into elite germplasm through marker-assisted selection (MAS) can accelerate the release of new C. pepo cultivars resistant to crown rot, but these tools are currently unavailable. Here we describe the identification of a quantitative trait locus (QTL), molecular markers and candidate genes associated with crown rot resistance in #181761-36P. Five hundred and twenty-three SNP markers were genotyped in an F2 (n = 83) population derived from a cross between #181761-36P (R) and Table Queen (S) using targeted genotyping by sequencing. A linkage map (2068.96 cM) consisting of twenty-one linkage groups and an average density of 8.1 markers/cM was developed for the F2 population. The F2:3 families were phenotyped in the greenhouse with a virulent strain of P. capsica, using the spore-spray method. A single QTL (QtlPC-C13) was consistently detected on LG 13 (chromosome 13) across three experiments and explained 17.92-21.47% of phenotypic variation observed in the population. Nine candidate disease resistance gene homologs were found within the confidence interval of QtlPC-C13. Single nucleotide polymorphism (SNP) markers within these genes were converted into Kompetitive Allele Specific PCR (KASP) assays and tested for association with resistance in the F2 population. One SNP marker (C002686) was significantly associated with resistance to crown rot in the F2 population (p < 0.05). This marker is a potential target for MAS for crown rot resistance in C. pepo.
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35
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Kay KM, Surget-Groba Y. The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understorey herbs. Mol Ecol 2021; 31:4351-4363. [PMID: 34487383 DOI: 10.1111/mec.16165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many co-adapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.
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Affiliation(s)
- Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yann Surget-Groba
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Département de Biologie, Université du Québec en Outaouais, Ripon, QC, Canada
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36
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Rillo-Bohn R, Adilardi R, Mitros T, Avşaroğlu B, Stevens L, Köhler S, Bayes J, Wang C, Lin S, Baskevitch KA, Rokhsar DS, Dernburg AF. Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage. eLife 2021; 10:70990. [PMID: 34427184 PMCID: PMC8455136 DOI: 10.7554/elife.70990] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022] Open
Abstract
Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages.
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Affiliation(s)
- Regina Rillo-Bohn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Renzo Adilardi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Barış Avşaroğlu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Lewis Stevens
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Darwin Tree of Life Project, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Simone Köhler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Joshua Bayes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Clara Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sabrina Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - K Alienor Baskevitch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Energy Joint Genome Institute, Berkeley, United States.,Okinawa Institute of Science and Technology Graduate University, Onna, Japan.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Abby F Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,California Institute for Quantitative Biosciences, Berkeley, United States
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Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans. PLoS One 2021; 16:e0251745. [PMID: 34010322 PMCID: PMC8133444 DOI: 10.1371/journal.pone.0251745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/30/2021] [Indexed: 11/24/2022] Open
Abstract
Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.
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de Almeida CP, de Carvalho Paulino JF, Bonfante GFJ, Perseguini JMKC, Santos IL, Gonçalves JGR, Patrício FRA, Taniguti CH, Gesteira GDS, Garcia AAF, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:647043. [PMID: 33927738 PMCID: PMC8078856 DOI: 10.3389/fpls.2021.647043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Angular leaf spot (ALS) is a disease that causes major yield losses in the common bean crop. Studies based on different isolates and populations have already been carried out to elucidate the genetic mechanisms of resistance to ALS. However, understanding of the interaction of this resistance with the reproductive stages of common bean is lacking. The aim of the present study was to identify ALS resistance loci at different plant growth stages (PGS) by association and linkage mapping approaches. An BC2F3 inter-gene pool cross population (AND 277 × IAC-Milênio - AM population) profiled with 1,091 SNPs from genotyping by sequencing (GBS) was used for linkage mapping, and a carioca diversity panel (CDP) genotyped by 5,398 SNPs from BeadChip assay technology was used for association mapping. Both populations were evaluated for ALS resistance at the V2 and V3 PGSs (controlled conditions) and R8 PGS (field conditions). Different QTL (quantitative trait loci) were detected for the three PGSs and both populations, showing a different quantitative profile of the disease at different plant growth stages. For the three PGS, multiple interval mapping (MIM) identified seven significant QTL, and the Genome-wide association study (GWAS) identified fourteen associate SNPs. Several loci validated regions of previous studies, and Phg-1, Phg-2, Phg-4, and Phg-5, among the 5 loci of greatest effects reported in the literature, were detected in the CDP. The AND 277 cultivar contained both the Phg-1 and the Phg-5 QTL, which is reported for the first time in the descendant cultivar CAL143 as ALS10.1UC. The novel QTL named ALS11.1AM was located at the beginning of chromosome Pv11. Gene annotation revealed several putative resistance genes involved in the ALS response at the three PGSs, and with the markers and loci identified, new specific molecular markers can be developed, representing a powerful tool for common bean crop improvement and for gain in ALS resistance.
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Affiliation(s)
| | | | | | | | - Isabella Laporte Santos
- Centro de Pesquisa em Recursos Genéticos Vegetais, Instituto Agronômico - IAC, Campinas, Brazil
| | | | | | - Cristiane Hayumi Taniguti
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriel de Siqueira Gesteira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Antônio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Qijian Song
- USDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, United States
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Kushwah A, Bhatia D, Rani U, Yadav IS, Singh I, Bharadwaj C, Singh S. Molecular mapping of quantitative trait loci for ascochyta blight and botrytis grey mould resistance in an inter-specific cross in chickpea ( Cicer arietinum L.) using genotyping by sequencing. BREEDING SCIENCE 2021; 71:229-239. [PMID: 34377071 PMCID: PMC8329888 DOI: 10.1270/jsbbs.20085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/23/2020] [Indexed: 06/13/2023]
Abstract
Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F8 Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.
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Affiliation(s)
- Ashutosh Kushwah
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Upasana Rani
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
| | - C Bharadwaj
- ICAR-Indian Agricultural Research Institute, New Delhi, India, 110012
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India, 141004
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Zhou H, Xia D, Li P, Ao Y, Xu X, Wan S, Li Y, Wu B, Shi H, Wang K, Gao G, Zhang Q, Wang G, Xiao J, Li X, Yu S, Lian X, He Y. Genetic architecture and key genes controlling the diversity of oil composition in rice grains. MOLECULAR PLANT 2021; 14:456-469. [PMID: 33307246 DOI: 10.1016/j.molp.2020.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/28/2020] [Accepted: 12/04/2020] [Indexed: 05/25/2023]
Abstract
Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for 11 oil-related traits was observed, and the oil composition of rice grains showed differentiation among the subpopulations. We identified 46 loci that are significantly associated with grain oil concentration or composition, 16 of which were detected in three recombinant inbred line populations. Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci, four of which (PAL6, LIN6, MYR2, and ARA6) were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations. Interestingly, population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice. Based on these results, we propose a possible oil biosynthetic pathway in rice grains. Collectively, our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.
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Affiliation(s)
- Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yiting Ao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodong Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Wan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Kaiyue Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Quezada M, Amadeu RR, Vignale B, Cabrera D, Pritsch C, Garcia AAF. Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:626811. [PMID: 33708232 PMCID: PMC7940835 DOI: 10.3389/fpls.2021.626811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.
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Affiliation(s)
- Marianella Quezada
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Rodrigo Rampazo Amadeu
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Beatriz Vignale
- Mejoramiento Genético, Departamento de Producción Vegetal, Estación Experimental de la Facultad de Agronomía, Universidad de la República, Salto, Uruguay
| | - Danilo Cabrera
- Programa de Investigación en Producción Fruticola, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental “Wilson Ferreira Aldunate”, Canelones, Uruguay
| | - Clara Pritsch
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Antonio Augusto Franco Garcia
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
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Diaz-Garcia L, Garcia-Ortega LF, González-Rodríguez M, Delaye L, Iorizzo M, Zalapa J. Chromosome-Level Genome Assembly of the American Cranberry ( Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum. FRONTIERS IN PLANT SCIENCE 2021; 12:633310. [PMID: 33643360 PMCID: PMC7902871 DOI: 10.3389/fpls.2021.633310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/19/2021] [Indexed: 05/25/2023]
Abstract
The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.
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Affiliation(s)
- Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Pabellón, Aguascalientes, Mexico
| | | | | | - Luis Delaye
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, WI, United States
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, United States
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Costa LC, Nalin RS, Dias MA, Ferreira ME, Song Q, Pastor-Corrales MA, Hurtado-Gonzales OP, de Souza EA. Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:543-556. [PMID: 33130954 DOI: 10.1007/s00122-020-03713-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/17/2020] [Indexed: 05/03/2023]
Abstract
Linkage and genome-wide association analyses using high-throughput SNP genotyping revealed different loci controlling resistance to different isolates of race 65 of Colletotrichum lindemuthianum in common bean. Development of varieties with durable resistance to anthracnose is a major challenge in common bean breeding programs because of the extensive virulence diversity of Colletotrichum lindemuthianum fungus. We used linkage and genome-wide association analyses to tap the genomic regions associated with resistance to different isolates of race 65. Linkage mapping was done using an F2 population derived from the cross between the Mesoamerican common beans BRS Estilo x Ouro Vermelho, inoculated with two different isolates of race 65. Association genetics relied on a diversity common bean panel containing 189 common bean accessions inoculated with five different isolates of race 65 as an attempt to validate the linkage analysis findings and, eventually, identify other genomic regions associated with resistance to race 65. The F2 population and diversity panel were genotyped with the BARCBean6K_3 Illumina BeadChip containing 5398 SNP markers. Both linkage and genome-wide association analyses identified different loci controlling resistance to different isolates of race 65 on linkage group Pv04. Genome-wide association analysis also detected loci on Pv05, Pv10 and Pv11 associated with resistance to race 65. These findings indicate that resistance to race 65 can be overcome by the virulence diversity among different isolates of the same race and could lead to the loss of resistance after cultivar release. We identified 25 resistant common bean cultivars to all five isolates of race 65 in the diversity panel. The accessions should be useful to develop cultivars combining different resistance genes that favor durable resistance to anthracnose in common bean.
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Affiliation(s)
| | - Rafael Storto Nalin
- Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, São Paulo, Brazil
| | - Mariana Andrade Dias
- Department of Biology, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Márcio Elias Ferreira
- Plant Genetics Laboratory, EMBRAPA-Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, BARC-West, Beltsville, MD, 20705, USA
| | | | - Oscar P Hurtado-Gonzales
- Soybean Genomics and Improvement Laboratory, USDA-ARS, BARC-West, Beltsville, MD, 20705, USA
- Plant Germplasm Quarantine Program, USDA-APHIS, BARC-East, Beltsville, MD, 20705, USA
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Optimizing imputation of marker data from genotyping-by-sequencing (GBS) for genomic selection in non-model species: Rubber tree (Hevea brasiliensis) as a case study. Genomics 2021; 113:655-668. [PMID: 33508443 DOI: 10.1016/j.ygeno.2021.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/07/2020] [Accepted: 01/22/2021] [Indexed: 11/24/2022]
Abstract
Genotyping-by-sequencing (GBS) provides the marker density required for genomic predictions (GP). However, GBS gives a high proportion of missing SNP data which, for species without a chromosome-level genome assembly, must be imputed without knowing the SNP physical positions. Here, we compared GP accuracy with seven map-independent and two map-dependent imputation approaches, and when using all SNPs against the subset of genetically mapped SNPs. We used two rubber tree (Hevea brasiliensis) datasets with three traits. The results showed that the best imputation approaches were LinkImputeR, Beagle and FImpute. Using the genetically mapped SNPs increased GP accuracy by 4.3%. Using LinkImputeR on all the markers allowed avoiding genetic mapping, with a slight decrease in GP accuracy. LinkImputeR gave the highest level of correctly imputed genotypes and its performances were further improved by its ability to define a subset of SNPs imputed optimally. These results will contribute to the efficient implementation of genomic selection with GBS. For Hevea, GBS is promising for rubber yield improvement, with GP accuracies reaching 0.52.
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Qi X, Ogden EL, Bostan H, Sargent DJ, Ward J, Gilbert J, Iorizzo M, Rowland LJ. High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population. FRONTIERS IN PLANT SCIENCE 2021; 12:692628. [PMID: 34234801 PMCID: PMC8256855 DOI: 10.3389/fpls.2021.692628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/24/2021] [Indexed: 05/11/2023]
Abstract
Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85-20) with the parent W85-23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.
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Affiliation(s)
- Xinpeng Qi
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Elizabeth L. Ogden
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Hamed Bostan
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | | | - Judson Ward
- Driscoll’s Inc., Watsonville, CA, United States
| | | | - Massimo Iorizzo
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Lisa J. Rowland
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- *Correspondence: Lisa J. Rowland, ;
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Miki Y, Yoshida K, Enoki H, Komura S, Suzuki K, Inamori M, Nishijima R, Takumi S. GRAS-Di system facilitates high-density genetic map construction and QTL identification in recombinant inbred lines of the wheat progenitor Aegilops tauschii. Sci Rep 2020; 10:21455. [PMID: 33293651 PMCID: PMC7723059 DOI: 10.1038/s41598-020-78589-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
Due to large and complex genomes of Triticeae species, skim sequencing approaches have cost and analytical advantages for detecting genetic markers and building linkage maps. Here, we develop a high-density linkage map and identify quantitative trait loci (QTLs) for recombinant inbred lines of Aegilops tauschii, a D-genome donor of bread wheat, using the recently developed genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) system, which facilitates skimming of the large and complicated genome and generates a large number of genetic markers. The deduced linkage groups based on the GRAS-Di genetic markers corresponded to the chromosome number of Ae. tauschii. We successfully identified stable QTLs for flowering time and spikelet shape-related traits. Genotype differences of RILs at the QTL-linked markers were significantly associated with the trait variations. In particular, one of the QTL-linked markers for flowering time was mapped close to VRN3 (also known as FLOWERING LOCUS T), which controls flowering. The GRAS-Di system is, therefore, an efficient and useful application for genotyping and linkage mapping in species with large and complex genomes, such as Triticeae species.
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Affiliation(s)
- Yuka Miki
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan.
| | - Hiroyuki Enoki
- toyota Motor Corporation, 1099, Marune, Kurozasa-cho, Miyoshi, Aichi, Japan
| | - Shoya Komura
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan
| | - Kazuyo Suzuki
- toyota Motor Corporation, 1099, Marune, Kurozasa-cho, Miyoshi, Aichi, Japan
| | - Minoru Inamori
- toyota Motor Corporation, 1099, Marune, Kurozasa-cho, Miyoshi, Aichi, Japan
| | - Ryo Nishijima
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, Japan
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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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Lou P, Woody S, Greenham K, VanBuren R, Colle M, Edger PP, Sartor R, Zheng Y, Levendoski N, Lim J, So C, Stoveken B, Woody T, Zhao J, Shen S, Amasino RM, McClung CR. Genetic and genomic resources to study natural variation in Brassica rapa. PLANT DIRECT 2020; 4:e00285. [PMID: 33364543 PMCID: PMC7755128 DOI: 10.1002/pld3.285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The globally important crop Brassica rapa, a close relative of Arabidopsis, is an excellent system for modeling our current knowledge of plant growth on a morphologically diverse crop. The long history of B. rapa domestication across Asia and Europe provides a unique collection of locally adapted varieties that span large climatic regions with various abiotic and biotic stress-tolerance traits. This diverse gene pool provides a rich source of targets with the potential for manipulation toward the enhancement of productivity of crops both within and outside the Brassicaceae. To expand the genetic resources available to study natural variation in B. rapa, we constructed an Advanced Intercross Recombinant Inbred Line (AI-RIL) population using B. rapa subsp. trilocularis (Yellow Sarson) R500 and the B. rapa subsp. parachinensis (Cai Xin) variety L58. Our current understanding of genomic structure variation across crops suggests that a single reference genome is insufficient for capturing the genetic diversity within a species. To complement this AI-RIL population and current and future B. rapa genomic resources, we generated a de novo genome assembly of the B. rapa subsp. trilocularis (Yellow Sarson) variety R500, the maternal parent of the AI-RIL population. The genetic map for the R500 x L58 population generated using this de novo genome was used to map Quantitative Trait Loci (QTL) for seed coat color and revealed the improved mapping resolution afforded by this new assembly.
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Affiliation(s)
- Ping Lou
- Department of Biological SciencesDartmouth CollegeHanoverNHUSA
| | - Scott Woody
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
| | - Kathleen Greenham
- Department of Biological SciencesDartmouth CollegeHanoverNHUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMNUSA
| | - Robert VanBuren
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Marivi Colle
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Ryan Sartor
- Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Yakun Zheng
- Department of Biological SciencesDartmouth CollegeHanoverNHUSA
- State Key Laboratory of North China Crop Improvement and RegulationLaboratory of Vegetable Germplasm Innovation and Utilization of HebeiCollaborative Innovation Center of Vegetable Industry in HebeiDepartment of HorticultureHebei Agricultural UniversityBaodingChina
| | | | - Jan Lim
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
| | - Calvin So
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
| | - Brian Stoveken
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
| | - Timothy Woody
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and RegulationLaboratory of Vegetable Germplasm Innovation and Utilization of HebeiCollaborative Innovation Center of Vegetable Industry in HebeiDepartment of HorticultureHebei Agricultural UniversityBaodingChina
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and RegulationLaboratory of Vegetable Germplasm Innovation and Utilization of HebeiCollaborative Innovation Center of Vegetable Industry in HebeiDepartment of HorticultureHebei Agricultural UniversityBaodingChina
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Furman BLS, Cauret CMS, Knytl M, Song XY, Premachandra T, Ofori-Boateng C, Jordan DC, Horb ME, Evans BJ. A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome. PLoS Genet 2020; 16:e1009121. [PMID: 33166278 PMCID: PMC7652241 DOI: 10.1371/journal.pgen.1009121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/16/2020] [Indexed: 11/18/2022] Open
Abstract
In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among-and even within-species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.
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Affiliation(s)
- Benjamin L. S. Furman
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
- Department of Zoology, University of British Columbia, 6270 University Blvd Vancouver, British Columbia, V6T 1Z4 Canada
| | - Caroline M. S. Cauret
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
- Department of Cell Biology, Charles University, 7 Vinicna Street, Prague, 12843, Czech Republic
| | - Xue-Ying Song
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Tharindu Premachandra
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | | | - Danielle C. Jordan
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543 USA
| | - Marko E. Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543 USA
| | - Ben J. Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
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50
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Zhou C, Olukolu B, Gemenet DC, Wu S, Gruneberg W, Cao MD, Fei Z, Zeng ZB, George AW, Khan A, Yencho GC, Coin LJM. Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. Nat Genet 2020; 52:1256-1264. [PMID: 33128049 DOI: 10.1038/s41588-020-00717-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 09/15/2020] [Indexed: 12/31/2022]
Abstract
Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.
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Affiliation(s)
- Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bode Olukolu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Dorcus C Gemenet
- International Potato Center, Lima, Peru
- CGIAR Excellence in Breeding Platform, International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | | | - Minh Duc Cao
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Zhao-Bang Zeng
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andrew W George
- Data61, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Queensland, Australia
| | - Awais Khan
- International Potato Center, Lima, Peru
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia.
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
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