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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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Grierson ERP, Thrimawithana AH, van Klink JW, Lewis DH, Carvajal I, Shiller J, Miller P, Deroles SC, Clearwater MJ, Davies KM, Chagné D, Schwinn KE. A phosphatase gene is linked to nectar dihydroxyacetone accumulation in mānuka (Leptospermum scoparium). THE NEW PHYTOLOGIST 2024. [PMID: 38532557 DOI: 10.1111/nph.19714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
Floral nectar composition beyond common sugars shows great diversity but contributing genetic factors are generally unknown. Mānuka (Leptospermum scoparium) is renowned for the antimicrobial compound methylglyoxal in its derived honey, which originates from the precursor, dihydroxyacetone (DHA), accumulating in the nectar. Although this nectar trait is highly variable, genetic contribution to the trait is unclear. Therefore, we investigated key gene(s) and genomic regions underpinning this trait. We used RNAseq analysis to identify nectary-associated genes differentially expressed between high and low nectar DHA genotypes. We also used a mānuka high-density linkage map and quantitative trait loci (QTL) mapping population, supported by an improved genome assembly, to reveal genetic regions associated with nectar DHA content. Expression and QTL analyses both pointed to the involvement of a phosphatase gene, LsSgpp2. The expression pattern of LsSgpp2 correlated with nectar DHA accumulation, and it co-located with a QTL on chromosome 4. The identification of three QTLs, some of the first reported for a plant nectar trait, indicates polygenic control of DHA content. We have established plant genetics as a key influence on DHA accumulation. The data suggest the hypothesis of LsSGPP2 releasing DHA from DHA-phosphate and variability in LsSgpp2 gene expression contributing to the trait variability.
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Affiliation(s)
- Ella R P Grierson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3216, New Zealand
| | | | - John W van Klink
- PFR, Chemistry Department, University of Otago, Dunedin, 9016, New Zealand
| | - David H Lewis
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | | | - Jason Shiller
- PFR, Te Puke Research Centre, Te Puke, 3182, New Zealand
| | - Poppy Miller
- PFR, Te Puke Research Centre, Te Puke, 3182, New Zealand
| | | | - Michael J Clearwater
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3216, New Zealand
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
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Asins MJ, Bullones A, Raga V, Romero-Aranda MR, Espinosa J, Triviño JC, Bernet GP, Traverso JA, Carbonell EA, Claros MG, Belver A. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus. Int J Mol Sci 2023; 24:15759. [PMID: 37958745 PMCID: PMC10650496 DOI: 10.3390/ijms242115759] [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: 09/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The excessive accumulation of chloride (Cl-) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl-, Na+, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (Citrus reshni) and the disease-resistant donor Poncirus trifoliata were performed with the aim to identify repeatable QTLs that regulate leaf Cl- (and/or Na+) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl- was detected in chromosome 6 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided.
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Affiliation(s)
- Maria J. Asins
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Amanda Bullones
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
| | - Veronica Raga
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - Maria R. Romero-Aranda
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
| | - Jesus Espinosa
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
| | - Juan C. Triviño
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Guillermo P. Bernet
- Sistemas Genómicos S.L., Ronda de Guglielmo Marconi, 6, 46980 Paterna, Spain; (J.C.T.); (G.P.B.)
| | - Jose A. Traverso
- Department of Cellular Biology, Faculty of Sciences, Universidad de Granada, 18071 Granada, Spain;
| | - Emilio A. Carbonell
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain; (V.R.)
| | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain; (A.B.); (M.G.C.)
- Integrative Biology for Plant Stress Group, La Mayora Institute of Subtropical and Mediterranean Horticulture, IHSM-CSIC-UMA, 29750 Malaga, Spain;
- CIBER de Enfermedades Raras (CIBERER) U741, 29071 Málaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Málaga, Spain
| | - Andres Belver
- Department of Stress, Development and Signaling of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (EEZ CSIC), C/Prof. Albareda 1, 18008 Granada, Spain; (J.E.); (A.B.)
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Molinier C, Lenormand T, Haag CR. No recombination suppression in asexually produced males of Daphnia pulex. Evolution 2023; 77:1987-1999. [PMID: 37345677 DOI: 10.1093/evolut/qpad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Obligate parthenogenesis (OP) is often thought to evolve by disruption of reductional meiosis and suppression of crossover recombination. In the crustacean Daphnia pulex, OP lineages, which have evolved from cyclical parthenogenetic (CP) ancestors, occasionally produce males that are capable of reductional meiosis. Here, by constructing high-density linkage maps, we find that these males show only slightly and nonsignificantly reduced recombination rates compared to CP males and females. Both meiosis disruption and recombination suppression are therefore sex-limited (or partly so), which speaks against the evolution of OP by disruption of a gene that is essential for meiosis or recombination in both sexes. The findings may be explained by female-limited action of genes that suppress recombination, but previously identified candidate genes are known to be expressed in both sexes. Alternatively, and equally consistent with the data, OP might have evolved through a reuse of the parthenogenesis pathways already present in CP and through their extension to all events of oogenesis. The causal mutations for the CP to OP transition may therefore include mutations in genes involved in oogenesis regulation and may not necessarily be restricted to genes of the "meiosis toolkit." More generally, our study emphasizes that there are many ways to achieve asexuality, and elucidating the possible mechanisms is key to ultimately identify the genes and traits involved.
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Affiliation(s)
- Cécile Molinier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tuebingen, Germany
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Chang Y, Li J, Zhang L. Genetic diversity and molecular diagnosis of Giardia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105482. [PMID: 37451417 DOI: 10.1016/j.meegid.2023.105482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Giardia is a genus of flagellated protozoan parasites that infect the small intestine of humans and animals, causing the diarrheal illness known as giardiasis. Giardia exhibits significant genetic diversity among its isolates, which can have important implications for disease transmission and clinical presentation. This diversity is influenced by the coevolution of Giardia with its host, resulting in the development of unique genetic assemblages with distinct phenotypic characteristics. Although panmixia has not been observed, some assemblages appear to have a broader host range and exhibit higher transmission rates. Molecular diagnostic methods enable researchers to examine the genetic diversity of Giardia populations, enhancing our understanding of the genetic diversity, population structure, and transmission patterns of this pathogen and providing insights into clinical presentations of giardiasis.
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Affiliation(s)
- Yankai Chang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan 450046, China
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan 450046, China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan 450046, China.
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Kho KH, Sukhan ZP, Hossen S, Cho Y, Lee WK, Nou IS. Age-Dependent Growth-Related QTL Variations in Pacific Abalone, Haliotis discus hannai. Int J Mol Sci 2023; 24:13388. [PMID: 37686194 PMCID: PMC10488178 DOI: 10.3390/ijms241713388] [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: 07/26/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Pacific abalone is a high-value, commercially important marine invertebrate. It shows low growth as well as individual and yearly growth variation in aquaculture. Marker-assisted selection breeding could potentially resolve the problem of low and variable growth and increase genetic gain. Expression of quantitative trait loci (QTLs) for growth-related traits, viz., body weight, shell length, and shell width were analyzed at the first, second, and third year of age using an F1 cross population. A total of 37 chromosome-wide QTLs were identified in linkage groups 01, 02, 03, 04, 06, 07, 08, 10, 11, 12, and 13 at different ages. None of the QTLs detected at any one age were expressed in all three age groups. This result suggests that growth-related traits at different ages are influenced by different QTLs in each year. However, multiple-trait QTLs (where one QTL affects all three traits) were detected each year that are also age-specific. Eleven multiple-trait QTLs were detected at different ages: two QTLs in the first year; two QTLs in the second year; and seven QTLs in the third year. As abalone hatcheries use three-year-old abalone for breeding, QTL-linked markers that were detected at the third year of age could potentially be used in marker-assisted selection breeding programs.
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Affiliation(s)
- Kang Hee Kho
- Department of Fisheries Science, Chonnam National University, Yeosu 59626, Republic of Korea; (Z.P.S.); (S.H.); (Y.C.); (W.-K.L.)
| | - Zahid Parvez Sukhan
- Department of Fisheries Science, Chonnam National University, Yeosu 59626, Republic of Korea; (Z.P.S.); (S.H.); (Y.C.); (W.-K.L.)
| | - Shaharior Hossen
- Department of Fisheries Science, Chonnam National University, Yeosu 59626, Republic of Korea; (Z.P.S.); (S.H.); (Y.C.); (W.-K.L.)
| | - Yusin Cho
- Department of Fisheries Science, Chonnam National University, Yeosu 59626, Republic of Korea; (Z.P.S.); (S.H.); (Y.C.); (W.-K.L.)
| | - Won-Kyo Lee
- Department of Fisheries Science, Chonnam National University, Yeosu 59626, Republic of Korea; (Z.P.S.); (S.H.); (Y.C.); (W.-K.L.)
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon 57922, Republic of Korea;
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Koji T, Iwata H, Ishimori M, Takanashi H, Yamasaki Y, Tsujimoto H. Multispectral Phenotyping and Genetic Analyses of Spring Appearance in Greening Plant, Phedimus spp. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0063. [PMID: 37383728 PMCID: PMC10292581 DOI: 10.34133/plantphenomics.0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
The change in appearance during the seasonal transitions in ornamental greening plants is an important characteristic. In particular, the early onset of green leaf color is a desirable trait for a cultivar. In this study, we established a method for phenotyping leaf color change by multispectral imaging and performed genetic analysis based on the phenotypes to clarify the potential of the approach in breeding greening plants. We performed multispectral phenotyping and quantitative trait locus (QTL) analysis of an F1 population derived from 2 parental lines of Phedimus takesimensis, known to be a drought and heat-tolerant rooftop plant species. The imaging was conducted in April of 2019 and 2020 when dormancy breakage occurs and growth extension begins. Principal component analysis of 9 different wavelength values showed a high contribution from the first principal component (PC1), which captured variation in the visible light range. The high interannual correlation in PC1 and in the intensity of visible light indicated that the multispectral phenotyping captured genetic variation in the color of leaves. We also performed restriction site-associated DNA sequencing and obtained the first genetic linkage map of Phedimus spp. QTL analysis revealed 2 QTLs related to early dormancy breakage. Based on the genotypes of the markers underlying these 2 QTLs, the F1 phenotypes with early (late) dormancy break, green (red or brown) leaves, and a high (low) degree of vegetative growth were classified. The results suggest the potential of multispectral phenotyping in the genetic dissection of seasonal leaf color changes in greening plants.
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Affiliation(s)
- Taeko Koji
- The United Graduate School of Agricultural Sciences,
Tottori University, 4-101 Koyamacho minami, Tottori-shi, Tottori 680-8553, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences,
The University of Tokyo, 1-1-1 Yayoi-chou, Bunkyo, Tokyo 113-8657, Japan
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori-shi, Tottori 680-0001, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori-shi, Tottori 680-0001, Japan
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Srivastav M, Radadiya N, Ramachandra S, Jayaswal PK, Singh N, Singh S, Mahato AK, Tandon G, Gupta A, Devi R, Subrayagowda SH, Kumar G, Prakash P, Singh S, Sharma N, Nagaraja A, Kar A, Rudra SG, Sethi S, Jaiswal S, Iquebal MA, Singh R, Singh SK, Singh NK. High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids. FRONTIERS IN PLANT SCIENCE 2023; 14:1135285. [PMID: 37351213 PMCID: PMC10282835 DOI: 10.3389/fpls.2023.1135285] [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: 12/31/2022] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Introduction Mango (Mangifera indica L.), acclaimed as the 'king of fruits' in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood. Methods For mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array. Results and discussion Initially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.
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Affiliation(s)
- Manish Srivastav
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nidhi Radadiya
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sridhar Ramachandra
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Pawan Kumar Jayaswal
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Nisha Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Sangeeta Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Ajay Kumar Mahato
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
| | - Gitanjali Tandon
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankit Gupta
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Rajni Devi
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sreekanth Halli Subrayagowda
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Gulshan Kumar
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Pragya Prakash
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Singh
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nimisha Sharma
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - A. Nagaraja
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Abhijit Kar
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shalini Gaur Rudra
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Shruti Sethi
- Division of Food Science and Postharvest Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR)- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute, New Delhi, India
| | - Nagendra Kumar Singh
- Genomics Laboratory, Indian Council of Agricultural Research (ICAR)- National Institute for Plant Biotechnology, New Delhi, India
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Kumar K, Yu Q, Bhatia D, Honsho C, Gmitter FG. Construction of a high density genetic linkage map to define the locus conferring seedlessness from Mukaku Kishu mandarin. FRONTIERS IN PLANT SCIENCE 2023; 14:1087023. [PMID: 36875618 PMCID: PMC9976630 DOI: 10.3389/fpls.2023.1087023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Mukaku Kishu ('MK'), a small sized mandarin, is an important source of seedlessness in citrus breeding. Identification and mapping the gene(s) governing 'MK' seedlessness will expedite seedless cultivar development. In this study, two 'MK'-derived mapping populations- LB8-9 Sugar Belle® ('SB') × 'MK' (N=97) and Daisy ('D') × 'MK' (N=68) were genotyped using an Axiom_Citrus56 Array encompassing 58,433 SNP probe sets, and population specific male and female parent linkage maps were constructed. The parental maps of each population were integrated to produce sub-composite maps, which were further merged to develop a consensus linkage map. All the parental maps (except 'MK_D') had nine major linkage groups, and contained 930 ('SB'), 810 ('MK_SB'), 776 ('D') and 707 ('MK_D') SNPs. The linkage maps displayed 96.9 ('MK_D') to 98.5% ('SB') chromosomal synteny with the reference Clementine genome. The consensus map was comprised of 2588 markers including a phenotypic seedless (Fs)-locus and spanned a genetic distance of 1406.84 cM, with an average marker distance of 0.54 cM, which is substantially lower than the reference Clementine map. For the phenotypic Fs-locus, the distribution of seedy and seedless progenies in both 'SB' × 'MK' (55:42, χ2 = 1.74) and 'D' × 'MK' populations (33:35, χ2 = 0.06) followed a test cross pattern. The Fs-locus mapped on chromosome 5 with SNP marker 'AX-160417325' at 7.4 cM in 'MK_SB' map and between two SNP markers 'AX-160536283' and 'AX-160906995' at a distance of 2.4 and 4.9 cM, respectively in 'MK_D' map. The SNPs 'AX-160417325' and 'AX-160536283' correctly predicted seedlessness of 25-91.9% progenies in this study. Based on the alignment of flanking SNP markers to the Clementine reference genome, the candidate gene for seedlessness hovered in a ~ 6.0 Mb region between 3.97 Mb (AX-160906995) to 10.00 Mb (AX-160536283). This region has 131 genes of which 13 genes (belonging to seven gene families) reportedly express in seed coat or developing embryo. The findings of the study will prove helpful in directing future research for fine mapping this region and eventually underpinning the exact causative gene governing seedlessness in 'MK'.
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Affiliation(s)
- Krishan Kumar
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
- Punjab Agricultural University, Dr. JC Bakhshi Regional Research Station, Abohar, India
| | - Qibin Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chitose Honsho
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
- Laboratory of Pomology, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Frederick G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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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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Bettinelli P, Nicolini D, Costantini L, Stefanini M, Hausmann L, Vezzulli S. Towards Marker-Assisted Breeding for Black Rot Bunch Resistance: Identification of a Major QTL in the Grapevine Cultivar 'Merzling'. Int J Mol Sci 2023; 24:ijms24043568. [PMID: 36834979 PMCID: PMC9961920 DOI: 10.3390/ijms24043568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Black rot (BR), caused by Guignardia bidwellii, is an emergent fungal disease threatening viticulture and affecting several mildew-tolerant varieties. However, its genetic bases are not fully dissected yet. For this purpose, a segregating population derived from the cross 'Merzling' (hybrid, resistant) × 'Teroldego' (V. vinifera, susceptible) was evaluated for BR resistance at the shoot and bunch level. The progeny was genotyped with the GrapeReSeq Illumina 20K SNPchip, and 7175 SNPs were combined with 194 SSRs to generate a high-density linkage map of 1677 cM. The QTL analysis based on shoot trials confirmed the previously identified Resistance to Guignardia bidwellii (Rgb)1 locus on chromosome 14, which explained up to 29.2% of the phenotypic variance, reducing the genomic interval from 2.4 to 0.7 Mb. Upstream of Rgb1, this study revealed a new QTL explaining up to 79.9% of the variance for bunch resistance, designated Rgb3. The physical region encompassing the two QTLs does not underlie annotated resistance (R)-genes. The Rgb1 locus resulted enriched in genes belonging to phloem dynamics and mitochondrial proton transfer, while Rgb3 presented a cluster of pathogenesis-related Germin-like protein genes, promoters of the programmed cell death. These outcomes suggest a strong involvement of mitochondrial oxidative burst and phloem occlusion in BR resistance mechanisms and provide new molecular tools for grapevine marker-assisted breeding.
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Affiliation(s)
- Paola Bettinelli
- Center Agriculture Food Environment (C3A), University of Trento, 38098 San Michele all’Adige, TN, Italy
- Grapevine Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, TN, Italy
| | - Daniela Nicolini
- Grapevine Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, TN, Italy
| | - Laura Costantini
- Grapevine Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, TN, Italy
| | - Marco Stefanini
- Grapevine Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, TN, Italy
| | - Ludger Hausmann
- JKI Institute for Grapevine Breeding, Geilweilerhof, 76833 Siebeldingen, Germany
| | - Silvia Vezzulli
- Grapevine Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, TN, Italy
- Correspondence: ; Tel.: +39-0461-615387
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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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Vidal A, Gauthier F, Rodrigez W, Guiglielmoni N, Leroux D, Chevrolier N, Jasson S, Tourrette E, Martin OC, Falque M. SeSAM: software for automatic construction of order-robust linkage maps. BMC Bioinformatics 2022; 23:499. [PMCID: PMC9675223 DOI: 10.1186/s12859-022-05045-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
Background Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs. Results In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++. Conclusions SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-05045-7.
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Affiliation(s)
- Adrien Vidal
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Franck Gauthier
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Willy Rodrigez
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Damien Leroux
- grid.507621.7INRAE, Unité de Mathématiques et Informatique Appliquées - Toulouse, Toulouse, France
| | - Nicolas Chevrolier
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Sylvain Jasson
- grid.507621.7INRAE, Unité de Mathématiques et Informatique Appliquées - Toulouse, Toulouse, France
| | - Elise Tourrette
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Olivier C. Martin
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France ,grid.503243.3Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France ,Université Paris Cité, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Younessi-Hamzekhanlu M, Gailing O. Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection. Int J Mol Sci 2022; 23:ijms232012315. [PMID: 36293169 PMCID: PMC9604372 DOI: 10.3390/ijms232012315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/30/2022] Open
Abstract
The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.
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Affiliation(s)
- Mehdi Younessi-Hamzekhanlu
- Department of Forestry and Medicinal Plants, Ahar Faculty of Agriculture and Natural Resources, University of Tabriz, 29 Bahman Blvd., Tabriz P.O. Box 5166616471, Iran
- Correspondence: (M.Y.-H.); (O.G.)
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Correspondence: (M.Y.-H.); (O.G.)
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A Novel Strategy for Constructing an Integrated Linkage Map in an F1 Hybrid Population of Populus deltoides and Populus simonii. Genes (Basel) 2022; 13:genes13101731. [PMID: 36292616 PMCID: PMC9601732 DOI: 10.3390/genes13101731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic linkage maps of the traditional F2 population in inbred lines were estimated from the frequency of recombination events in both parents, providing full genetic information for genetic and genomic studies. However, in outbred forest trees, it is almost impossible to generate the F2 population because of their high heterozygosity and long generation times. We proposed a novel strategy to construct an integrated genetic linkage map that contained both parental recombination information, with restriction-site-associated DNA sequencing (RADSeq) data in an F1 hybrid population of Populus deltoides and Populus simonii. We selected a large number of specific RAD tags to construct the linkage map, each of which contained two SNPs, one heterozygous only in the female parent and the other heterozygous only in the male. Consequently, the integrated map contained a total of 1154 RAD tags and 19 linkage groups, with a total length of 5255.49 cM and an average genetic distance of 4.63 cM. Meanwhile, the two parent-specific linkage maps were also constructed with SNPs that were heterozygous in one parent and homozygous in the other. We found that the integrated linkage map was more consensus with the genomic sequences of P. simonii and P. deltoides. Additionally, the likelihood of the marker order in each linkage group of the integrated map was greater than that in both parental maps. The integrated linkage map was more accurate than the parent-specific linkage maps constructed in the same F1 hybrid population, providing a powerful genetic resource for identifying the quantitative trait loci (QTLs) with dominant effects, assembling genomic sequences, and performing comparative genomics in related Populus species. More importantly, this novel strategy can be used in other outbred species to build an integrated linkage map.
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Habe I, Miyatake K. Identification and characterization of resistance quantitative trait loci against bacterial wilt caused by the Ralstonia solanacearum species complex in potato. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:50. [PMID: 37313419 PMCID: PMC10248640 DOI: 10.1007/s11032-022-01321-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) represents one of the most serious diseases affecting potato cultivation. The development of BW-resistant cultivars represents the most efficient strategy to control this disease. The resistance-related quantitative trait loci (QTLs) in plants against different RSSC strains have not been studied extensively. Therefore, we performed QTL analysis for evaluating BW resistance using a diploid population derived from Solanum phureja, S. chacoense, and S. tuberosum. Plants cultivated in vitro were inoculated with different strains (phylotype I/biovar 3, phylotype I/biovar 4, and phylotype IV/biovar 2A) and incubated at 24 °C or 28 °C under controlled conditions. Composite interval mapping was performed for the disease indexes using a resistant parent-derived map and a susceptible parent-derived map consisting of single-nucleotide polymorphism markers. We identified five major and five minor resistance QTLs on potato chromosomes 1, 3, 5, 6, 7, 10, and 11. The major QTLs PBWR-3 and PBWR-7 conferred stable resistance against Ralstonia pseudosolanacearum (phylotype I) and Ralstonia syzygii (phylotype IV), whereas PBWR-6b was a strain-specific major resistance QTL against phylotype I/biovar 3 and was more effective at a lower temperature. Therefore, we suggest that broad-spectrum QTLs and strain-specific QTLs can be combined to develop the most effective BW-resistant cultivars for specific areas. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01321-9.
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Affiliation(s)
- Ippei Habe
- Nagasaki Agriculture and Forestry Technical Development Center, 3118 Kaizu, Isahaya, Nagasaki, 854-0063 Japan
| | - Koji Miyatake
- Institute of Vegetable and Floriculture Science, NARO, Kusawa 360, Mie, Tsu, 514-2392 Japan
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Possamai T, Wiedemann-Merdinoglu S. Phenotyping for QTL identification: A case study of resistance to Plasmopara viticola and Erysiphe necator in grapevine. FRONTIERS IN PLANT SCIENCE 2022; 13:930954. [PMID: 36035702 PMCID: PMC9403010 DOI: 10.3389/fpls.2022.930954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Vitis vinifera is the most widely cultivated grapevine species. It is highly susceptible to Plasmopara viticola and Erysiphe necator, the causal agents of downy mildew (DM) and powdery mildew (PM), respectively. Current strategies to control DM and PM mainly rely on agrochemical applications that are potentially harmful to humans and the environment. Breeding for resistance to DM and PM in wine grape cultivars by introgressing resistance loci from wild Vitis spp. is a complementary and more sustainable solution to manage these two diseases. During the last two decades, 33 loci of resistance to P. viticola (Rpv) and 15 loci of resistance to E. necator (Ren and Run) have been identified. Phenotyping is salient for QTL characterization and understanding the genetic basis of resistant traits. However, phenotyping remains a major bottleneck for research on Rpv and Ren/Run loci and disease resistance evaluation. A thorough analysis of the literature on phenotyping methods used for DM and PM resistance evaluation highlighted phenotyping performed in the vineyard, greenhouse or laboratory with major sources of variation, such as environmental conditions, plant material (organ physiology and age), pathogen inoculum (genetic and origin), pathogen inoculation (natural or controlled), and disease assessment method (date, frequency, and method of scoring). All these factors affect resistance assessment and the quality of phenotyping data. We argue that the use of new technologies for disease symptom assessment, and the production and adoption of standardized experimental guidelines should enhance the accuracy and reliability of phenotyping data. This should contribute to a better replicability of resistance evaluation outputs, facilitate QTL identification, and contribute to streamline disease resistance breeding programs.
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Affiliation(s)
- Tyrone Possamai
- CREA—Research Centre for Viticulture and Enology, Conegliano, Italy
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Sohi HS, Gill MIS, Chhuneja P, Arora NK, Maan SS, Singh J. Construction of Genetic Linkage Map and Mapping QTL Specific to Leaf Anthocyanin Colouration in Mapping Population 'Allahabad Safeda' × 'Purple Guava (Local)' of Guava ( Psidium guajava L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:2014. [PMID: 35956491 PMCID: PMC9370526 DOI: 10.3390/plants11152014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
In the present investigation, F1 hybrids were developed in guava (Psidium guajava L.) by crossing high leaf-anthocyanin reflective-index (ARI1) content cultivars purple guava (local) 'PG', 'CISH G-1' and low leaf-ARI1 content cultivar Seedless 'SL' with Allahabad Safeda 'AS'. On the basis of phenotypic observations, high ARI1 content was observed in the cross 'AS' × 'PG' (0.214). Further, an SSR-markers-based genetic linkage map was developed from a mapping population of 238 F1 individuals derived from cross 'AS' × 'PG'. The linkage map comprised 11 linkage groups (LGs), spanning 1601.7 cM with an average marker interval distance of 29.61 cM between adjacent markers. Five anthocyanin-content related gene-specific markers from apple were tested for parental polymorphism in the genotypes 'AS' and 'PG'. Subsequently, a marker, viz., 'MdMYB10F1', revealed a strong association with leaf anthocyanin content in the guava mapping population. QTL (qARI-6-1) on LG6 explains much of the variation (PVE = 11.51% with LOD = 4.67) in levels of leaf anthocyanin colouration. This is the first report of amplification/utilization of apple anthocyanin-related genes in guava. The genotypic data generated from the genetic map can be further exploited in future for the enrichment of linkage maps and for identification of complex quantitative trait loci (QTLs) governing economically important fruit quality traits in guava.
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Affiliation(s)
- Harjot Singh Sohi
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Manav Indra Singh Gill
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India;
| | - Naresh Kumar Arora
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Sukhjinder Singh Maan
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
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20
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Sosa-Zuniga V, Vidal Valenzuela Á, Barba P, Espinoza Cancino C, Romero-Romero JL, Arce-Johnson P. Powdery Mildew Resistance Genes in Vines: An Opportunity to Achieve a More Sustainable Viticulture. Pathogens 2022; 11:pathogens11060703. [PMID: 35745557 PMCID: PMC9230758 DOI: 10.3390/pathogens11060703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 12/10/2022] Open
Abstract
Grapevine (Vitis vinifera) is one of the main fruit crops worldwide. In 2020, the total surface area planted with vines was estimated at 7.3 million hectares. Diverse pathogens affect grapevine yield, fruit, and wine quality of which powdery mildew is the most important disease prior to harvest. Its causal agent is the biotrophic fungus Erysiphe necator, which generates a decrease in cluster weight, delays fruit ripening, and reduces photosynthetic and transpiration rates. In addition, powdery mildew induces metabolic reprogramming in its host, affecting primary metabolism. Most commercial grapevine cultivars are highly susceptible to powdery mildew; consequently, large quantities of fungicide are applied during the productive season. However, pesticides are associated with health problems, negative environmental impacts, and high costs for farmers. In paralleled, consumers are demanding more sustainable practices during food production. Therefore, new grapevine cultivars with genetic resistance to powdery mildew are needed for sustainable viticulture, while maintaining yield, fruit, and wine quality. Two main gene families confer resistance to powdery mildew in the Vitaceae, Run (Resistance to Uncinula necator) and Ren (Resistance to Erysiphe necator). This article reviews the powdery mildew resistance genes and loci and their use in grapevine breeding programs.
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Affiliation(s)
- Viviana Sosa-Zuniga
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O’Higgins 340, Santiago 8331150, Chile;
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4560, Santiago 7820436, Chile
| | - Álvaro Vidal Valenzuela
- Foundazione Edmund Mach, Via Edmund Mach 1, San Michele all’Adige (TN), 38010 Trento, Italy;
| | - Paola Barba
- Instituto de Investigaciones Agropecuarias, Avenida Santa Rosa 11610, Santiago 8831314, Chile;
| | - Carmen Espinoza Cancino
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Avenida El Llano Subercaseaux 2801, Santiago 8900000, Chile;
| | - Jesus L. Romero-Romero
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Unidad Sinaloa, Bvd. Juan de Dios Bátiz Paredes 250, Culiacan Rosales 81101, Mexico;
| | - Patricio Arce-Johnson
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O’Higgins 340, Santiago 8331150, Chile;
- Agrijohnson Ltda., Parcela 16b, Miraflores, Curacavi 9630000, Chile
- Correspondence:
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21
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Razar RM, Qi P, Devos KM, Missaoui AM. Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F 1 Populations (Lowland x Coastal and Coastal x Upland). FRONTIERS IN PLANT SCIENCE 2022; 13:739133. [PMID: 35665173 PMCID: PMC9162799 DOI: 10.3389/fpls.2022.739133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of genetic diversity in switchgrass germplasm can be exploited to capture favorable alleles that increase its range of adaptation and biomass yield. The objectives of the study were to analyze the extent of polymorphism and patterns of segregation distortion in two F1 populations and use the linkage maps to locate QTL for biomass yield. We conducted genotyping-by-sequencing on two populations derived from crosses between the allotetraploid lowland genotype AP13 (a selection from "Alamo") and coastal genotype B6 (a selection from PI 422001) with 285 progeny (AB population) and between B6 and the allotetraploid upland VS16 (a selection from "Summer") with 227 progeny (BV population). As predictable from the Euclidean distance between the parents, a higher number of raw variants was discovered in the coastal × upland BV cross (6 M) compared to the lowland × coastal AB cross (2.5 M). The final number of mapped markers was 3,107 on the BV map and 2,410 on the AB map. More segregation distortion of alleles was seen in the AB population, with 75% distorted loci compared to 11% distorted loci in the BV population. The distortion in the AB population was seen across all chromosomes in both the AP13 and B6 maps and likely resulted from zygotic or post-zygotic selection for increased levels of heterozygosity. Our results suggest lower genetic compatibility between the lowland AP13 and the coastal B6 ecotype than between B6 and the upland ecotype VS16. Four biomass QTLs were mapped in the AB population (LG 2N, 6K, 6N, and 8N) and six QTLs in the BV population [LG 1N (2), 8N (2), 9K, and 9N]. The QTL, with the largest and most consistent effect across years, explaining between 8.4 and 11.5% of the variation, was identified on 6N in the AP13 map. The cumulative effect of all the QTLs explained a sizeable portion of the phenotypic variation in both AB and BV populations and the markers associated with them may potentially be used for the marker-assisted improvement of biomass yield. Since switchgrass improvement is based on increasing favorable allele frequencies through recurrent selection, the transmission bias within individuals and loci needs to be considered as this may affect the genetic gain if the favorable alleles are distorted.
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Affiliation(s)
- Rasyidah M. Razar
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Genetic Resources and Improvement Unit, RRIM Research Station, Malaysian Rubber Board, Selangor, Malaysia
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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22
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Du C, Sun P, Cheng X, Zhang L, Wang L, Hu J. QTL mapping of drought-related traits in the hybrids of Populus deltoides 'Danhong'×Populus simonii 'Tongliao1'. BMC PLANT BIOLOGY 2022; 22:238. [PMID: 35545765 PMCID: PMC9092850 DOI: 10.1186/s12870-022-03613-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Poplar trees provide a large amount of wood material, but many parts of the world are arid or semi-arid areas because of insufficient annual precipitation, which seriously affects the growth of poplar trees. Populus simonii 'Tongliao1' shows strong tolerance to stress environments, and Populus deltoides 'Danhong' shows a stronger growth rate in a suitable environment. To identify drought tolerance-related QTLs and genes, an F1 population derived from the cross between the 'Danhong' and 'Tongliao 1' Populus was assessed under drought stress. RESULTS We measured drought-related traits such as the relative height growth, relative diameter growth, leaf senescence number, specific leaf area, and leaf relative water content in the population under control and drought environments. The results showed that drought stress reduced the plant height relative growth, ground diameter relative growth, specific leaf area and leaf relative water content and increased the number of leaf drops. A total of 208 QTLs were identified by QTL mapping analysis, and they consisted of 92, 63 and 53 QTLs under control, drought stress treatment and drought index conditions, respectively. A molecular identification marker for drought tolerance, np2841, which was associated with a QTL (qDLRWC-LG10-1) for relative leaf water content, was initially developed. We mined 187 candidate genes for QTL regions of five traits under a drought environment. The reference genome annotation for Populus trichocarpa and a homologous gene analysis of Arabidopsis thaliana identified two candidate genes, Potri.003G171300 and Potri.012G123900, with significant functions in response to drought stress. We identified five key regulatory genes (Potri.006G273500, Potri.007G111500, Potri.007G111600, Potri.007G111700, and Potri.007G111800) related to drought tolerance through the poplar coexpression network. CONCLUSION In this study, our results indicate that the QTLs can effectively enhance the drought tolerance of poplar. It is a step closer towards unravelling the genetic basis of poplar drought tolerance-related traits, and to providing validated candidate genes and molecular markers for future genetic improvement.
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Affiliation(s)
- Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Xingqi Cheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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23
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High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Flowering Dogwood (Cornus florida). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding for resistance has been recognized as an ideal strategy for controlling the disease in C. florida, but efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. In this study, we mapped quantitative trait loci (QTL) associated with PM resistance/tolerance in two full sibling populations segregating for PM response: Rutgers H4AR15P25 (P25) × Rutgers H4AR15R28 (P28) (n = 195) and Rutgers H4AR15R25 × Rutgers H4AR15P35 (P35) (n = 83). High-density genetic linkage maps were constructed for the mapping populations using double digest restriction-site associated DNA sequencing-derived single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). The P25 × P28 map consisted of 2265 markers, spanning 1520 cM and 11 linkage groups (LGs) with an average marker spacing of 0.69 cM. The P25 × P35 map was constructed with 1788 markers, spanning 1256 cM and 11 LGs, with an average marker spacing of 0.72 cM. The maps had 604 markers in common and exhibited excellent collinearity. Through multiple QTL model mapping, one major QTL (LOD = 11.36 and R2 = 58.9%) was identified in P25 × P35. Furthermore, a minor QTL (LOD = 3.30 and R2 = 7.8%) was detected in P25 × P28. Due to their proximity onLG3, these QTL may be designating the same locus or tightly linked loci. The negative additive effects of both QTL signify that the PM susceptible male parents were contributing susceptibility alleles to the progeny. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs.
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24
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Li Z, Zhao W, Zhang J, Pan Z, Bai S, Tong C. A Novel Strategy to Reveal the Landscape of Crossovers in an F1 Hybrid Population of Populus deltoides and Populus simonii. PLANTS 2022; 11:plants11081046. [PMID: 35448774 PMCID: PMC9025136 DOI: 10.3390/plants11081046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/03/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022]
Abstract
Although the crossover (CO) patterns of different species have been extensively investigated, little is known about the landscape of CO patterns in Populus because of its high heterozygosity and long-time generation. A novel strategy was proposed to reveal the difference of CO rate and interference between Populus deltoides and Populus simonii using their F1 hybrid population. We chose restriction site-associated DNA (RAD) tags that contained two SNPs, one only receiving the CO information from the female P. deltoides and the other from the male P. simonii. These RAD tags allowed us to investigate the CO patterns between the two outbred species, instead of using the traditional backcross populations in inbred lines. We found that the CO rate in P. deltoides was generally greater than that in P. simonii, and that the CO interference was a common phenomenon across the two genomes. The COs landscape of the different Populus species facilitates not only to understand the evolutionary mechanism for adaptability but also to rebuild the statistical model for precisely constructing genetic linkage maps that are critical in genome assembly in Populus. Additionally, the novel strategy could be applied in other outbred species for investigating the CO patterns.
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Affiliation(s)
| | | | | | | | | | - Chunfa Tong
- Correspondence: ; Tel.: +86-025-85428817 (ext. 815)
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25
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Shen F, Bianco L, Wu B, Tian Z, Wang Y, Wu T, Xu X, Han Z, Velasco R, Fontana P, Zhang X. A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple. J Adv Res 2022; 42:149-162. [PMID: 36513410 PMCID: PMC9788957 DOI: 10.1016/j.jare.2022.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants. OBJECTIVES We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes. METHODS A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted. RESULTS By using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively. CONCLUSION The BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.
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Affiliation(s)
- Fei Shen
- College of Horticulture, China Agricultural University, Beijing 100193, China,Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, CREA, Conegliano, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Corresponding authors.
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
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Development of Novel Markers for Yield in Hevea brasiliensis Muell. Arg. Based on Candidate Genes from Biosynthetic Pathways Associated with Latex Production. Biochem Genet 2022; 60:2171-2199. [PMID: 35296963 DOI: 10.1007/s10528-022-10211-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022]
Abstract
Scarcity of functional genetic markers associated with candidate genes (CGs) is a serious constraint for marker-assisted selection in the natural rubber producing tree, Hevea brasiliensis. In order to develop markers associated with rubber yield, five CGs involved in latex biosynthesis were characterized from 16 popular Hevea varieties. Novel SNPs and indels were identified and developed into markers using simple genotyping techniques like allele-specific PCR, CAPS, etc. A progeny population was genotyped using these markers to validate them, to understand their segregation pattern and to map them to a genetic linkage map. Parent-specific maps were constructed using pseudo-test cross strategy with the help of additional markers. The sequence structure information generated will be useful for future studies on gene mapping, functional relevance of coding SNPs and evolution of rubber biosynthesis genes in Hevea. Concurrently, the markers developed may serve as powerful tools for yield-based selection and for genetic diversity and pedigree studies in Hevea. Above all, the marker assays designed for genotyping could be economically carried out in any laboratory having basic molecular biology infrastructure and expertise.
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Branchereau C, Quero-García J, Zaracho-Echagüe NH, Lambelin L, Fouché M, Wenden B, Donkpegan A, Le Dantec L, Barreneche T, Alletru D, Parmentier J, Dirlewanger E. New insights into flowering date in Prunus: fine mapping of a major QTL in sweet cherry. HORTICULTURE RESEARCH 2022; 9:uhac042. [PMID: 35184200 PMCID: PMC9070640 DOI: 10.1093/hr/uhac042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Flowering date is an important trait in Prunus fruit species, especially for their adaptation in a global warming context. Numerous quantitative trait loci (QTLs) have been identified and a major one was previously located on LG4. The objectives of this study were to fine-map this QTL in sweet cherry, to identify robust candidate genes by using the new sweet cherry genome sequence of the cultivar 'Regina' and to define markers usable in marker-assisted selection (MAS). We performed QTL analyses on two populations derived from crosses using cultivars 'Regina' and 'Garnet' as parents. The first one (n = 117) was phenotyped over ten years, while the second one (n = 1386) was evaluated during three years. Kompetitive allele specific PCR (KASP) markers located within the QTL region on LG4 were developed and mapped within this region, consisting in the first fine mapping in sweet cherry. The QTL interval was narrowed from 380 kb to 68 kb and candidate genes were identified by using the genome sequence of 'Regina'. Their expression was analyzed from bud dormancy period to flowering in cultivars 'Regina' and 'Garnet'. Several genes, such as PavBOI-E3, PavSR45a and PavSAUR71, were differentially expressed in these two cultivars and could be then considered as promising candidate genes. Two KASP markers were validated using a population derived from a cross between cultivars 'Regina' and 'Lapins' and two collections, including landraces and modern cultivars. Thanks to the high synteny within the Prunus genus, these results give new insights into the control of flowering date in Prunus species and pave the way for the development of molecular breeding strategies.
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Affiliation(s)
- Camille Branchereau
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - José Quero-García
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Nathalia Helena Zaracho-Echagüe
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA, Centre de Recerca en Agrigenómica CSIC-IRTAUAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Laurine Lambelin
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Mathieu Fouché
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Bénédicte Wenden
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Armel Donkpegan
- SYSAAF-Centre INRAE Val de Loire, UMR BOA, 37380 Nouzilly France
| | - Loïck Le Dantec
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Teresa Barreneche
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - David Alletru
- INRAE, UE 0393, Unité Expérimentale Arboricole, F-33210 Toulenne, France
| | - Julien Parmentier
- INRAE, UE 0393, Unité Expérimentale Arboricole, F-33210 Toulenne, France
| | - Elisabeth Dirlewanger
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
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Wang Z, Ren H, Pang C, Lu G, Xu F, Cheng W, Que Y, Xu L. An autopolyploid-suitable polyBSA-seq strategy for screening candidate genetic markers linked to leaf blight resistance in sugarcane. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:623-636. [PMID: 34775519 DOI: 10.1007/s00122-021-03989-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
An autopolyploid-suitable polyBSA-seq strategy was developed for screening candidate genetic markers linked to leaf blight resistance in sugarcane. Due to the complex genome architecture, the quantitative trait loci mappings and linkage marker selections for agronomic traits of autopolyploid crops were mainly limited to the time-consuming and cost intensive construction of genetic maps. To map resistance-linked markers for sugarcane leaf blight (SLB) caused by Stagonospora tainanensis, the autopolyploid-suitable bulk-segregant analysis based on the sequencing (polyBSA-seq) strategy was successfully applied for the first time. Resistant- and susceptible-bulks (R- and S-bulks) constructed from the extreme-phenotypic sugarcane F1 lines of YT93-159 × ROC22 were deep sequenced with 195.0 × for bulks and 74.4 × for parents. Informative single-dose variants (ISDVs) present as one copy in one parent and null in the other parent were detected based on the genome sequence of LA Purple, an autooctoploid Saccharum officinarum, to screen candidate linkage markers (CLMs). The proportion of the number of short reads harboring ISDVs in the total short reads covering a given genomic position was defined as ISDV index and the ISDVs with indices met the threshold set in this study (0.04-0.14) were selected as CLMs. In total, three resistance- and one susceptibility-related CLMs for SLB resistance were identified by the polyBSA-seq. Among them, two markers on chromosome 10 were less than 300 Kb apart. Furthermore, the RNA-seq was used to calculate the expression level of genes within 1.0 Mb from the aforementioned four CLMs, which demonstrated that twelve genes were differentially expressed between resistant and susceptible clones, including a receptor-like kinase and an ethylene-responsive transcription factor. This is the first reported polyBSA-seq in autopolyploid sugarcane, which specifically tailored for the fast selection of the CLMs and causal genes associated with important agronomic traits.
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Affiliation(s)
- Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, 661600, China
| | - Hui Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guilong Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Cheng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Jinnan W, Ruyue W, Jihong L, Yanting T, Haoping G, Lili H, Dongyue W, Xueling W. Construction of a high-density genetic map using specific-length amplified fragment markers and identification of QTLs for branching angle in poplar. Mol Genet Genomics 2022; 297:345-356. [PMID: 35015131 DOI: 10.1007/s00438-021-01850-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/18/2021] [Indexed: 11/28/2022]
Abstract
Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80 cM for the female and male maps, and 3142.61 cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28 cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64-11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.
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Affiliation(s)
- Wang Jinnan
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Ruyue
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Li Jihong
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China. .,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China. .,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China.
| | - Tian Yanting
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Guo Haoping
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Hou Lili
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Dongyue
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
| | - Wang Xueling
- College of Forestry, Shandong Agricultural University, Taian, 271018, Shangdong, China.,Mountain Tai Forest Ecosystem Research Station of State Forestry and Grassland Administration, Shandong Agricultural University, Taian, 271018, Shangdong, China.,State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Taian, 271018, Shangdong, China
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Lin P, Wang K, Wang Y, Hu Z, Yan C, Huang H, Ma X, Cao Y, Long W, Liu W, Li X, Fan Z, Li J, Ye N, Ren H, Yao X, Yin H. The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. Genome Biol 2022; 23:14. [PMID: 35012630 PMCID: PMC8744323 DOI: 10.1186/s13059-021-02599-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/31/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production. However, the molecular mechanism of the domestication of oil-Camellia is still limited due to the lack of sufficient genomic information. RESULTS To elucidate the genetic and genomic basis of evolution and domestication, here we report a chromosome-scale reference genome of wild oil-Camellia (2.95 Gb), together with transcriptome sequencing data of 221 cultivars. The oil-Camellia genome, assembled by an integrative approach of multiple sequencing technologies, consists of a large proportion of repetitive elements (76.1%) and high heterozygosity (2.52%). We construct a genetic map of high-density corrected markers by sequencing the controlled-pollination hybrids. Genome-wide association studies reveal a subset of artificially selected genes that are involved in the oil biosynthesis and phytohormone pathways. Particularly, we identify the elite alleles of genes encoding sugar-dependent triacylglycerol lipase 1, β-ketoacyl-acyl carrier protein synthase III, and stearoyl-acyl carrier protein desaturases; these alleles play important roles in enhancing the yield and quality of seed oil during oil-Camellia domestication. CONCLUSIONS We generate a chromosome-scale reference genome for oil-Camellia plants and demonstrate that the artificial selection of elite alleles of genes involved in oil biosynthesis contributes to oil-Camellia domestication.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Kailiang Wang
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Chao Yan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Hu Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Yongqing Cao
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Wei Long
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Weixin Liu
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Xinlei Li
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Zhengqi Fan
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Jiyuan Li
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Ning Ye
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Huadong Ren
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China.
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Martins CR, Borghetti F, Moretzsohn MDC, Noronha SED, Valls JFM. Strategies for reintroduction and conservation of Gymnopogon doellii, an endemic grass at risk of extinction. RODRIGUÉSIA 2022. [DOI: 10.1590/2175-7860202273088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract The Brazilian savanna, regionally known as Cerrado, is characterized by a great diversity of physiognomies and holds the highest species diversity and level of endemism among world savannas. However, due mainly to agribusiness, this vegetation is among the most threatened ones, currently presenting alarming rates of extinction. Among the species present in the “red list” we find the endemic Gymnopogon doellii, a grass whose distribution is restricted to a few sites. In the Federal District and surroundings, for example, only one population, with scattered subpopulations, is known, within the limits of the Brasilia National Park. By this study we raised information related to the biology of G. doellii, as population size and distribution, genetic variability and germination characteristics. Besides, we produced seedlings in greenhouse, planted in different physiognomies of the Cerrado and followed them for almost four years to check for their survival, growth and fruiting under natural conditions. Seedlings transplanted to the field presented high rates of recruitment (> 25%), growth patterns similar to wild plants and produced viable caryopses. We recommend transplanting of individuals of G. doellii for both in situ conservation as well as for the revegetation of degraded areas of the Cerrado.
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Hirao T, Matsunaga K, Shirasawa K. Quantitative Trait Loci Analysis Based on High-Density Mapping of Single-Nucleotide Polymorphisms by Genotyping-by-Sequencing Against Pine Wilt Disease in Japanese Black Pine ( Pinus thunbergii). FRONTIERS IN PLANT SCIENCE 2022; 13:850660. [PMID: 35463400 PMCID: PMC9022113 DOI: 10.3389/fpls.2022.850660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/09/2022] [Indexed: 05/05/2023]
Abstract
Identifying genes/loci for resistance to pine wilt disease (PWD) caused by the pine wood nematode (PWN) is beneficial for improving resistance breeding in Pinus thunbergii, but to date, genetic information using molecular markers has been limited. Here, we constructed a high-density linkage map using genotyping-by-sequencing (GBS) and conducted quantitative trait loci (QTL) analysis for PWD resistance for the self-pollinated progeny of "Namikata 73," which is the most resistant variety among resistant varieties of P. thunbergii, following inoculation tests with PWN. An S1 mapping population consisting of the 116 progenies derived from self-pollination of the resistant variety, "Namikata 73" (resistance rank 5 to PWN), was inoculated with PWN isolate Ka-4 and evaluated for disease symptoms. To construct a high-density linkage map, we used single-nucleotide polymorphisms (SNPs) identified by GBS based on next-generation sequencing technology and some anchor DNA markers, expressed sequence tag (EST)-derived SNP markers and EST-derived simple sequence repeat (SSR) markers, and genomic SSR markers. The linkage map had 13 linkage groups (LGs) consisting of 2,365 markers including 2,243 GBS-SNP markers over a total map distance of 1968.4 centimorgans (cM). Results from QTL analysis using phenotype data and the linkage map indicated that PWD resistance is controlled by a single locus located on LG-3, as identified in a previous study. This locus showed overdominant genetic action in the present study. With the confirmation of PWD1 in two different mapping populations (present study and a previous study), the locus associated with this region is thought to be a good target for marker-assisted selection in P. thunbergii breeding programs in order to obtain high levels of resistance to PWD caused by PWN.
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Affiliation(s)
- Tomonori Hirao
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan
- *Correspondence: Tomonori Hirao,
| | - Koji Matsunaga
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Koshi, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
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Possamai T, Wiedemann-Merdinoglu S, Lacombe MC, Dorne MA, Merdinoglu D, De Nardi B, Migliaro D, Velasco R, De Mori G, Cipriani G, Testolin R. Phenotyping and genetic analysis of the Caucasian grape resistance to Erysiphe necator. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20225002010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Oh S, Han H, Kim D. A Novel Pear Scab (Venturia nashicola) Resistance Gene, Rvn3, from Interspecific Hybrid Pear (Pyrus pyrifolia × P. communis). PLANTS 2021; 10:plants10122632. [PMID: 34961103 PMCID: PMC8705610 DOI: 10.3390/plants10122632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 12/03/2022]
Abstract
Asian pear scab is a fungal disease caused by Venturia nashicola. The identification of genes conferring scab resistance could facilitate the breeding of disease-resistant cultivars. Therefore, the present study aimed to identify a scab-resistance gene using an interspecific hybrid population ((Pyrus pyrifolia × P. communis) × P. pyrifolia). Artificial inoculation of V. nashicola was carried out for two years. The segregation ratio (1:1) of resistant to susceptible individuals indicated that resistance to V. nashicola was inherited from P. communis and controlled by a single dominant gene. Based on two years phenotypic data with the Kruskal–Wallis test and interval mapping, 12 common markers were significantly associated with scab resistance. A novel scab resistance gene, Rvn3, was mapped in linkage group 6 of the interspecific hybrid pear, and co-linearity between Rvn3 and one of the apple scab resistance genes, Rvi14, was confirmed. Notably, an insertion in pseudo-chromosome 6 of the interspecific hybrid cultivar showed homology with apple scab resistance genes. Hence, the newly discovered Rvn3 was considered an ortholog of the apple scab resistance gene. Since the mapping population used in the present study is a pseudo-BC1 population, pyramiding of multiple resistance genes to pseudo-BC1 could facilitate the breeding of pear cultivars with durable resistance.
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Affiliation(s)
| | | | - Daeil Kim
- Correspondence: ; Tel.: +82-43-261-2527
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Zhang X, Luan P, Cao D, Hu G. A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp ( Cyprinus carpio). Front Genet 2021; 12:778487. [PMID: 34868267 PMCID: PMC8633483 DOI: 10.3389/fgene.2021.778487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9-15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.
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Affiliation(s)
- Xiaofeng Zhang
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | | | | | - Guo Hu
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
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Possamai T, Wiedemann-Merdinoglu S, Merdinoglu D, Migliaro D, De Mori G, Cipriani G, Velasco R, Testolin R. Construction of a high-density genetic map and detection of a major QTL of resistance to powdery mildew (Erysiphe necator Sch.) in Caucasian grapes (Vitis vinifera L.). BMC PLANT BIOLOGY 2021; 21:528. [PMID: 34763660 PMCID: PMC8582213 DOI: 10.1186/s12870-021-03174-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/09/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Vitis vinifera L. is the most cultivated grapevine species worldwide. Erysiphe necator Sch., the causal agent of grape powdery mildew, is one of the main pathogens affecting viticulture. V. vinifera has little or no genetic resistances against E. necator and the grape industry is highly dependent on agrochemicals. Some Caucasian V. vinifera accessions have been reported to be resistant to E. necator and to have no genetic relationships to known sources of resistance to powdery mildew. The main purpose of this work was the study and mapping of the resistance to E. necator in the Caucasian grapes 'Shavtsitska' and 'Tskhvedianis tetra'. RESULTS The Caucasian varieties 'Shavtsitska' and 'Tskhvedianis tetra' showed a strong partial resistance to E. necator which segregated in two cross populations: the resistant genotypes delayed and limited the pathogen mycelium growth, sporulation intensity and number of conidia generated. A total of 184 seedlings of 'Shavtsitska' x 'Glera' population were genotyped through the Genotyping by Sequencing (GBS) technology and two high-density linkage maps were developed for the cross parents. The QTL analysis revealed a major resistance locus, explaining up to 80.15% of the phenotypic variance, on 'Shavtsitska' linkage group 13, which was associated with a reduced pathogen infection as well as an enhanced plant necrotic response. The genotyping of 105 Caucasian accessions with SSR markers flanking the QTL revealed that the resistant haplotype of 'Shavtsitska' was shared by 'Tskhvedianis tetra' and a total of 25 Caucasian grape varieties, suggesting a widespread presence of this resistance in the surveyed germplasm. The uncovered QTL was mapped in the region where the Ren1 locus of resistance to E. necator, identified in the V. vinifera 'Kishmish vatkana' and related grapes of Central Asia, is located. The genetic analysis conducted revealed that the Caucasian grapes in this study exhibit a resistant haplotype different from that of Central Asian grape accessions. CONCLUSIONS The QTL isolated in 'Shavtsitska' and present in the Caucasian V. vinifera varieties could be a new candidate gene of resistance to E. necator to use in breeding programmes. It co-localizes with the Ren1 locus but shows a different haplotype from that of grapevines of Central Asia. We therefore consider that the Caucasian resistance locus, named Ren1.2, contains a member of a cluster of R-genes, of which the region is rich, and to be linked with, or possibly allelic, to Ren1.
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Affiliation(s)
- Tyrone Possamai
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy.
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy.
| | | | - Didier Merdinoglu
- INRAE, Université de Strasbourg, SVQV UMR-A 1131, 28 rue de Herrlisheim, 68000, Colmar, France
| | - Daniele Migliaro
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy
| | - Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Riccardo Velasco
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
- Institute of Applied Genomics, Science & Technology Park "Luigi Danieli", via Jacopo Linussio 51, 33100, Udine, Italy
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37
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Fan M, Gao Y, Wu Z, Haider S, Zhang Q. Evidence for hexasomic inheritance in Chrysanthemum morifolium Ramat. based on analysis of EST-SSR markers. Genome 2021; 65:75-81. [PMID: 34756106 DOI: 10.1139/gen-2020-0155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chrysanthemums (Chrysanthemum morifolium Ramat.) are ornamental flowers, which are famous worldwide. The mode of inheritance has great implications for the genetic analysis of polyploid species. However, genetic analysis of chrysanthemum has been hampered because of its controversial inheritance mode (disomic or hexasomic). To classify the inheritance mode of chrysanthemums, an analysis of three approaches was carried out in an F1 progeny of 192 offspring using 223 expressed sequence tag-simple sequence repeat (EST-SSR) markers. The analysis included segregation analysis, the ratio of simplex marker alleles linked in coupling to repulsion, as well as the transmission and segregation patterns of EST-SSR marker alleles. After segregation analysis, 204 marker alleles fit hexasomic inheritance and 150 marker alleles fit disomic inheritance, showing that marker alleles were inherited predominantly in a hexasomic manner. Furthermore, the results of the analysis of allele configuration and segregation behavior of five EST-SSR markers also suggested random pairing of chromosomes. Additionally, the ratio of simplex marker alleles linked in coupling to repulsion was 1:0, further supporting hexasomic inheritance. Therefore, it could be inferred that chrysanthemum is a complete or near-complete hexasome.
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Affiliation(s)
- Min Fan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yike Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Zhiping Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Saba Haider
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.,Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Centre for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
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38
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Huff M, Seaman J, Wu D, Zhebentyayeva T, Kelly LJ, Faridi N, Nelson CD, Cooper E, Best T, Steiner K, Koch J, Romero Severson J, Carlson JE, Buggs R, Staton M. A high quality reference genome for Fraxinus pennsylvanica for ash species restoration and research. Mol Ecol Resour 2021; 22:1284-1302. [PMID: 34748273 PMCID: PMC9299157 DOI: 10.1111/1755-0998.13545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]
Abstract
Green ash (Fraxinus pennsylvanica) is the most widely distributed ash tree in North America. Once common, it has experienced high mortality from the non‐native invasive emerald ash borer (EAB; Agrilus planipennis). A small percentage of native green ash trees that remain healthy in long‐infested areas, termed “lingering ash,” display partial resistance to the insect, indicating that breeding and propagating populations with higher resistance to EAB may be possible. To assist in ash breeding, ecology and evolution studies, we report the first chromosome‐level assembly from the genus Fraxinus for F. pennsylvanica with over 99% of bases anchored to 23 haploid chromosomes, spanning 757 Mb in total, composed of 49.43% repetitive DNA, and containing 35,470 high‐confidence gene models assigned to 22,976 Asterid orthogroups. We also present results of range‐wide genetic variation studies, the identification of candidate genes for important traits including potential EAB‐resistance genes, and an investigation of comparative genome organization among Asterids based on this reference genome platform. Residual duplicated regions within the genome probably resulting from a recent whole genome duplication event in Oleaceae were visualized in relation to wild olive (Olea europaea var. sylvestris). We used our F. pennsylvanica chromosome assembly to construct reference‐guided assemblies of 27 previously sequenced Fraxinus taxa, including F. excelsior. Thus, we present a significant step forward in genomic resources for research and protection of Fraxinus species.
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Affiliation(s)
- Matt Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Josiah Seaman
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Di Wu
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tetyana Zhebentyayeva
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nurul Faridi
- USDA Forest Service, Southern Research Station, Saucier, Mississippi, USA.,Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas, USA
| | - Charles Dana Nelson
- USDA Forest Service, Southern Research Station, Saucier, Mississippi, USA.,Forest Health Research and Education Center, University of Kentucky, Lexington, Kentucky, USA
| | - Endymion Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Teodora Best
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kim Steiner
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jennifer Koch
- United States Department of Agriculture, Forest Service, Northern Research Station, Delaware, Ohio, USA
| | - Jeanne Romero Severson
- Department of Biological Sciences, Notre Dame University, 46556, Notre Dame, Indiana, USA
| | - John E Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Richard Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
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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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40
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Macnee N, Hilario E, Tahir J, Currie A, Warren B, Rebstock R, Hallett IC, Chagné D, Schaffer RJ, Bulley SM. Peridermal fruit skin formation in Actinidia sp. (kiwifruit) is associated with genetic loci controlling russeting and cuticle formation. BMC PLANT BIOLOGY 2021; 21:334. [PMID: 34261431 PMCID: PMC8278711 DOI: 10.1186/s12870-021-03025-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The skin (exocarp) of fleshy fruit is hugely diverse across species. Most fruit types have a live epidermal skin covered by a layer of cuticle made up of cutin while a few create an outermost layer of dead cells (peridermal layer). RESULTS In this study we undertook crosses between epidermal and peridermal skinned kiwifruit, and showed that epidermal skin is a semi-dominant trait. Furthermore, backcrossing these epidermal skinned hybrids to a peridermal skinned fruit created a diverse range of phenotypes ranging from epidermal skinned fruit, through fruit with varying degrees of patches of periderm (russeting), to fruit with a complete periderm. Quantitative trait locus (QTL) analysis of this population suggested that periderm formation was associated with four loci. These QTLs were aligned either to ones associated with russet formation on chromosome 19 and 24, or cuticle integrity and coverage located on chromosomes 3, 11 and 24. CONCLUSION From the segregation of skin type and QTL analysis, it appears that skin development in kiwifruit is controlled by two competing factors, cuticle strength and propensity to russet. A strong cuticle will inhibit russeting while a strong propensity to russet can create a continuous dead skinned periderm.
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Affiliation(s)
- Nikolai Macnee
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Jibran Tahir
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | | | - Ben Warren
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant and Food Research Ltd. (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - David Chagné
- PFR, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Robert J Schaffer
- School of Biological Science, The University of Auckland, Auckland, 1146, New Zealand
- PFR, 55 Old Mill Road, RD3, Motueka, 7198, New Zealand
| | - Sean M Bulley
- PFR, 412 No 1 Road RD 2, Te Puke, 3182, New Zealand.
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41
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Song Z, Li X. Recent Advances in Molecular Marker-Assisted Breeding for Quality Improvement of Traditional Chinese Medicine. Curr Pharm Biotechnol 2021; 22:867-875. [PMID: 32351179 DOI: 10.2174/1389201021666200430121013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The quality of Traditional Chinese Medicine (TCM), reflected by its bioactive compounds and associated contents, is directly linked to its clinical efficacy. Therefore, it is of great importance to improve the quality of TCM by increasing the bioactive compound content. METHODS Mapping the active component content-associated QTLs in TCM and further markerassisted breeding has enabled us to rapidly and effectively cultivate new varieties with high bioactive compound contents, which has opened the door for genetic breeding studies on medicinal plants. RESULTS In this paper, a strategy and technical molecular breeding method for TCM are discussed. The development of four methods and progress in functional marker development, as well as the applications of such markers in TCM, are reviewed. CONCLUSION The progress in, challenges of, and future of marker-assisted breeding for quality improvement of TCM are discussed, which provide valuable scientific references for future molecular breeding.
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Affiliation(s)
- Zhenqiao Song
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
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42
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Komaei Koma G, Şekerli M, Snelling JW, Mehlenbacher SA. New Sources of Eastern Filbert Blight Resistance and Simple Sequence Repeat Markers on Linkage Group 6 in Hazelnut ( Corylus avellana L.). FRONTIERS IN PLANT SCIENCE 2021; 12:684122. [PMID: 34194458 PMCID: PMC8238048 DOI: 10.3389/fpls.2021.684122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Commercial production of hazelnut (Corylus avellana) in Oregon's Willamette Valley is threatened by eastern filbert blight (EFB), a serious canker disease caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller. The fungus also prevents the establishment of hazelnut orchards in eastern North America. Genetic resistance is considered the most effective way to control the disease. A high level of EFB resistance was first discovered in 'Gasaway'. This resistance is conferred by a dominant allele at a single locus on linkage group 6 (LG6). Resistance from several additional sources has been assigned to the same chromosomal region. In this study, new simple sequence repeat (SSR) markers were developed for the resistance region on LG6 and new sources of resistance were investigated. Forty-two new SSR markers were developed from four contigs in the genome sequence of 'Jefferson' hazelnut, characterized, and nine of them were placed on LG6 of the genetic map. Accessions representing 12 new sources of EFB resistance were crossed with susceptible selections resulting in 18 seedling populations. Segregation ratios in the seedling populations fit the expected 1:1 ratio for 10 sources, while one source showed an excess of resistant seedlings and another showed an excess of susceptible seedlings. Based on correlation of disease response and scores of SSR markers in the 'Gasaway' resistance region in the seedlings, eight resistance sources were assigned to LG6. Linkage maps were constructed for each progeny using SSR markers. The LG6 resistance sources include two selections (#23 and #26) from the Russian Research Institute of Forestry and Mechanization near Moscow, four selections from southern Russia, one selection (OSU 1185.126) from Crimea, one selection (OSU 533.129) from Michigan, Corylus heterophylla 'Ogyoo' from the South Korea, and the interspecific hybrid 'Estrella #1'. These new LG6 resistance sources and SSR markers should be useful in breeding new cultivars, including the pyramiding of resistance genes. For the other four resistance sources (Moscow #37, hybrid selection OSU 401.014, C. americana 'Winkler' and C. americana OSU 366.060), SSR marker scores on linkage groups 6, 7 and 2 were not correlated with disease response and merit further investigation.
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43
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Quero-García J, Letourmy P, Campoy JA, Branchereau C, Malchev S, Barreneche T, Dirlewanger E. Multi-year analyses on three populations reveal the first stable QTLs for tolerance to rain-induced fruit cracking in sweet cherry (Prunus avium L.). HORTICULTURE RESEARCH 2021; 8:136. [PMID: 34059661 PMCID: PMC8166915 DOI: 10.1038/s41438-021-00571-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 06/01/2023]
Abstract
Rain-induced fruit cracking is a major problem in sweet cherry cultivation. Basic research has been conducted to disentangle the physiological and mechanistic bases of this complex phenomenon, whereas genetic studies have lagged behind. The objective of this work was to disentangle the genetic determinism of rain-induced fruit cracking. We hypothesized that a large genetic variation would be revealed, by visual field observations conducted on mapping populations derived from well-contrasted cultivars for cracking tolerance. Three populations were evaluated over 7-8 years by estimating the proportion of cracked fruits for each genotype at maturity, at three different areas of the sweet cherry fruit: pistillar end, stem end, and fruit side. An original approach was adopted to integrate, within simple linear models, covariates potentially related to cracking, such as rainfall accumulation before harvest, fruit weight, and firmness. We found the first stable quantitative trait loci (QTLs) for cherry fruit cracking, explaining percentages of phenotypic variance above 20%, for each of these three types of cracking tolerance, in different linkage groups, confirming the high complexity of this trait. For these and other QTLs, further analyses suggested the existence of at least two-linked QTLs in each linkage group, some of which showed confidence intervals close to 5 cM. These promising results open the possibility of developing marker-assisted selection strategies to select cracking-tolerant sweet cherry cultivars. Further studies are needed to confirm the stability of the reported QTLs over different genetic backgrounds and environments and to narrow down the QTL confidence intervals, allowing the exploration of underlying candidate genes.
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Affiliation(s)
- José Quero-García
- INRAE, Biologie du Fruit et Pathologie, Université de Bordeaux, UMR 1332, F-33140, Villenave d'Ornon, France.
| | - Philippe Letourmy
- CIRAD, UPR AIDA, University of Montpellier, TA B-115/02, Avenue Agropolis, 34398, Montpellier Cedex 5, France
| | - José Antonio Campoy
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, 50289, Cologne, Germany
| | - Camille Branchereau
- INRAE, Biologie du Fruit et Pathologie, Université de Bordeaux, UMR 1332, F-33140, Villenave d'Ornon, France
| | - Svetoslav Malchev
- Fruit Growing Institute - Plovdiv, 12 Ostromila Str., 4004, Plovdiv, Bulgaria
| | - Teresa Barreneche
- INRAE, Biologie du Fruit et Pathologie, Université de Bordeaux, UMR 1332, F-33140, Villenave d'Ornon, France
| | - Elisabeth Dirlewanger
- INRAE, Biologie du Fruit et Pathologie, Université de Bordeaux, UMR 1332, F-33140, Villenave d'Ornon, France
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44
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Popowski E, Thomson SJ, Knäbel M, Tahir J, Crowhurst RN, Davy M, Foster TM, Schaffer RJ, Tustin DS, Allan AC, McCallum J, Chagné D. Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing. G3-GENES GENOMES GENETICS 2021; 11:6261761. [PMID: 34009255 PMCID: PMC8495948 DOI: 10.1093/g3journal/jkab142] [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: 02/11/2021] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
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Affiliation(s)
- Elizabeth Popowski
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | | | | | | | - Marcus Davy
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | - Robert J Schaffer
- Plant & Food Research, Motueka, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Andrew C Allan
- Plant & Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - David Chagné
- Plant & Food Research, Palmerston North, New Zealand
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45
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Terakami S, Adachi Y, Takeuchi Y, Takada N, Nishio S, Saito T, Yamamoto T. Development of an SSR marker set for efficient selection for resistance to black spot disease in pear breeding. BREEDING SCIENCE 2021; 71:240-252. [PMID: 34377072 PMCID: PMC8329887 DOI: 10.1270/jsbbs.20136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/24/2020] [Indexed: 06/13/2023]
Abstract
Black spot disease, which is caused by Alternaria alternata (Fries) Keissler Japanese pear pathotype, is one of the most harmful diseases in Japanese pear cultivation. Because of the potential harm of fungicides to consumers and the environment, resistant cultivars are desired. In this study, to enable efficient marker-assisted selection in pear breeding, we conducted comprehensive inoculation tests and genotyping with 207 pear cultivars. We identified a marker set (Mdo.chr11.27 and Mdo.chr11.34) suitable for selection for black spot resistance. In most susceptible cultivars, Mdo.chr11.27 amplified a 220-bp band and Mdo.chr11.34 amplified a 259-bp band. The genotype of Mdo.chr11.34 corresponds perfectly to the estimated genotype of Japanese pears susceptible to black spot disease. Using linkage analysis, we identified the positions of the gene for susceptibility to black spot disease in Chinese pear. Mdo.chr11.27 and Mdo.chr11.34 were tightly linked to susceptibility in Chinese pear, and the susceptibility gene was mapped at the top of linkage group 11, similar to that in Japanese pear. This marker set and the accumulation of phenotypic data will enable efficient marker-assisted breeding for black spot resistance in pear breeding.
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Affiliation(s)
- Shingo Terakami
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Yoshihiko Adachi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Yukie Takeuchi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Norio Takada
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Toshihiro Saito
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
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46
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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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Candidate genes linked to QTL regions associated with fatty acid composition in oil palm. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00563-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Yu L, Ma X, Deng B, Yue J, Ming R. Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach. Mol Genet Genomics 2021; 296:41-53. [PMID: 32955620 DOI: 10.1007/s00438-020-01723-1724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/04/2020] [Indexed: 05/18/2023]
Abstract
Spinach (Spinacia olracea L.) is a dioecious leafy vegetable with a highly repetitive genome of around 990 Mb, which is challenging for de-novo genome assembly. In our study, a segregating F1 (double pseudo-testcross) population from 'Viroflay' × 'Cornell-NO. 9' was used for genetic mapping by resequencing genotyping. In the paternal 'Cornell-NO. 9' map, 212,414 SNPs were mapped, and the total linkage distance was 476.83 cM; the maternal 'Viroflay' map included 29,282 SNPs with 401.28 cM total genetic distance. Both paternal and maternal maps have the expected number of six linkage groups (LGs). A non-recombining region with 5678 SNPs (39 bin markers) co-segregates with sex type which located at 45.2 cM of LG1 in the 'Cornell-NO. 9' map while indicates the sex determination region (SDR). Integration of two maps into a consensus map guided us to anchor additional 1242 contigs to six pseudomolecules from the published reference genome, which improved additional 233 Mb (23.4%) assembly based on spinach estimated genome size. Particularly, the X counterpart of SDR in our assembly is estimated around 18.4 Mb which locates at the largest chromosome, as consensus with sex-biased FISH signals from previous cytogenetics studies. The region is featured by reduced gene density, higher percentage of repetitive sequences, and no recombination. Our linkage maps provide the resource for improving spinach genome de-novo assembly and identification of sex-determining genes in spinach.
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Affiliation(s)
- Li'ang Yu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ban Deng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jingjing Yue
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality. G3-GENES GENOMES GENETICS 2020; 10:4513-4529. [PMID: 33067307 PMCID: PMC7718743 DOI: 10.1534/g3.120.401452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied from 0.31 for glucose content with the Bayesian LASSO (BL) to 0.78 for ethylene production with RR-BLUP, which yielded the most accurate predictions in comparison to Bayesian models and only 10% out of 61,030 SNPs were sufficient to reach accurate predictions. Useful insights were provided on the genetic architecture of apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTL. Furthermore, multivariate modeling yielded promising outcomes in terms of PA within training partitions partially phenotyped for target traits. This provides a useful framework for the implementation of indirect selection based on easy-to-measure traits. Thus, we highlighted the main levers to take into account for the implementation of GS for fruit quality in apricot, but also to improve the genetic gain in perennial species.
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50
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Zeng D, Yang C, Li Q, Zhu W, Chen X, Peng M, Chen X, Lin Y, Wang H, Liu H, Liang J, Liu Q, Zhao Y. Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2020; 21:857. [PMID: 33267780 PMCID: PMC7709431 DOI: 10.1186/s12864-020-07254-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Background Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. Results In this study, we constructed a high-density genetic map of the Pacific white shrimp (Litopenaeus vannamei) using specific length amplified fragment sequencing (SLAF-seq). The constructed genetic map contained 17,338 polymorphic markers spanning 44 linkage groups, with a total distance of 6360.12 centimorgans (cM) and an average distance of 0.37 cM. Using this genetic map, we identified a quantitative trait locus (QTL) that explained 7.41–8.46% of the phenotypic variance in L. vannamei survival time under acute ammonia stress. We then sequenced the transcriptomes of the most ammonia-tolerant and the most ammonia-sensitive individuals from each of four genetically distinct L. vannamei families. We found that 7546 genes were differentially expressed between the ammonia-tolerant and ammonia-sensitive individuals. Using QTL analysis and the transcriptomes, we identified one candidate gene (annotated as an ATP synthase g subunit) associated with ammonia tolerance. Conclusions In this study, we constructed a high-density genetic map of L. vannamei and identified a QTL for ammonia tolerance. By combining QTL and transcriptome analyses, we identified a candidate gene associated with ammonia tolerance. Our work provides the basis for future genetic studies focused on molecular marker-assisted selective breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07254-x.
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Affiliation(s)
- Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, 430070, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jingzhen Liang
- Life Science Research Institute, Guangxi University, Nanning, 530004, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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