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Magon G, De Rosa V, Martina M, Falchi R, Acquadro A, Barcaccia G, Portis E, Vannozzi A, De Paoli E. Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1293186. [PMID: 38148866 PMCID: PMC10750425 DOI: 10.3389/fpls.2023.1293186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
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Affiliation(s)
- Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
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Kaya HB, Dilli Y, Oncu-Oner T, Ünal A. Exploring genetic diversity and population structure of a large grapevine ( Vitis vinifera L.) germplasm collection in Türkiye. FRONTIERS IN PLANT SCIENCE 2023; 14:1121811. [PMID: 37235025 PMCID: PMC10208073 DOI: 10.3389/fpls.2023.1121811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/06/2023] [Indexed: 05/28/2023]
Abstract
Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r2 was between 0.45 and 0.2 and became flat when r2 was 0.05. The average LD decay for the entire genome was 30 kb when r2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.
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Affiliation(s)
- Hilal Betul Kaya
- Department of Bioengineering, Manisa Celal Bayar University, Manisa, Türkiye
| | - Yıldız Dilli
- Republic of Türkiye Ministry of Agriculture and Forestry, Viticulture Research Institute, Manisa, Türkiye
| | - Tulay Oncu-Oner
- Department of Bioengineering, Manisa Celal Bayar University, Manisa, Türkiye
| | - Akay Ünal
- Republic of Türkiye Ministry of Agriculture and Forestry, Viticulture Research Institute, Manisa, Türkiye
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A 69 kbp Deletion at the Berry Color Locus Is Responsible for Berry Color Recovery in Vitis vinifera L. Cultivar 'Riesling Rot'. Int J Mol Sci 2022; 23:ijms23073708. [PMID: 35409066 PMCID: PMC8998622 DOI: 10.3390/ijms23073708] [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: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
‘Riesling Weiss’ is a white grapevine variety famous worldwide for fruity wines with higher acidity. Hardly known is ‘Riesling Rot’, a red-berried variant of ‘Riesling Weiss’ that disappeared from commercial cultivation but has increased in awareness in the last decades. The question arises of which variant, white or red, is the original and, consequently, which cultivar is the true ancestor. Sequencing the berry color locus of ‘Riesling Rot’ revealed a new VvmybA gene variant in one of the two haplophases called VvmybA3/1RR. The allele displays homologous recombination of VvmybA3 and VvmybA1 with a deletion of about 69 kbp between both genes that restores VvmybA1 transcripts. Furthermore, analysis of ‘Riesling Weiss’, ‘Riesling Rot’, and the ancestor ‘Heunisch Weiss’ along chromosome 2 using SSR (simple sequence repeat) markers elucidated that the haplophase of ‘Riesling Weiss’ was inherited from the white-berried parent variety ‘Heunisch Weiss’. Since no color mutants of ‘Heunisch Weiss’ are described that could have served as allele donors, we concluded that, in contrast to the public opinion, ‘Riesling Rot’ resulted from a mutational event in ‘Riesling Weiss’ and not vice versa.
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Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map. PLANTS 2022; 11:plants11050696. [PMID: 35270166 PMCID: PMC8912348 DOI: 10.3390/plants11050696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Abstract
Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.
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Men Y, Li JR, Shen HL, Yang YM, Fan ST, Li K, Guo YS, Lin H, Liu ZD, Guo XW. VaAPRT3 Gene is Associated With Sex Determination in Vitis amurensis. Front Genet 2022; 12:727260. [PMID: 35003203 PMCID: PMC8733387 DOI: 10.3389/fgene.2021.727260] [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: 06/18/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
In the past decade, progress has been made in sex determination mechanism in Vitis. However, genes responsible for sexual differentiation and its mechanism in V. amurensis remain unknown. Here, we identify a sex determination candidate gene coding adenine phosphoribosyl transferase 3 (VaAPRT3) in V. amurensis. Cloning and sequencing of the VaAPRT3 gene allowed us to develop a molecular marker able to discriminate female individuals from males or hermaphrodites based on a 22-bp InDel. Gene expression and endogenous cytokinin content analysis revealed that the VaAPRT3 gene is involved in sex determination or, to be precise, in female organ differentiation, through regulating cytokinin metabolism in V. amurensis. This study enlarged the understanding of sex determination mechanism in the genus Vitis, and the sex marker could be used as a helpful tool for sexual identification in breeding programs as well as in investigation and collection of V. amurensis germplasms.
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Affiliation(s)
- Yan Men
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Ji-Rui Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hai-Lin Shen
- Institute of Pomology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Yi-Ming Yang
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shu-Tian Fan
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yin-Shan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhen-Dong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiu-Wu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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Volynkin V, Vasylyk I, Volodin V, Grigoreva E, Karzhaev D, Lushchay E, Ulianich P, Volkov V, Risovannaya V, Blinova S, Alekseev J, Gorislavets S, Likhovskoi V, Beatovic A, Potokina E. The Assessment of Agrobiological and Disease Resistance Traits of Grapevine Hybrid Populations ( Vitis vinifera L. × Muscadinia rotundifolia Michx.) in the Climatic Conditions of Crimea. PLANTS 2021; 10:plants10061215. [PMID: 34203712 PMCID: PMC8232157 DOI: 10.3390/plants10061215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 11/24/2022]
Abstract
The Crimean autochthonous grape varieties are unique by their origin and serve as a valuable source for breeding new cultivars with increased salt and frost resistance, as well as high-quality berries. However, they suffer from fungal pathogens, as the dry and hot summer months contribute to the epiphytotic course of diseases. An increase in the resistance of Crimean grape varieties is currently achieved through interspecific hybridization. In this study, we describe the genetic and agrobiological diversity of three hybrid populations obtained using the Vitis interspecific hybrid ‘Magarach 31-77-10′ as a female parent and Muscadinia rotundifolia × Vitis vinifera BC5 hybrid plants as male parents. The hybrid nature of the populations was assessed using RADseq high-throughput genotyping. We discovered 12,734 SNPs, which were common to all three hybrid populations. We also proved with the SSR markers that the strong powdery and downy mildew resistance of the paternal genotypes is determined by the dominant Run1/Rpv1 locus inherited from M. rotundifolia. As a result, the disease development score (R, %) for both mildew diseases in the female parent ‘Magarach 31-77-10’ was three times higher than in male parents 2000-305-143 and 2000-305-163 over two years of phytopathological assessment. The highest values of yield-contributing traits (average bunch weight ~197 g and 1.3 kg as yield per plant) were detected in the population 4-11 (♀M. No. 31-77-10 × 2000-305-163). Despite the epiphytotic development of PM, the spread of oidium to the vegetative organs of hybrids 4-11 did not exceed 20%. Some hybrid genotypes with high productivity and resistance to pathogens were selected for further assessment as promising candidates for new varieties.
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Affiliation(s)
- Vladimir Volynkin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Irina Vasylyk
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Vitalii Volodin
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Elizaveta Grigoreva
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia;
| | - Dmitry Karzhaev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
| | - Ekaterina Lushchay
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Pavel Ulianich
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- All-Russian Research Institute of Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Vladimir Volkov
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
| | - Valentina Risovannaya
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Sofiya Blinova
- Syntol, 127434 Moscow, Russia;
- All-Russian Research Institute of Agricultural Biotechnology, 127434 Moscow, Russia
| | - Jakov Alekseev
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Syntol, 127434 Moscow, Russia;
| | - Svetlana Gorislavets
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Vladimir Likhovskoi
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
| | - Aleksandar Beatovic
- Information Technologies and Programming Faculty, ITMO University, 197101 St. Petersburg, Russia;
| | - Elena Potokina
- All-Russian National Research Institute of Viticulture and Winemaking ‘Magarach’ RAS, 298600 Yalta, Russia; (V.V.); (I.V.); (V.V.); (E.G.); (D.K.); (E.L.); (P.U.); (V.V.); (V.R.); (J.A.); (S.G.); (V.L.)
- Institute of Forest and Natural Resources Management, Saint Petersburg State Forest Technical University, 194021 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-911-084-1422
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Identification of genomic regions associated with early plant vigour in lentil (Lens culinaris). J Genet 2020. [DOI: 10.1007/s12041-020-1182-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhao Y, Zhao Y, Guo Y, Su K, Shi X, Liu D, Zhang J. High-density genetic linkage-map construction of hawthorn and QTL mapping for important fruit traits. PLoS One 2020; 15:e0229020. [PMID: 32045463 PMCID: PMC7012432 DOI: 10.1371/journal.pone.0229020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/28/2020] [Indexed: 11/30/2022] Open
Abstract
Few reports exist on QTL mapping of the important economic traits of hawthorn. We hybridized the cultivars ‘Shandongdamianqiu’ (female parent) and ‘Xinbinruanzi’ (male parent), and 130 F1 individuals and the two parents were used for RAD-seq, SNP development, and high-density linkage map construction. Three genetic maps were obtained, one for each of the parents and an integrated one. In these three maps, 17 linkage groups were constructed. The female and male parent maps contained 2657 and 4088 SNP markers, respectively, and had genetic distances of 2689.65 and 2558.41 cM, respectively, whereas the integrated map was 2470.02 cM, and contained 6,384 SNP markers. QTL mapping based on six agronomic traits, namely fruit transverse diameter, vertical diameter, single fruit weight, pericarp brittleness, pericarp puncture hardness, and average sarcocarp firmness were conducted, and 25 QTLs were detected in seven linkage groups. Explained phenotypic variation rate ranged from 17.7% to 35%. This genetic map contains the largest number of molecular markers ever obtained from hawthorn and will provide an important future reference for fine QTL mapping of economic traits and molecular assisted selection of hawthorn.
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Affiliation(s)
- Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Yidi Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, P.R.C
- * E-mail: (YG); (JZ)
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Xiaochang Shi
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Di Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R.C
| | - Jijun Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and technology, Qinhuangdao, P.R.C
- * E-mail: (YG); (JZ)
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Zhu J, Guo Y, Su K, Liu Z, Ren Z, Li K, Guo X. Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing. BMC PLANT BIOLOGY 2018; 18:347. [PMID: 30541441 PMCID: PMC6291968 DOI: 10.1186/s12870-018-1575-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/26/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding. Development of a large set of single nucleotide polymorphisms (SNPs) via next-generation sequencing (NGS)-based methods, restriction-site associated DNA sequencing (RAD-seq), and the generation of a highly saturated genetic map help improve fine mapping of quantitative trait loci (QTL). RESULTS We generated a highly saturated genetic map to identify significant traits in two elite grape cultivars and 176 F1 plants. In total, 1,426,967 high-quality restriction site-associated DNA tags were detected; 51,365, 23,683, and 70,061 markers were assessed in 19 linkage groups (LGs) for the maternal, paternal, and integrated maps, respectively. Our map was highly saturated in terms of marker density and average "Gap ≤ 5 cM" percentage. CONCLUSIONS In this study, RAD-seq of 176 F1 plants and their parents yielded 8,481,484 SNPs and 1,646,131 InDel markers, of which 65,229 and 4832, respectively, were used to construct a highly saturated genetic map for grapevine. This map is expected to facilitate genetic studies on grapevine, including an evaluation of grapevine and deciphering the genetic basis of economically and agronomically important traits. Our findings provide basic essential genetic data the grapevine genetic research community, which will lead to improvements in grapevine breeding.
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Affiliation(s)
- Junchi Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
- Ministry of Education Key Laboratory of Protected Horticulture, Shenyang, 110866 People’s Republic of China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Zhihua Ren
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
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Dong Z, Liu W, Li X, Tan W, Zhao Q, Wang M, Ren R, Ma X, Tang X. Genetic relationships of 34 grapevine varieties and construction of molecular fingerprints by SSR markers. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1450162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Zhigang Dong
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Wei Liu
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Xiaomei Li
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Wei Tan
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Qifeng Zhao
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Min Wang
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Rui Ren
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Xiaohe Ma
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
| | - Xiaoping Tang
- Shanxi Academy of Agricultural Sciences /Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Pomology Institute, Taiyuan, Shanxi, PR China
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Wang J, Su K, Guo Y, Xing H, Zhao Y, Liu Z, Li K, Guo X. Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing. PLoS One 2017; 12:e0181728. [PMID: 28746364 PMCID: PMC5528875 DOI: 10.1371/journal.pone.0181728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/06/2017] [Indexed: 12/30/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.
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Affiliation(s)
- Jiahui Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
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Teh SL, Fresnedo-Ramírez J, Clark MD, Gadoury DM, Sun Q, Cadle-Davidson L, Luby JJ. Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:1. [PMID: 28127252 PMCID: PMC5226326 DOI: 10.1007/s11032-016-0586-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 11/01/2016] [Indexed: 05/22/2023]
Abstract
Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F1 families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from 'Seyval blanc', through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.
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Affiliation(s)
- Soon Li Teh
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108 USA
| | | | - Matthew D. Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108 USA
| | - David M. Gadoury
- School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456 USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853 USA
| | | | - James J. Luby
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108 USA
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Chen J, Wang N, Fang LC, Liang ZC, Li SH, Wu BH. Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries. BMC PLANT BIOLOGY 2015; 15:28. [PMID: 25644551 PMCID: PMC4329212 DOI: 10.1186/s12870-015-0428-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/15/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND QTLs controlling individual sugars and acids (fructose, glucose, malic acid and tartaric acid) in grape berries have not yet been identified. The present study aimed to construct a high-density, high-quality genetic map of a winemaking grape cross with a complex parentage (V. vinifera × V. amurensis) × ((V. labrusca × V. riparia) × V. vinifera), using next-generation restriction site-associated DNA sequencing, and then to identify loci related to phenotypic variability over three years. RESULTS In total, 1 826 SNP-based markers were developed. Of these, 621 markers were assembled into 19 linkage groups (LGs) for the maternal map, 696 for the paternal map, and 1 254 for the integrated map. Markers showed good linear agreement on most chromosomes between our genetic maps and the previously published V. vinifera reference sequence. However marker order was different in some chromosome regions, indicating both conservation and variation within the genome. Despite the identification of a range of QTLs controlling the traits of interest, these QTLs explained a relatively small percentage of the observed phenotypic variance. Although they exhibited a large degree of instability from year to year, QTLs were identified for all traits but tartaric acid and titratable acidity in the three years of the study; however only the QTLs for malic acid and β ratio (tartaric acid-to-malic acid ratio) were stable in two years. QTLs related to sugars were located within ten LGs (01, 02, 03, 04, 07, 09, 11, 14, 17, 18), and those related to acids within three LGs (06, 13, 18). Overlapping QTLs in LG14 were observed for fructose, glucose and total sugar. Malic acid, total acid and β ratio each had several QTLs in LG18, and malic acid also had a QTL in LG06. A set of 10 genes underlying these QTLs may be involved in determining the malic acid content of berries. CONCLUSION The genetic map constructed in this study is potentially a high-density, high-quality map, which could be used for QTL detection, genome comparison, and sequence assembly. It may also serve to broaden our understanding of the grape genome.
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Affiliation(s)
- Jie Chen
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Nian Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Lin-Chuan Fang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Zhen-Chang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China.
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China.
| | - Ben-Hong Wu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China.
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Guo Y, Shi G, Liu Z, Zhao Y, Yang X, Zhu J, Li K, Guo X. Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.). FRONTIERS IN PLANT SCIENCE 2015; 6:393. [PMID: 26089826 PMCID: PMC4454882 DOI: 10.3389/fpls.2015.00393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/16/2015] [Indexed: 05/04/2023]
Abstract
In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.
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Affiliation(s)
| | | | | | - Yuhui Zhao
- *Correspondence: Yuhui Zhao and Xiuwu Guo, College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning, China ;
| | | | | | | | - Xiuwu Guo
- *Correspondence: Yuhui Zhao and Xiuwu Guo, College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning, China ;
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Fechter I, Hausmann L, Zyprian E, Daum M, Holtgräwe D, Weisshaar B, Töpfer R. QTL analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in Vitis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1857-72. [PMID: 25112201 PMCID: PMC4145202 DOI: 10.1007/s00122-014-2310-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/05/2014] [Indexed: 05/21/2023]
Abstract
In the recent past, genetic analyses of grapevine focused mainly on the identification of resistance loci for major diseases such as powdery and downy mildew. Currently, breeding programs make intensive use of these results by applying molecular markers linked to the resistance traits. However, modern genetics also allows to address additional agronomic traits that have considerable impact on the selection of grapevine cultivars. In this study, we have used linkage mapping for the identification and characterization of flowering time and ripening traits in a mapping population from a cross of V3125 ('Schiava Grossa' × 'Riesling') and the interspecific rootstock cultivar 'Börner' (Vitis riparia × Vitis cinerea). Comparison of the flowering time QTL mapping with data derived from a second independent segregating population identified several common QTLs. Especially a large region on linkage group 1 proved to be of special interest given the genetic divergence of the parents of the two populations. The proximity of the QTL region contains two CONSTANS-like genes. In accordance with data from other plants such as Arabidopsis thaliana and Oryza sativa, we hypothesize that these genes are major contributors to control the time of flowering in Vitis.
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Affiliation(s)
- Iris Fechter
- Institute for Grapevine Breeding, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany,
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16
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Guo Y, Lin H, Liu Z, Zhao Y, Guo X, Li K. SSR and SRAP marker-based linkage map of Vitis vinifera L. BIOTECHNOL BIOTEC EQ 2014; 28:221-229. [PMID: 26019507 PMCID: PMC4434142 DOI: 10.1080/13102818.2014.907996] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/09/2013] [Indexed: 11/13/2022] Open
Abstract
An F1 population was created by the cross ‘87-1’ × ‘9-22’. The female parent ‘87-1’ was an extremely early maturing cultivar with strong flavour. The male parent was an excellent breeding line producing large berries maturing late. The mapping population included 149 randomly chosen individuals. Molecular genetic map for each parent and the consensus map were constructed using simple sequence repeat and sequence-related amplified polymorphism markers by software JoinMap 3.0. The ‘87-1’ map covers a total length of 1272.9 cM distributed in 21 linkage groups and consists of 163 molecular markers with an average distance between adjacent markers of 8.9 cM. The ‘9-22’ map covers a total length of 1267.4 cM distributed in 20 linkage groups and consists of 158 molecular markers with an average distance between adjacent markers of 9.1 cM. The consensus map covers a total length of 1537.1 cM distributed in 21 linkage groups and one doublet and consists of 217 molecular markers with an average distance of 7.8 cM between adjacent markers. The length of the linkage groups is 69.8 cM on average. The map covers the 19 chromosomes of the Vitis genome and can lay a solid foundation for further studies such as quantative trait loci (QTL) mapping of correlated traits and marker-assisted selection.
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Affiliation(s)
- Yinshan Guo
- Pomology Department, College of Horticulture, Shenyang Agricultural University, Shenyang , P.R. China
| | - Hong Lin
- Pomology Department, College of Horticulture, Shenyang Agricultural University, Shenyang , P.R. China
| | - Zhendong Liu
- Pomology Department, College of Horticulture, Shenyang Agricultural University, Shenyang , P.R. China
| | - Yuhui Zhao
- Pomology Department, College of Horticulture, Shenyang Agricultural University, Shenyang , P.R. China
| | - Xiuwu Guo
- Pomology Department, College of Horticulture, Shenyang Agricultural University, Shenyang , P.R. China
| | - Kun Li
- Pomology Department, College of Horticulture, Shenyang Agricultural University, Shenyang , P.R. China
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17
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Liu C, Fan X, Jiang J, Guo D, Sun H, Zhang Y, Feng J. Genetic Diversity of Chinese Wild Grape Species by SSR and SRAP Markers. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Chonghuai Liu
- Henan Agricultural University, College of Horticulture, Zhengzhou, Henan Province, P.R. China
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou, Henan Province, P.R. China
| | - Xiucai Fan
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou, Henan Province, P.R. China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou, Henan Province, P.R. China
| | - Dalong Guo
- Henan University of Science and Technology, College of Forestry, Luoyang, Henan Province, P.R. China
| | - Haisheng Sun
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou, Henan Province, P.R. China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou, Henan Province, P.R. China
| | - Jiancan Feng
- Henan Agricultural University, College of Horticulture, Zhengzhou, Henan Province, P.R. China
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18
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Hvarleva T, Russanov K, Bakalova A, Zhiponova M, Djakova G, Atanassov A, Atanassov I. Microsatellite Linkage Map Based on F2 Population from Bulgarian Grapevine Cultivar Storgozia. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10817626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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20
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Barba P, Cadle-Davidson L, Harriman J, Glaubitz JC, Brooks S, Hyma K, Reisch B. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:73-84. [PMID: 24072208 DOI: 10.1007/s00122-013-2202-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
Abstract
Improved efficacy and durability of powdery mildew resistance can be enhanced via knowledge of the genetics of resistance and susceptibility coupled with the development of high-resolution maps to facilitate the stacking of multiple resistance genes and other desirable traits. We studied the inheritance of powdery mildew (Erysiphe necator) resistance and susceptibility of wild Vitis rupestris B38 and cultivated V. vinifera 'Chardonnay', finding evidence for quantitative variation. Molecular markers were identified using genotyping-by-sequencing, resulting in 16,833 single nucleotide polymorphisms (SNPs) based on alignment to the V. vinifera 'PN40024' reference genome sequence. With an average density of 36 SNPs/Mbp and uniform coverage of the genome, this 17K set was used to identify 11 SNPs on chromosome 7 associated with a resistance locus from V. rupestris B38 and ten SNPs on chromosome 9 associated with a locus for susceptibility from 'Chardonnay' using single marker association and linkage disequilibrium analysis. Linkage maps for V. rupestris B38 (1,146 SNPs) and 'Chardonnay' (1,215 SNPs) were constructed and used to corroborate the 'Chardonnay' locus named Sen1 (Susceptibility to Erysiphe necator 1), providing the first insight into the genetics of susceptibility to powdery mildew from V. vinifera. The identification of markers associated with a susceptibility locus in a V. vinifera background can be used for negative selection among breeding progenies. This work improves our understanding of the nature of powdery mildew resistance in V. rupestris B38 and 'Chardonnay', while applying next-generation sequencing tools to advance grapevine genomics and breeding.
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Affiliation(s)
- Paola Barba
- Department of Plant Breeding, Cornell University, Ithaca, NY, 14853, USA
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21
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Riaz S, Boursiquot JM, Dangl GS, Lacombe T, Laucou V, Tenscher AC, Walker MA. Identification of mildew resistance in wild and cultivated Central Asian grape germplasm. BMC PLANT BIOLOGY 2013; 13:149. [PMID: 24093598 PMCID: PMC3851849 DOI: 10.1186/1471-2229-13-149] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/30/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species. RESULTS A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: 'Kishmish vatkana' and 'Karadzhandal'. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with 'Kishmish vatkana' and 'Karadzhandal', and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups. CONCLUSIONS This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Jean-Michel Boursiquot
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, Montpellier SupAgro, 2 Place Viala, Montpellier 34060, France
| | - Gerald S Dangl
- Foundation Plant Services, University of California, Davis, CA 95616, USA
| | - Thierry Lacombe
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Valerie Laucou
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Alan C Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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22
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Viana AP, Riaz S, Walker MA. Genetic dissection of agronomic traits within a segregating population of breeding table grapes. GENETICS AND MOLECULAR RESEARCH 2013; 12:951-64. [PMID: 23613241 DOI: 10.4238/2013.april.2.11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Grapes (Vitis vinifera) are of great economic importance worldwide. We genetically dissected a table grape breeding population, using hidden Markov models (HMM) applied to quantitative trait locus (QTL) analyses. We evaluated and dissected the following traits: total number of clusters, leaf score, peduncle length, cluster length, number of berries, weight of 10 berries, average seed number, nature of seeds, berry skin color, soluble solids, titratable acidity, and berry anthocyanin. A consensus map was developed with 255 SSR molecular markers, ordered into 19 linkage groups. The observed length of this map was 1871.4 cM, with 89.7% coverage. QTL were identified using interval mapping with HMM. The number of QTL detected for each trait varied between 1 and 8, reflecting the quantitative nature of these traits. The percentage of variation explained by these QTL was small, varying between 1.56 and 11.98%. We found QTL across linkage groups 2, 7, 12, 13, and 14 for berry anthocyanin.
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Affiliation(s)
- A P Viana
- Laboratório de Melhoramento Genético Vegetal, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brasil.
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23
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Blanc S, Wiedemann-Merdinoglu S, Dumas V, Mestre P, Merdinoglu D. A reference genetic map of Muscadinia rotundifolia and identification of Ren5, a new major locus for resistance to grapevine powdery mildew. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1663-75. [PMID: 22865124 DOI: 10.1007/s00122-012-1942-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/15/2012] [Indexed: 05/02/2023]
Abstract
Muscadinia rotundifolia, a species closely related to cultivated grapevine Vitis vinifera, is a major source of resistance to grapevine downy and powdery mildew, two major threats to cultivated traditional cultivars of V. vinifera respectively caused by the oomycete Plasmopara viticola and the ascomycete Erisyphe necator. The aim of the present work was to develop a reference genetic linkage map based on simple sequence repeat (SSR) markers for M. rotundifolia. This map was created using S1 M. rotundifolia cv. Regale progeny, and covers 948 cM on 20 linkage groups, which corresponds to the expected chromosome number for muscadine. The comparison of the genetic maps of V. vinifera and M. rotundifolia revealed a high macrosynteny between the genomes of both species. The S1 progeny was used to assess the general level of resistance of M. rotundifolia to P. viticola and E. necator, by scoring different parameters of pathogen development. A quantitative trait locus (QTL) analysis allowed us to highlight a major QTL on linkage group 14 controlling resistance to powdery mildew, which explained up to 58 % of the total phenotypic variance. This QTL was named 'Resistance to Erysiphe Necator 5' (Ren5). A microscopic evaluation E. necator mycelium development on resistant and susceptible genotypes of the S1 progeny showed that Ren5 exerts its action after the formation of the first appressorium, and acts by delaying, and then stopping, mycelium development.
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Affiliation(s)
- Sophie Blanc
- Santé de la Vigne et Qualité du Vin, INRA-UDS, UMR 1131, 28 rue de Herrlisheim, BP 20507, 68021 Colmar Cedex, France
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Riaz S, Hu R, Walker MA. A framework genetic map of Muscadinia rotundifolia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1195-1210. [PMID: 22688272 DOI: 10.1007/s00122-012-1906-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 05/25/2012] [Indexed: 06/01/2023]
Abstract
This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n = 20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879 cM on 18 chromosomes. The average distance between the markers was 4.1 cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841 cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088 cM, which represented 66 % of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome.
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Affiliation(s)
- S Riaz
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
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Wang N, Fang L, Xin H, Wang L, Li S. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC PLANT BIOLOGY 2012; 12:148. [PMID: 22908993 PMCID: PMC3528476 DOI: 10.1186/1471-2229-12-148] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/18/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. RESULTS An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. CONCLUSIONS The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Linchuan Fang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lijun Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
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Wang N, Fang L, Xin H, Wang L, Li S. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC PLANT BIOLOGY 2012. [PMID: 22908993 DOI: 10.1186/1471-2229-12148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. RESULTS An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. CONCLUSIONS The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Cai X, Feng Z, Hou B, Xing W, Ding X. Development of microsatellite markers for genetic diversity analysis of Dendrobium loddigesii Rolfe, an endangered orchid in China. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Choudhary S, Gaur R, Gupta S. EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1449-62. [PMID: 22301907 DOI: 10.1007/s00122-012-1800-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/05/2012] [Indexed: 05/17/2023]
Abstract
Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.
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Affiliation(s)
- Shalu Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No 10531, New Delhi 110067, India
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Fechter I, Hausmann L, Daum M, Rosleff Sörensen T, Viehöver P, Weisshaar B, Töpfer R. Candidate genes within a 143 kb region of the flower sex locus in Vitis. Mol Genet Genomics 2012; 287:247-59. [DOI: 10.1007/s00438-012-0674-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 01/05/2012] [Indexed: 12/18/2022]
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EST-SSRs characterization and in-silico alignments with linkage map SSR loci in grape (Vitis L.) genome. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0121-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Shokeen B, Choudhary S, Sethy NK, Bhatia S. Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus. ANNALS OF BOTANY 2011; 108:321-336. [PMID: 21788377 PMCID: PMC3143056 DOI: 10.1093/aob/mcr162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/27/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Catharanthus roseus is a plant of great medicinal importance, yet inadequate knowledge of its genome structure and the unavailability of genomic resources have been major impediments in the development of improved varieties. The aims of this study were to develop co-dominant sequence-tagged microsatellite sites (STMS) and gene-targeted markers (GTMs) and utilize them for the construction of a framework intraspecific linkage map of C. roseus. METHODS For simple sequence repeat (SSR) isolation, a genomic library enriched for (GA)(n) repeats was constructed from C. roseus 'Nirmal' (CrN1). In addition, GTMs were also designed from 12 genes of the TIA (terpenoid indole alkaloid) pathway - the medicinally most significant pathway in C. roseus. An F(2) mapping population was also generated by crossing two diverse accessions of C. roseus CrN1 (Nirmal)×CrN82 (Kew). KEY RESULTS A new set of 314 STMS markers and 64 GTMs were developed in this study. A segregating F(2) mapping population consisting of 111 F(2) individuals was generated. For generating the linkage map, a set of 423 co-dominant markers (378 newly developed and 45 published earlier) were screened for polymorphism between the parental genotypes, of which 134 were identified to be polymorphic. A total of 114 markers were mapped on eight linkage groups that spanned a 632·7 cM region of the genome with an average marker distance of 5·55 cM. Further, the mechanism of hypervariability at the gene-targeted loci was investigated at the sequence level. CONCLUSIONS For the first time, a large array of STMS markers and GTMs was generated in the model medicinal plant C. roseus. Moreover, the first microsatellite marker-based linkage map was described in this study. Together, these will serve as a foundation for future genomics studies related to quantitative trait loci analysis and molecular breeding in C. roseus.
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Affiliation(s)
- Bhumika Shokeen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Shalu Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Niroj Kumar Sethy
- Peptide and Proteomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Timarpur, Delhi-110054, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
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Huang H, Lu J, Ren Z, Hunter W, Dowd SE, Dang P. Mining and validating grape (Vitis L.) ESTs to develop EST-SSR markers for genotyping and mapping. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2011; 28:241-254. [PMID: 21841909 PMCID: PMC3132434 DOI: 10.1007/s11032-010-9477-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 06/19/2010] [Indexed: 05/20/2023]
Abstract
Grape expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping. An integrated pipeline including several computational tools for SSR identification and functional annotation was developed to identify 6,447 EST-SSR sequences from a total collection of 215,609 grape ESTs retrieved from NCBI. The 6,447 EST-SSRs were further reduced to 1,701 non-redundant sequences via clustering analysis, and 1,037 of them were successfully designed with primer pairs flanking the SSR motifs. From them, 150 pairs of primers were randomly selected for PCR amplification, polymorphism and heterozygosity analysis in V. vinifera cvs. Riesling and Cabernet Sauvignon, and V. rotundifolia (muscadine grape) cvs. Summit and Noble, and 145 pairs of these primers yielded PCR products. Pairwise comparisons of loci between the parents Riesling and Cabernet Sauvignon showed that 72 were homozygous in both cultivars, while 70 loci were heterozygous in at least one cultivar of the two. Muscadine parents Noble and Summit had 90 homozygous SSR loci in both parents and contained 50 heterozygous loci in at least one of the two. These EST-SSR functional markers are a useful addition for grape genotyping and genome mapping. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-010-9477-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hong Huang
- Center for Viticulture and Small Fruits Research, Florida A&M University, Tallahassee, FL 32317 USA
- School of Library and Information Science, University of South Florida, Tampa, FL 33620 USA
| | - Jiang Lu
- Center for Viticulture and Small Fruits Research, Florida A&M University, Tallahassee, FL 32317 USA
| | - Zhongbo Ren
- Center for Viticulture and Small Fruits Research, Florida A&M University, Tallahassee, FL 32317 USA
| | - Wayne Hunter
- United States Department of Agriculture, Agriculture Research Service, United States Horticultural Research Laboratory, 2001 South Rock Road, Fort Pierce, FL 34945 USA
| | - Scot E. Dowd
- Research and Testing Laboratory, 4321 Marsha Sharp Hwy, Lubbock, TX 79407 USA
| | - Phat Dang
- United States Department of Agriculture, Agricultural Research Service, National Peanut Research Laboratory, 10011 Forrester Drive, Dawson, GA 39842 USA
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Blasi P, Blanc S, Wiedemann-Merdinoglu S, Prado E, Rühl EH, Mestre P, Merdinoglu D. Construction of a reference linkage map of Vitis amurensis and genetic mapping of Rpv8, a locus conferring resistance to grapevine downy mildew. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:43-53. [PMID: 21404060 DOI: 10.1007/s00122-011-1565-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 02/26/2011] [Indexed: 05/08/2023]
Abstract
Downy mildew, caused by the oomycete Plasmopara viticola, is one of the major threats to grapevine. All traditional cultivars of grapevine (Vitis vinifera) are susceptible to downy mildew, the control of which requires regular application of fungicides. In contrast, many sources of resistance to P. viticola have been described in the Vitis wild species, among which is V. amurensis Rupr. (Vitaceae), a species originating from East Asia. A genetic linkage map of V. amurensis, based on 122 simple sequence repeat and 6 resistance gene analogue markers, was established using S1 progeny. This map covers 975 cM on 19 linkage groups, which represent 82% of the physical coverage of the V. vinifera reference genetic map. To measure the general level of resistance, the sporulation of P. viticola and the necrosis produced in response to infection, five quantitative and semi-quantitative parameters were scored 6 days post-inoculation on the S1 progeny. A quantitative trait locus (QTL) analysis allowed us to identify on linkage group 14 a major QTL controlling the resistance to downy mildew found in V. amurensis, which explained up to 86.3% of the total phenotypic variance. This QTL was named 'Resistance to Plasmopara viticola 8' (Rpv8).
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Affiliation(s)
- Paule Blasi
- UMR 1131 Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique, 28 rue de Herrlisheim, BP 20507, 68021, Colmar Cedex, France
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Riaz S, Tenscher AC, Ramming DW, Walker MA. Using a limited mapping strategy to identify major QTLs for resistance to grapevine powdery mildew (Erysiphe necator) and their use in marker-assisted breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1059-73. [PMID: 21188350 PMCID: PMC3056998 DOI: 10.1007/s00122-010-1511-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 12/04/2010] [Indexed: 05/18/2023]
Abstract
A limited genetic mapping strategy based on simple sequence repeat (SSR) marker data was used with five grape populations segregating for powdery mildew (Erysiphe necator) resistance in an effort to develop genetic markers from multiple sources and enable the pyramiding of resistance loci. Three populations derived their resistance from Muscadinia rotundifolia 'Magnolia'. The first population (06708) had 97 progeny and was screened with 137 SSR markers from seven chromosomes (4, 7, 9, 12, 13, 15, and 18) that have been reported to be associated with powdery or downy mildew resistance. A genetic map was constructed using the pseudo-testcross strategy and QTL analysis was carried out. Only markers from chromosome 13 and 18 were mapped in the second (04327) and third (06712) populations, which had 47 and 80 progeny, respectively. Significant QTLs for powdery mildew resistance with overlapping genomic regions were identified for different tissue types (leaf, stem, rachis, and berry) on chromosome 18, which distinguishes the resistance in 'Magnolia' from that present in other accessions of M. rotundifolia and controlled by the Run1 gene on chromosome 12. The 'Magnolia' resistance locus was termed as Run2.1. Powdery mildew resistance was also mapped in a fourth population (08391), which had 255 progeny and resistance from M. rotundifolia 'Trayshed'. A locus accounting for 50% of the phenotypic variation mapped to chromosome 18 and was named Run2.2. This locus overlapped the region found in the 'Magnolia'-based populations, but the allele sizes of the flanking markers were different. 'Trayshed' and 'Magnolia' shared at least one allele for 68% of the tested markers, but alleles of the other 32% of the markers were not shared indicating that the two M. rotundifolia selections were very different. The last population, 08306 with 42 progeny, derived its resistance from a selection Vitis romanetii C166-043. Genetic mapping discovered a major powdery mildew resistance locus termed Ren4 on chromosome 18, which explained 70% of the phenotypic variation in the same region of chromosome 18 found in the two M. rotundifolia resistant accessions. The mapping results indicate that powdery mildew resistance genes from different backgrounds reside on chromosome 18, and that genetic markers can be used as a powerful tool to pyramid these loci and other powdery mildew resistance loci into a single line.
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Affiliation(s)
- S. Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - A. C. Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - D. W. Ramming
- USDA-Agricultural Research Service, Parlier, CA 93468 USA
| | - M. A. Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
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Mejía N, Soto B, Guerrero M, Casanueva X, Houel C, de los Ángeles Miccono M, Ramos R, Le Cunff L, Boursiquot JM, Hinrichsen P, Adam-Blondon AF. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC PLANT BIOLOGY 2011; 11:57. [PMID: 21447172 PMCID: PMC3076230 DOI: 10.1186/1471-2229-11-57] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 03/29/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. RESULTS Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development.Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation.For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. CONCLUSION We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.
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Affiliation(s)
- Nilo Mejía
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Braulio Soto
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Marcos Guerrero
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Ximena Casanueva
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Cléa Houel
- UMR INRA CNRS University of Evry on Plant Genomics, 2 rue Gaston Crémieux, BP 5708, 91057, Evry, France
| | | | - Rodrigo Ramos
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
| | - Loïc Le Cunff
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Jean-Michel Boursiquot
- INRA - Montpellier SupAgro, UMR 1097, Equipe Diversité Génétique et Génomique Vigne, 2 place P. Viala, F-34060 Montpellier Cedex 1, France
| | - Patricio Hinrichsen
- Biotechnology Unit, La Platina Experimental Station, INIA, Av. Santa Rosa 11610, 8831314, Santiago, Chile
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Houel C, Bounon R, Chaïb J, Guichard C, Péros JP, Bacilieri R, Dereeper A, Canaguier A, Lacombe T, N'Diaye A, Le Paslier MC, Vernerey MS, Coriton O, Brunel D, This P, Torregrosa L, Adam-Blondon AF. Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions. BMC PLANT BIOLOGY 2010; 10:284. [PMID: 21176183 PMCID: PMC3022909 DOI: 10.1186/1471-2229-10-284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 12/22/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the fleshless berry mutation (flb) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication. RESULTS In total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both V. vinifera cv. Chardonnay and a genotype carrying the flb mutation, V. vinifera cv. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that flb could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the flb region, representing 48,874 bp in a highly diverse set of cultivated and wild V. vinifera genotypes, to identify possible signatures of domestication in the cultivated V. vinifera compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the flb region. CONCLUSIONS We observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the flb region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the flb gene in a F2 population when available.
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Affiliation(s)
- Cléa Houel
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Rémi Bounon
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
- Unité INRA Etude du Polymorphisme des Végétaux (EPGV), 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Jamila Chaïb
- CSIRO Plant Industry, PO BOX 350, Glen Osmond SA 5064, Australia
| | - Cécile Guichard
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Jean-Pierre Péros
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Roberto Bacilieri
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Alexis Dereeper
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Aurélie Canaguier
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Thierry Lacombe
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Amidou N'Diaye
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | | | - Marie-Stéphanie Vernerey
- Unité mixte de Recherche Amélioration des Plantes et Biotechnologies Végétales (APBV), INRA Agrocampus Rennes, Plate-forme cytologique moléculaire, 35 653 Le Rheu Cedex, France
- Unité mixte de Recherche Biologie et Génétique des Interactions Plantes-Agents Pathogènes (BGPI), INRA SupAgro CIRAD, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Olivier Coriton
- Unité mixte de Recherche Amélioration des Plantes et Biotechnologies Végétales (APBV), INRA Agrocampus Rennes, Plate-forme cytologique moléculaire, 35 653 Le Rheu Cedex, France
| | - Dominique Brunel
- Unité INRA Etude du Polymorphisme des Végétaux (EPGV), 2 rue Gaston Crémieux, 91 057 Evry cedex, France
| | - Patrice This
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Laurent Torregrosa
- Unité mixte de Recherche Diversité et Adaptation des Plantes Cultivées (DiaPC), INRA SupAgro, 2 place Pierre Viala, 34 060 Montpellier Cedex, France
| | - Anne-Françoise Adam-Blondon
- Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France
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Ibáñez J, Vélez MD, de Andrés MT, Borrego J. Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1213-22. [PMID: 19680623 DOI: 10.1007/s00122-009-1122-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 07/20/2009] [Indexed: 05/04/2023]
Abstract
Distinctness, uniformity and stability (DUS) testing of varieties is usually required to apply for Plant Breeders' Rights. This exam is currently carried out using morphological traits, where the establishment of distinctness through a minimum distance is the key issue. In this study, the possibility of using microsatellite markers for establishing the minimum distance in a vegetatively propagated crop (grapevine) has been evaluated. A collection of 991 accessions have been studied with nine microsatellite markers and pair-wise compared, and the highest intra-variety distance and the lowest inter-variety distance determined. The collection included 489 different genotypes, and synonyms and sports. Average values for number of alleles per locus (19), Polymorphic Information Content (0.764) and heterozygosities observed (0.773) and expected (0.785) indicated the high level of polymorphism existing in grapevine. The maximum intra-variety variability found was one allele between two accessions of the same variety, of a total of 3,171 pair-wise comparisons. The minimum inter-variety variability found was two alleles between two pairs of varieties, of a total of 119,316 pair-wise comparisons. In base to these results, the minimum distance required to set distinctness in grapevine with the nine microsatellite markers used could be established in two alleles. General rules for the use of the system as a support for establishing distinctness in vegetatively propagated crops are discussed.
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Affiliation(s)
- Javier Ibáñez
- IMIDRA (Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario), Finca El Encín, Carretera A-2, PK 38,200, 28800 Alcalá de Henares, Spain.
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Zhang J, Hausmann L, Eibach R, Welter LJ, Töpfer R, Zyprian EM. A framework map from grapevine V3125 (Vitis vinifera 'Schiava grossa' x 'Riesling') x rootstock cultivar 'Börner' (Vitis riparia x Vitis cinerea) to localize genetic determinants of phylloxera root resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1039-51. [PMID: 19626311 DOI: 10.1007/s00122-009-1107-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 06/30/2009] [Indexed: 05/05/2023]
Abstract
Grapevine rootstock cultivar 'Börner' is a hybrid of Vitis riparia and Vitis cinerea Arnold that shows high resistance to phylloxera (Daktulosphaira vitifoliae Fitch). To localize the determinants of phylloxera root resistance, the susceptible grapevine V3125 (Vitis vinifera 'Schiava grossa' x 'Riesling') was crossed to 'Börner'. Genetic framework maps were built from the progeny. 235 microsatellite markers were placed on the integrated parental map. They cover 1,155.98 cM on 19 linkage groups with an average marker distance of 4.8 cM. Phylloxera resistance was scored by counting nodosities after inoculation of the root system. Progeny plants were triplicated and experimentally infected in 2 years. A scan of the genetic maps indicated a quantitative trait locus on linkage group 13. This region was targeted by six microsatellite-type markers newly developed from the V. vinifera model genome sequence. Two of these appear closely linked to the trait, and can be useful for marker-assisted breeding.
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Affiliation(s)
- Junke Zhang
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany
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Marguerit E, Boury C, Manicki A, Donnart M, Butterlin G, Némorin A, Wiedemann-Merdinoglu S, Merdinoglu D, Ollat N, Decroocq S. Genetic dissection of sex determinism, inflorescence morphology and downy mildew resistance in grapevine. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1261-78. [PMID: 19238349 DOI: 10.1007/s00122-009-0979-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 01/22/2009] [Indexed: 05/20/2023]
Abstract
A genetic linkage map of grapevine was constructed using a pseudo-testcross strategy based upon 138 individuals derived from a cross of Vitis vinifera Cabernet Sauvignon x Vitis riparia Gloire de Montpellier. A total of 212 DNA markers including 199 single sequence repeats (SSRs), 11 single strand conformation polymorphisms (SSCPs) and two morphological markers were mapped onto 19 linkage groups (LG) which covered 1,249 cM with an average of 6.7 cM between markers. The position of SSR loci in the maps presented here is consistent with the genome sequence. Quantitative traits loci (QTLs) for several traits of inflorescence and flower morphology, and downy mildew resistance were investigated. Two novel QTLs for downy mildew resistance were mapped on linkage groups 9 and 12, they explain 26.0-34.4 and 28.9-31.5% of total variance, respectively. QTLs for inflorescence morphology with a large effect (14-70% of total variance explained) were detected close to the Sex locus on LG 2. The gene of the enzyme 1-aminocyclopropane-1-carboxylic acid synthase, involved in melon male organ development and located in the confidence interval of all QTLs detected on the LG 2, could be considered as a putative candidate gene for the control of sexual traits in grapevine. Co-localisations were found between four QTLs, detected on linkage groups 1, 14, 17 and 18, and the position of the floral organ development genes GIBBERELLIN INSENSITIVE1, FRUITFULL, LEAFY and AGAMOUS. Our results demonstrate that the sex determinism locus also determines both flower and inflorescence morphological traits.
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Affiliation(s)
- Elisa Marguerit
- Université de Bordeaux, UMR Ecophysiologie et Génomique Fonctionelle de la Vigne, Gradignan, France
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Duchêne E, Butterlin G, Claudel P, Dumas V, Jaegli N, Merdinoglu D. A grapevine (Vitis vinifera L.) deoxy-D: -xylulose synthase gene colocates with a major quantitative trait loci for terpenol content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:541-52. [PMID: 19002427 DOI: 10.1007/s00122-008-0919-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 10/14/2008] [Indexed: 05/18/2023]
Abstract
Linalool, geraniol, nerol, citronellol and alpha-terpineol are isoprenoid molecules responsible for specific aromas found in grapes and wines. Total concentrations (free and bound forms) of these compounds were measured in the skins of mature berries during 2 successive years in two progenies obtained from Muscat Ottonel and Gewurztraminer selfings. Partial genetic maps based on microsatellite markers were constructed and several quantitative trait loci (QTLs) related to terpenol content were detected. A major QTL on linkage group (LG) 5 colocated with a deoxy-D: -xylulose synthase gene, coding for the first enzyme of the plastidial isoprenoid biosynthesis pathway. The number of favourable alleles at this locus determined the level of terpenol synthesis. A second QTL, on LG 10, was found to determine the balance linalool versus geraniol and nerol in the Muscat self-progeny plants.
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Affiliation(s)
- Eric Duchêne
- INRA, UMR 1131 Santé de la Vigne et Qualité du Vin, 28, rue de Herrlisheim, BP 20507, 68021, Colmar, France.
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Ramezani A, Haddad R, Dorostkar M. Genetic diversity of grapevine accessions from Iran, Russia and USA using microsatellite markers. Pak J Biol Sci 2009; 12:152-157. [PMID: 19579936 DOI: 10.3923/pjbs.2009.152.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
To discover marker information content and differentiation among grapevine accessions from Iran, USA and Russia, nine microsatellite markers were used. A total of 75 alleles were detected, giving a mean of 8.3 alleles per 9 loci. The total number of alleles per locus varied between 6 to 11 and the polymorphism information content ranged from 0.65 to 0.88, indicating that these loci were highly informative. A positive correlation (r = 0.870) was observed between the number of alleles and the level of polymorphism. Two SSRs loci including SSrVrZAG47 and VVMD27 were found to be probably synonymous. Gene diversities were high in all populations with values ranging from 0.709 to 0.784. In all populations, the mean number (averaged over loci) of heterozygous individuals was higher than expected. PCO analysis could not be so clearly differentiated accessions from Iran and Russia. The pattern of clustering of the Vitis vinifera populations was according to their geographic distribution. It is suggested that accessions could possibly be assigned to their regions of origin according to their genotypes.
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Affiliation(s)
- A Ramezani
- Department of Agricultural Biotechnology, Imam Khomeini International University, Gazvin, Iran
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Riaz S, Tenscher AC, Rubin J, Graziani R, Pao SS, Walker MA. Fine-scale genetic mapping of two Pierce's disease resistance loci and a major segregation distortion region on chromosome 14 of grape. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:671-681. [PMID: 18516585 DOI: 10.1007/s00122-008-0802-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 05/09/2008] [Indexed: 05/26/2023]
Abstract
A refined genetic map of chromosome 14, which contains the Pierce's disease (PD) resistance locus, was created from three grape mapping populations. The source of PD resistance in these populations was b43-17, a male form of Vitis arizonica Engelm. that is homozygous resistant. The resistance locus segregated as a single dominant gene and mapped as PdR1a in the F1 selection F8909-17 (9621 population) and as PdR1b in a sibling F1 selection F8909-08 (04190 population). These two full sibs inherited either allele of the Pierce's disease resistance locus from the b43-17 parent, which is homozygous at that locus. The 9621 population consisted of 425 progeny and PdR1a mapped between markers VvCh14-56/VvCh14-02 and UDV095 within a 0.6 cM genetic distance. The 04190 population consisted of 361 progeny and PdR1b mapped between markers VvCh14-02 and UDV095/VvCh14-10 within a 0.4 cM distance. Many of the markers present on chromosome 14 were distorted with an excess of female alleles in the 04190 and 04373 population (developed from a cross of V. vinifera L. F2-35 x b43-17) indicating that potential gametophytic factors are present in this region. Common markers from this region within the 9621 population were not distorted except Scu15. When these markers were compared to V. vinifera-based maps of chromosome 14 they were also distorted suggesting the involvement of gametophytic factors, and prompting the identification of this region as Vitis-segregation distortion region 1 (V-SDR1). The refined genetic maps developed from this study can be used to identify and clone genes that confer resistance to Pierce's disease.
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Affiliation(s)
- S Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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Vezzulli S, Troggio M, Coppola G, Jermakow A, Cartwright D, Zharkikh A, Stefanini M, Grando MS, Viola R, Adam-Blondon AF, Thomas M, This P, Velasco R. A reference integrated map for cultivated grapevine (Vitis vinifera L.) from three crosses, based on 283 SSR and 501 SNP-based markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:499-511. [PMID: 18504538 DOI: 10.1007/s00122-008-0794-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Accepted: 05/02/2008] [Indexed: 05/17/2023]
Abstract
We have developed an integrated map from five elite cultivars of Vitis vinifera L.; Syrah, Pinot Noir, Grenache, Cabernet Sauvignon and Riesling which are parents of three segregating populations. A new source of markers, SNPs, identified in ESTs and unique BAC-end sequences was added to the available IGGP reference set of SSRs. The complete integrated map comprises 1,134 markers (350 AFLP, 332 BESs, 169 ESTs, 283 SSRs) spanning 1,443 cM over 19 linkage groups and shows a mean distance between neighbouring loci of 1.27 cM. Marker order was mainly conserved between the integrated map and the highly dense SyrahxPinot Noir consensus map except for few inversions. Moreover, the marker order has been validated through the assembled genome sequence of Pinot Noir. We have also assessed the transferability of SNP-based markers among five V. vinifera varieties, enabling marker validation across different genotypes. This integrated map can serve as a fundamental tool for molecular breeding in V. vinifera and related species and provide a basis for studies of genome organization and evolution in grapevines.
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Moroldo M, Paillard S, Marconi R, Fabrice L, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M, Adam-Blondon AF. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance. BMC PLANT BIOLOGY 2008; 8:66. [PMID: 18554400 PMCID: PMC2442077 DOI: 10.1186/1471-2229-8-66] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 06/13/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. RESULTS The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. CONCLUSION Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.
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Affiliation(s)
- Marco Moroldo
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Sophie Paillard
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
- UMR118, INRA-Agrocampus, University of Rennes, Amélioration des Plantes et Biotechnologies Végétales, F-35650 Le Rheu, France
| | - Raffaella Marconi
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
| | - Legeai Fabrice
- Unité de Recherche Génomique-Info, URGI, Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France
| | - Aurelie Canaguier
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Corinne Cruaud
- Gnoscope, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
| | | | - Cecile Guichard
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Veronique Brunaud
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Isabelle Le Clainche
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Simone Scalabrin
- Dipartimento di Scienze Matematiche, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Raffaele Testolin
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Gabriele Di Gaspero
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
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Salmaso M, Malacarne G, Troggio M, Faes G, Stefanini M, Grando MS, Velasco R. A grapevine (Vitis vinifera L.) genetic map integrating the position of 139 expressed genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:1129-43. [PMID: 18347774 DOI: 10.1007/s00122-008-0741-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 03/01/2008] [Indexed: 05/20/2023]
Abstract
Grapevine molecular maps based on microsatellites, AFLP and RAPD markers are now available. SSRs are essential to allow cross-talks between maps, thus upgrading any growing grapevine maps. In this work, single nucleotide polymorphisms (SNPs) were developed from coding sequences and from unique BAC-end sequences, and nested in a SSR framework map of grapevine. Genes participating to flavonoids metabolism and defence, and signal transduction pathways related genes were also considered. Primer pairs for 351 loci were developed from ESTs present on public databases and screened for polymorphism in the "Merzling" (a complex genotype Freiburg 993-60 derived from multiple crosses also involving wild Vitis species) x Vitis vinifera (cv. Teroldego) cross population. In total 138 SNPs, 108 SSR markers and a phenotypic trait (berry colour) were mapped in 19 major linkage groups of the consensus map. In specific cases, ESTs with putatively related functions mapped near QTLs previously identified for resistance and berry ripening. Genes related to anthocyanin metabolism mapped in different linkage groups. A myb gene, which has been correlated with anthocyanin biosynthesis, cosegregated with berry colour on linkage group 2. The possibility of associating candidate genes to known position of QTL is discussed for this plant.
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Affiliation(s)
- Marzia Salmaso
- Genetics and Molecular Biology Department, Istituto Agrario San Michele all'Adige, via Mach 1, 38010 San Michele a/A (TN), Italy.
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Costantini L, Battilana J, Lamaj F, Fanizza G, Grando MS. Berry and phenology-related traits in grapevine (Vitis vinifera L.): from quantitative trait loci to underlying genes. BMC PLANT BIOLOGY 2008; 8:38. [PMID: 18419811 PMCID: PMC2395262 DOI: 10.1186/1471-2229-8-38] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 04/17/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND The timing of grape ripening initiation, length of maturation period, berry size and seed content are target traits in viticulture. The availability of early and late ripening varieties is desirable for staggering harvest along growing season, expanding production towards periods when the fruit gets a higher value in the market and ensuring an optimal plant adaptation to climatic and geographic conditions. Berry size determines grape productivity; seedlessness is especially demanded in the table grape market and is negatively correlated to fruit size. These traits result from complex developmental processes modified by genetic, physiological and environmental factors. In order to elucidate their genetic determinism we carried out a quantitative analysis in a 163 individuals-F1 segregating progeny obtained by crossing two table grape cultivars. RESULTS Molecular linkage maps covering most of the genome (2n = 38 for Vitis vinifera) were generated for each parent. Eighteen pairs of homologous groups were integrated into a consensus map spanning over 1426 cM with 341 markers (mainly microsatellite, AFLP and EST-derived markers) and an average map distance between loci of 4.2 cM. Segregating traits were evaluated in three growing seasons by recording flowering, veraison and ripening dates and by measuring berry size, seed number and weight. QTL (Quantitative Trait Loci) analysis was carried out based on single marker and interval mapping methods. QTLs were identified for all but one of the studied traits, a number of them steadily over more than one year. Clusters of QTLs for different characters were detected, suggesting linkage or pleiotropic effects of loci, as well as regions affecting specific traits. The most interesting QTLs were investigated at the gene level through a bioinformatic analysis of the underlying Pinot noir genomic sequence. CONCLUSION Our results revealed novel insights into the genetic control of relevant grapevine features. They provide a basis for performing marker-assisted selection and testing the role of specific genes in trait variation.
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Affiliation(s)
- Laura Costantini
- Genetics and Molecular Biology Department, IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Juri Battilana
- Genetics and Molecular Biology Department, IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
| | - Flutura Lamaj
- DIBCA, University of Bari, Via Amendola 165/A, 70100 Bari, Italy
| | - Girolamo Fanizza
- DIBCA, University of Bari, Via Amendola 165/A, 70100 Bari, Italy
| | - Maria Stella Grando
- Genetics and Molecular Biology Department, IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
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Troggio M, Malacarne G, Coppola G, Segala C, Cartwright DA, Pindo M, Stefanini M, Mank R, Moroldo M, Morgante M, Grando MS, Velasco R. A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 2007; 176:2637-50. [PMID: 17603124 PMCID: PMC1950661 DOI: 10.1534/genetics.106.067462] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Accepted: 06/14/2007] [Indexed: 11/18/2022] Open
Abstract
The construction of a dense genetic map for Vitis vinifera and its anchoring to a BAC-based physical map is described: it includes 994 loci mapped onto 19 linkage groups, corresponding to the basic chromosome number of Vitis. Spanning 1245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 single-nucleotide polymorphism (SNP)-based genetic markers, 132 simple sequence repeats (SSRs), and 379 AFLP markers in a mapping population of 94 F(1) individuals derived from a V. vinifera cross of the cultivars Syrah and Pinot Noir. Of these markers, 623 were anchored to 367 contigs that are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. On the basis of contigs containing two or more genetically mapped markers, region-dependent estimations of physical and recombinational distances are presented. The markers used in this study include 118 SSRs common to an integrated map derived from five segregating populations of V. vinifera. The positions of these SSR markers in the two maps are conserved across all Vitis linkage groups. The addition of SNP-based markers introduces polymorphisms that are easy to database, are useful for evolutionary studies, and significantly increase the density of the map. The map provides the most comprehensive view of the Vitis genome reported to date and will be relevant for future studies on structural and functional genomics and genetic improvement.
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Affiliation(s)
- Michela Troggio
- IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
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48
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Carmona MJ, Cubas P, Calonje M, Martínez-Zapater JM. Flowering transition in grapevine (Vitis viniferaL.)This review is one of a selection of papers presented at the symposium onVitisat the XVII International Botanical Congress held in Vienna, Austria, 2005. ACTA ACUST UNITED AC 2007. [DOI: 10.1139/b07-059] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The available information on the regulation of flowering transition in model systems, such as Arabidopsis and rice, provides a framework to undertake the study of this process in plant species with different growth strategies. The grapevine ( Vitis vinifera L.) is the most widely cultivated and economically important fruit crop in the world. Understanding the regulation of flowering transition in this species can be relevant for the improvement of yield and quality of the crop. The grapevine is a representative of the family Vitaceae, whose species mostly grow as vines and have evolved climbing organs, tendrils, which are ontogenetically related to the reproductive organs. Here, we summarize the available information on the flowering transition in the grapevine. With this purpose, we first describe the vegetative and reproductive development of the grapevine as well as the reports on the physiology of flowering induction in this species. As well, we review the recent information on the molecular genetics of flowering signal integrator and flower meristem identity genes in the grapevine and compare the process with what is already known in model systems such as Arabidopsis. Finally, we propose a preliminary model to explain the regulation of flower initiation in the grapevine that is useful to identify its differential features and infer future prospects in the understanding of this process.
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Affiliation(s)
- María José Carmona
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Pilar Cubas
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Myriam Calonje
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - José Miguel Martínez-Zapater
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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49
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Cabezas JA, Cervera MT, Ruiz-García L, Carreño J, Martínez-Zapater JM. A genetic analysis of seed and berry weight in grapevine. Genome 2007; 49:1572-85. [PMID: 17426772 DOI: 10.1139/g06-122] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fruit size and seedlessness are highly relevant traits in many fruit crop species, and both are primary targets of breeding programs for table grapes. In this work we performed a quantitative genetic analysis of size and seedlessness in an F1 segregating population derived from the cross between a classical seeded (Vitis vinifera L. 'Dominga') and a newly bred seedless ('Autumn Seedless') cultivar. Fruit size was scored as berry weight (BW), and for seedlessness we considered both seed fresh weight (SFW) and the number of seeds and seed traces (SN) per berry. Quantitative trait loci (QTL) analysis of BW detected 3 QTLs affecting this trait and accounting for up to 67% of the total phenotypic variance. QTL analysis for seedlessness detected 3 QTLs affecting SN (explaining up to 35% of total variance) and 6 affecting SFW (explaining up to 90% of total variance). Among them, a major effect QTL explained almost half of the phenotypic variation for SFW. Comparative analysis of QTLs for these traits reduced the number of grapevine genomic regions involved, one of them being a major effect QTL for seedlessness. Association analyses showed that microsatellite locus VMC7F2, closely linked to this QTL, is a useful marker for selection of seedlessnes.
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Affiliation(s)
- J A Cabezas
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), C/ Darwin 3, 28049 Madrid, Spain
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50
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Di Gaspero G, Cipriani G, Adam-Blondon AF, Testolin R. Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers for R-gene candidates. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1249-63. [PMID: 17380315 DOI: 10.1007/s00122-007-0516-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 01/28/2007] [Indexed: 05/14/2023]
Abstract
Genetic maps functionally oriented towards disease resistance have been constructed in grapevine by analysing with a simultaneous maximum-likelihood estimation of linkage 502 markers including microsatellites and resistance gene analogs (RGAs). Mapping material consisted of two pseudo-testcrosses, 'Chardonnay' x 'Bianca' and 'Cabernet Sauvignon' x '20/3' where the seed parents were Vitis vinifera genotypes and the male parents were Vitis hybrids carrying resistance to mildew diseases. Individual maps included 320-364 markers each. The simultaneous use of two mapping crosses made with two pairs of distantly related parents allowed mapping as much as 91% of the markers tested. The integrated map included 420 Simple Sequence Repeat (SSR) markers that identified 536 SSR loci and 82 RGA markers that identified 173 RGA loci. This map consisted of 19 linkage groups (LGs) corresponding to the grape haploid chromosome number, had a total length of 1,676 cM and a mean distance between adjacent loci of 3.6 cM. Single-locus SSR markers were randomly distributed over the map (CD = 1.12). RGA markers were found in 18 of the 19 LGs but most of them (83%) were clustered on seven LGs, namely groups 3, 7, 9, 12, 13, 18 and 19. Several RGA clusters mapped to chromosomal regions where phenotypic traits of resistance to fungal diseases such as downy mildew and powdery mildew, bacterial diseases such as Pierce's disease, and pests such as dagger and root-knot nematode, were previously mapped in different segregating populations. The high number of RGA markers integrated into this new map will help find markers linked to genetic determinants of different pest and disease resistances in grape.
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Affiliation(s)
- G Di Gaspero
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100, Udine, Italy.
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