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García-Abadillo J, Barba P, Carvalho T, Sosa-Zuñiga V, Lozano R, Carvalho HF, Garcia-Rojas M, Salazar E, y Sánchez JI. Dissecting the complex genetic basis of pre- and post-harvest traits in Vitis vinifera L. using genome-wide association studies. HORTICULTURE RESEARCH 2024; 11:uhad283. [PMID: 38487297 PMCID: PMC10939405 DOI: 10.1093/hr/uhad283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding. We also mapped novel QTL associated with post-harvest traits across chromosomes 2, 4, 9, 11, 15, 18, and 19, broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior, including decay, shriveling, and weight loss. Leveraging gene ontology annotations, we drew parallels between traits and scrutinized candidate genes, laying a robust groundwork for future trait-feature identification endeavors in plant breeding. We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses, as the use of best linear unbiased estimators (BLUEs) corrections in our study may have led to the suppression of some common QTL in grapevine traits. Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits, offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.
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Affiliation(s)
- Julian García-Abadillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo - Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Paola Barba
- Genetic Resources Unit and Germplasm Bank, La Platina, Instituto de Investigaciones Agropecuarias, Av Santa Rosa 11610, La pintana, Santiago, Chile
- Sun World International, 28994 Gromer Av, Wasco, 93280, California, USA
| | | | - Viviana Sosa-Zuñiga
- Instituto de Ciencias Químicas y Aplicadas (ICQA), Universidad Autónoma de Chile, El Llano Subercaseaux 2801, Santiago, Chile
| | | | - Humberto Fanelli Carvalho
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo - Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Miguel Garcia-Rojas
- Genetic Resources Unit and Germplasm Bank, La Platina, Instituto de Investigaciones Agropecuarias, Av Santa Rosa 11610, La pintana, Santiago, Chile
| | - Erika Salazar
- Genetic Resources Unit and Germplasm Bank, La Platina, Instituto de Investigaciones Agropecuarias, Av Santa Rosa 11610, La pintana, Santiago, Chile
| | - Julio Isidro y Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo - Pozuelo de Alarcón, 28223, Madrid, Spain
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Park S, Park YO, Park Y. Population Genetic Analysis in Persimmons ( Diospyros kaki Thunb.) Based on Genome-Wide Single-Nucleotide Polymorphisms. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112097. [PMID: 37299077 DOI: 10.3390/plants12112097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/13/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
This study investigated the genetic diversity and population structure of a persimmon (Diospyros kaki Thunb., 2n = 6x = 90) collection in South Korea by evaluating 9751 genome-wide single-nucleotide polymorphisms (SNPs) detected using genotyping-by-sequencing in 93 cultivars. The results of neighbor-joining clustering, principal component analysis, and STRUCTURE analysis based on SNPs indicated clear separation between cultivar groups (pollination-constant nonastringent (PCNA, 40 cultivars), pollination-constant astringent (PCA, 19), pollination-variant nonastringent (PVNA, 23), and the pollination-variant astringent type (PVA, 9)) based on the astringency types, while separation between PVA and PVNA-type cultivars was unclear. Population genetic diversity based on SNPs showed that the proportions of polymorphic SNPs within each group ranged from 99.01% (PVNA) to 94.08% (PVA), and the PVNA group exhibited the highest genetic diversity (He = 3.86 and uHe = 0.397). F (fixation index) values were low ranging from -0.024 (PVA) to 0.176 (PCA) with an average of 0.089, indicating a deficiency of heterozygosity. Analysis of molecular variance (AMOVA) and Fst among cultivar groups indicated that variation within individuals was higher than that among the groups. Pairwise Fst values among the groups ranged from 0.01566 (between PVA and PVNA) to 0.09416 (between PCA and PCNA), indicating a low level of cultivar type differentiation. These findings highlight the potential application of biallelic SNPs in population genetics studies of allopolyploids species and provide valuable insights that may have significant implications for breeding and cultivar identification in persimmon.
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Affiliation(s)
- Seoyeon Park
- Department of Horticultural Science, Pusan National University, Miryang 50463, Republic of Korea
| | - Ye-Ok Park
- Sweet Persimmon Research Institute, Gyeongsangnam-do Agricultural Research and Extension Services, Gimhae 50871, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Science, Pusan National University, Miryang 50463, Republic of Korea
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Tympakianakis S, Trantas E, Avramidou EV, Ververidis F. Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1139647. [PMID: 37180393 PMCID: PMC10169827 DOI: 10.3389/fpls.2023.1139647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.
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Affiliation(s)
- Stylianos Tympakianakis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
| | - Emmanouil Trantas
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organisation “DIMITRA“, Athens, Greece
| | - Filippos Ververidis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
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4
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Vervalle JA, Costantini L, Lorenzi S, Pindo M, Mora R, Bolognesi G, Marini M, Lashbrooke JG, Tobutt KR, Vivier MA, Roodt-Wilding R, Grando MS, Bellin D. A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4371-4390. [PMID: 36271055 PMCID: PMC9734222 DOI: 10.1007/s00122-022-04225-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars 'Cabernet Sauvignon', 'Corvina' and 'Rhine Riesling', the lesser-known wine variety 'Deckrot', and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965-0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.
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Affiliation(s)
- Jessica A Vervalle
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Laura Costantini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Silvia Lorenzi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Riccardo Mora
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giada Bolognesi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Martina Marini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Justin G Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Ken R Tobutt
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Melané A Vivier
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Center Agriculture Food and Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy.
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Possamai T, Wiedemann-Merdinoglu S. Phenotyping for QTL identification: A case study of resistance to Plasmopara viticola and Erysiphe necator in grapevine. FRONTIERS IN PLANT SCIENCE 2022; 13:930954. [PMID: 36035702 PMCID: PMC9403010 DOI: 10.3389/fpls.2022.930954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
Vitis vinifera is the most widely cultivated grapevine species. It is highly susceptible to Plasmopara viticola and Erysiphe necator, the causal agents of downy mildew (DM) and powdery mildew (PM), respectively. Current strategies to control DM and PM mainly rely on agrochemical applications that are potentially harmful to humans and the environment. Breeding for resistance to DM and PM in wine grape cultivars by introgressing resistance loci from wild Vitis spp. is a complementary and more sustainable solution to manage these two diseases. During the last two decades, 33 loci of resistance to P. viticola (Rpv) and 15 loci of resistance to E. necator (Ren and Run) have been identified. Phenotyping is salient for QTL characterization and understanding the genetic basis of resistant traits. However, phenotyping remains a major bottleneck for research on Rpv and Ren/Run loci and disease resistance evaluation. A thorough analysis of the literature on phenotyping methods used for DM and PM resistance evaluation highlighted phenotyping performed in the vineyard, greenhouse or laboratory with major sources of variation, such as environmental conditions, plant material (organ physiology and age), pathogen inoculum (genetic and origin), pathogen inoculation (natural or controlled), and disease assessment method (date, frequency, and method of scoring). All these factors affect resistance assessment and the quality of phenotyping data. We argue that the use of new technologies for disease symptom assessment, and the production and adoption of standardized experimental guidelines should enhance the accuracy and reliability of phenotyping data. This should contribute to a better replicability of resistance evaluation outputs, facilitate QTL identification, and contribute to streamline disease resistance breeding programs.
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Affiliation(s)
- Tyrone Possamai
- CREA—Research Centre for Viticulture and Enology, Conegliano, Italy
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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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Reshef N, Karn A, Manns DC, Mansfield AK, Cadle-Davidson L, Reisch B, Sacks GL. Stable QTL for malate levels in ripe fruit and their transferability across Vitis species. HORTICULTURE RESEARCH 2022; 9:uhac009. [PMID: 35369130 PMCID: PMC8968676 DOI: 10.1093/hr/uhac009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%), and based on two and five years of data, respectively, their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.
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Affiliation(s)
| | - Avinash Karn
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - David C Manns
- Department of Food Science, Cornell AgriTech, Geneva, NY 14456, USA
| | | | | | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Gavin L Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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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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Karn A, Diaz-Garcia L, Reshef N, Zou C, Manns DC, Cadle-Davidson L, Mansfield AK, Reisch BI, Sacks GL. The Genetic Basis of Anthocyanin Acylation in North American Grapes ( Vitis spp.). Genes (Basel) 2021; 12:1962. [PMID: 34946911 PMCID: PMC8701791 DOI: 10.3390/genes12121962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Hydroxycinnamylated anthocyanins (or simply 'acylated anthocyanins') increase color stability in grape products, such as wine. Several genes that are relevant for anthocyanin acylation in grapes have been previously described; however, control of the degree of acylation in grapes is complicated by the lack of genetic markers quantitatively associated with this trait. To characterize the genetic basis of anthocyanin acylation in grapevine, we analyzed the acylation ratio in two closely related biparental families, Vitis rupestris B38 × 'Horizon' and 'Horizon' × Illinois 547-1, for 2 and 3 years, respectively. The acylation ratio followed a bimodal and skewed distribution in both families, with repeatability estimates larger than 0.84. Quantitative trait locus (QTL) mapping with amplicon-based markers (rhAmpSeq) identified a strong QTL from 'Horizon' on chromosome 3, near 15.85 Mb in both families and across years, explaining up to 85.2% of the phenotypic variance. Multiple candidate genes were identified in the 14.85-17.95 Mb interval, in particular, three copies of a gene encoding an acetyl-CoA-benzylalcohol acetyltransferase-like protein within the two most strongly associated markers. Additional population-specific QTLs were found in chromosomes 9, 10, 15, and 16; however, no candidate genes were described. The rhAmpSeq markers reported here, which were previously shown to be highly transferable among the Vitis genus, could be immediately implemented in current grapevine breeding efforts to control the degree of anthocyanin acylation and improve the quality of grapes and their products.
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Affiliation(s)
- Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Pabellón, Aguascalientes 20676, Mexico
| | - Noam Reshef
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA;
| | - David C. Manns
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.C.M.); (A.K.M.)
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anna Katharine Mansfield
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.C.M.); (A.K.M.)
| | - Bruce I. Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
| | - Gavin L. Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
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Possamai T, Wiedemann-Merdinoglu S, Merdinoglu D, Migliaro D, De Mori G, Cipriani G, Velasco R, Testolin R. Construction of a high-density genetic map and detection of a major QTL of resistance to powdery mildew (Erysiphe necator Sch.) in Caucasian grapes (Vitis vinifera L.). BMC PLANT BIOLOGY 2021; 21:528. [PMID: 34763660 PMCID: PMC8582213 DOI: 10.1186/s12870-021-03174-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/09/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Vitis vinifera L. is the most cultivated grapevine species worldwide. Erysiphe necator Sch., the causal agent of grape powdery mildew, is one of the main pathogens affecting viticulture. V. vinifera has little or no genetic resistances against E. necator and the grape industry is highly dependent on agrochemicals. Some Caucasian V. vinifera accessions have been reported to be resistant to E. necator and to have no genetic relationships to known sources of resistance to powdery mildew. The main purpose of this work was the study and mapping of the resistance to E. necator in the Caucasian grapes 'Shavtsitska' and 'Tskhvedianis tetra'. RESULTS The Caucasian varieties 'Shavtsitska' and 'Tskhvedianis tetra' showed a strong partial resistance to E. necator which segregated in two cross populations: the resistant genotypes delayed and limited the pathogen mycelium growth, sporulation intensity and number of conidia generated. A total of 184 seedlings of 'Shavtsitska' x 'Glera' population were genotyped through the Genotyping by Sequencing (GBS) technology and two high-density linkage maps were developed for the cross parents. The QTL analysis revealed a major resistance locus, explaining up to 80.15% of the phenotypic variance, on 'Shavtsitska' linkage group 13, which was associated with a reduced pathogen infection as well as an enhanced plant necrotic response. The genotyping of 105 Caucasian accessions with SSR markers flanking the QTL revealed that the resistant haplotype of 'Shavtsitska' was shared by 'Tskhvedianis tetra' and a total of 25 Caucasian grape varieties, suggesting a widespread presence of this resistance in the surveyed germplasm. The uncovered QTL was mapped in the region where the Ren1 locus of resistance to E. necator, identified in the V. vinifera 'Kishmish vatkana' and related grapes of Central Asia, is located. The genetic analysis conducted revealed that the Caucasian grapes in this study exhibit a resistant haplotype different from that of Central Asian grape accessions. CONCLUSIONS The QTL isolated in 'Shavtsitska' and present in the Caucasian V. vinifera varieties could be a new candidate gene of resistance to E. necator to use in breeding programmes. It co-localizes with the Ren1 locus but shows a different haplotype from that of grapevines of Central Asia. We therefore consider that the Caucasian resistance locus, named Ren1.2, contains a member of a cluster of R-genes, of which the region is rich, and to be linked with, or possibly allelic, to Ren1.
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Affiliation(s)
- Tyrone Possamai
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy.
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy.
| | | | - Didier Merdinoglu
- INRAE, Université de Strasbourg, SVQV UMR-A 1131, 28 rue de Herrlisheim, 68000, Colmar, France
| | - Daniele Migliaro
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy
| | - Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - Riccardo Velasco
- CREA - Research Centre for Viticulture and Enology, viale XXVIII Aprile 26, 31015, Conegliano, TV, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
- Institute of Applied Genomics, Science & Technology Park "Luigi Danieli", via Jacopo Linussio 51, 33100, Udine, Italy
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Abstract
We studied the grape sex-determining region (SDR) in 12 Vitis genomes and demonstrated its conservation across 556 genotypes including 193 accessions from 47 world-wide wild grapevine species and 363 accessions of cultivated grapevine. Although the grape SDR is recombination free in all wild species, we found two distinct hermaphrodite (H) haplotypes (H1 and H2) among the cultivated grapevines, both chimeras of male (M) and female (f) haplotypes. The two independent recombinations carry different genetic signatures which long predate the domestication of grapevine, suggesting independent evolutions of this trait in wild European grapevine gene pools prior to human domestication. Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.
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Su K, Guo Y, Zhong W, Lin H, Liu Z, Li K, Li Y, Guo X. High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing. PHYTOPATHOLOGY 2021; 111:659-670. [PMID: 33635092 DOI: 10.1094/phyto-12-19-0480-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca 'Zhuosexiang') and white rot-susceptible cultivar (V. vinifera 'Victoria'). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.
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Affiliation(s)
- Kai Su
- 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
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, People's Republic of China
| | - Weihao Zhong
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Hong Lin
- 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
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, People's Republic of China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, People's Republic of China
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13
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Yousaf MF, Demirel U, Naeem M, Çalışkan ME. Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato ( Solanum tuberosum L.). 3 Biotech 2021; 11:174. [PMID: 33927965 DOI: 10.1007/s13205-021-02727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022] Open
Abstract
Tuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software "WinRHIZO" (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r 2 = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases "StPP1"), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02727-6.
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Yin L, Karn A, Cadle-Davidson L, Zou C, Underhill A, Atkins P, Treiber E, Voytas D, Clark M. Fine Mapping of Leaf Trichome Density Revealed a 747-kb Region on Chromosome 1 in Cold-Hardy Hybrid Wine Grape Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:587640. [PMID: 33746993 PMCID: PMC7965957 DOI: 10.3389/fpls.2021.587640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/21/2021] [Indexed: 05/25/2023]
Abstract
Segregation for leaf trichome density was observed in a cold-hardy hybrid grape population GE1025 (N = ∼125, MN1264 × MN1246) that was previously used to detect a quantitative trait locus (QTL) underlying foliar phylloxera resistance on chromosome 14. Our hypothesis was that high trichome density was associated with resistance to phylloxera. Existing literature found trichome density QTL on chromosomes 1 and 15 using a hybrid grape population of "Horizon" × Illinois 547-1 and suggested a few candidate genes. To validate the reported QTL and our hypothesis, interval mapping was conducted in GE1025 with previous genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) genotype data and phenotypic scores collected using a 0-6 trichome density scale at several leaf positions. Evaluations were done on replicated forced dormant cuttings in 2 years and on field-grown leaves in 1 year. There was no strong relationship between trichome density and phylloxera resistance except for a Pearson's correlation (r) of about -0.2 between a few trichome density traits and phylloxera severity traits at 2 and 3 weeks after infestation. Two genetic regions were repeatedly detected for multiple trichome density traits: from 10 to 20.7 Mbp (∼10 Mbp) on chromosome 1 for ribbon and simple density traits and from 2.4 to 8.9 Mbp on chromosome 10 for ribbon density traits, explaining 12.1-48.2 and 12.6-27.5% of phenotypic variation, respectively. To fine map, we genotyped a larger population, GE1783 (N = ∼1,023, MN1264 × MN1246), with conserved rhAmpSeq haplotype markers across multiple Vitis species and phenotyped 233 selected potential recombinants. Evaluations were conducted on field-grown leaves in a single year. The QTL for ribbon trichome density on adaxial vein and adaxial leaf and simple density on abaxial vein was fine mapped to 12.63-13.38 Mbp (747 kb) on chromosome 1. We found variations of MN1264 and MN1246 at candidate genes NAC transcription factor 29, EF-hand protein, and MYB140 in this region and three other surrounding candidate genes proposed previously. Even though no strong relationship between foliar phylloxera resistance and trichome density was found, this study validated and fine mapped a major QTL for trichome density using a cold-hardy hybrid grape population and shed light on a few candidate genes that have implications for different breeding programs.
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Affiliation(s)
- Lu Yin
- Department of Horticultural Science, University of Minnesota, Twin Cities, MN, United States
| | - Avinash Karn
- Institute of Biotechnology, Bioinformatics Facility, Cornell University, Ithaca, NY, United States
| | - Lance Cadle-Davidson
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, United States
| | - Cheng Zou
- Institute of Biotechnology, Bioinformatics Facility, Cornell University, Ithaca, NY, United States
| | - Anna Underhill
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, United States
| | - Paul Atkins
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, United States
| | - Erin Treiber
- Department of Horticultural Science, University of Minnesota, Twin Cities, MN, United States
| | - Daniel Voytas
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, United States
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, Twin Cities, MN, United States
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Quezada M, Amadeu RR, Vignale B, Cabrera D, Pritsch C, Garcia AAF. Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:626811. [PMID: 33708232 PMCID: PMC7940835 DOI: 10.3389/fpls.2021.626811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.
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Affiliation(s)
- Marianella Quezada
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Rodrigo Rampazo Amadeu
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Beatriz Vignale
- Mejoramiento Genético, Departamento de Producción Vegetal, Estación Experimental de la Facultad de Agronomía, Universidad de la República, Salto, Uruguay
| | - Danilo Cabrera
- Programa de Investigación en Producción Fruticola, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental “Wilson Ferreira Aldunate”, Canelones, Uruguay
| | - Clara Pritsch
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Antonio Augusto Franco Garcia
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
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16
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Naegele RP, Londo JP, Zou C, Cousins P. Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera. PeerJ 2021; 9:e10773. [PMID: 33614279 PMCID: PMC7877238 DOI: 10.7717/peerj.10773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Macro and micro nutrient accumulation affects all stages of plant growth and development. When nutrient deficiencies or excesses occur, normal plant growth is altered resulting in symptoms such as leaf chlorosis, plant stunting or death. In grapes, few genomic regions associated with nutrient accumulation or deficiencies have been identified. Our study evaluated micro and macro nutrient concentrations in Vitis vinifera L. to identify associated SNPs using an association approach with genotype by sequencing data. Nutrient concentrations and foliar symptoms (leaf chlorosis and stunting) were compared among 249 F1Vitis vinifera individuals in 2015 and 2016. Foliar symptoms were consistent (≥90%) between years and correlated with changes in nutrient concentrations of magnesium (r = 0.65 and r = 0.38 in 2015 and 2016, respectively), aluminum (r = 0.24 and r = 0.49), iron (r = 0.21 and r = 0.49), and sodium (r = 0.32 and r = 0.21). Single nucleotide polymorphisms associated with symptoms, sodium, and magnesium were detected on each chromosome with the exception of 5, 7 and 17 depending on the trait and genome used for analyses explaining up to 40% of the observed variation. Symptoms and magnesium concentration were primarily associated with SNPs on chromosome 3, while SNPs associated with increased sodium content were primarily found on chromosomes 11 and 18. Mean concentrations for each nutrient varied between years in the population between symptomatic and asymptomatic plants, but relative relationships were mostly consistent. These data suggest a complex relationship among foliar symptoms and micro and macro nutrients accumulating in grapevines.
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Affiliation(s)
- Rachel P Naegele
- San Joaquin Valley Agricultural Sciences Center, USDA ARS, Parlier, CA, United States of America
| | - Jason P Londo
- Grape Genetics Unit, USDA ARS, Geneva, NY, United States of America
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States of America
| | - Peter Cousins
- E&J Gallo Winery, Modesto, CA, United States of America
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Pina A, Irisarri P, Errea P, Zhebentyayeva T. Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot ( Prunus armeniaca L.). FRONTIERS IN PLANT SCIENCE 2021; 12:622906. [PMID: 33679836 PMCID: PMC7933020 DOI: 10.3389/fpls.2021.622906] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/08/2021] [Indexed: 05/29/2023]
Abstract
Graft incompatibility (GI) between the most popular Prunus rootstocks and apricot cultivars is one of the major problems for rootstock usage and improvement. Failure in producing long-leaving healthy grafts greatly affects the range of available Prunus rootstocks for apricot cultivation. Despite recent advances related to the molecular mechanisms of a graft-union formation between rootstock and scion, information on genetic control of this trait in woody plants is essentially missing because of a lack of hybrid crosses, segregating for the trait. In this study, we have employed the next-generation sequencing technology to generate the single-nucleotide polymorphism (SNP) markers and construct parental linkage maps for an apricot F1 population "Moniqui (Mo)" × "Paviot (Pa)" segregating for ability to form successful grafts with universal Prunus rootstock "Marianna 2624". To localize genomic regions associated with this trait, we genotyped 138 individuals from the "Mo × Pa" cross and constructed medium-saturated genetic maps. The female "Mo" and male "Pa" maps were composed of 557 and 501 SNPs and organized in eight linkage groups that covered 780.2 and 690.4 cM of genetic distance, respectively. Parental maps were aligned to the Prunus persica v2.0 genome and revealed a high colinearity with the Prunus reference map. Two-year phenotypic data for characters associated with unsuccessful grafting such as necrotic line (NL), bark and wood discontinuities (BD and WD), and an overall estimate of graft (in)compatibility (GI) were collected for mapping quantitative trait loci (QTLs) on both parental maps. On the map of the graft-compatible parent "Pa", two genomic regions on LG5 (44.9-60.8 cM) and LG8 (33.2-39.2 cM) were associated with graft (in)compatibility characters at different significance level, depending on phenotypic dataset. Of these, the LG8 QTL interval was most consistent between the years and supported by two significant and two putative QTLs. To our best knowledge, this is the first report on QTLs for graft (in)compatibility in woody plants. Results of this work will provide a valuable genomic resource for apricot breeding programs and facilitate future efforts focused on candidate genes discovery for graft (in)compatibility in apricot and other Prunus species.
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Affiliation(s)
- Ana Pina
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Patricia Irisarri
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Pilar Errea
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
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18
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Ma KB, Yang SJ, Jo YS, Kang SS, Nam M. Development of Kompetitive Allele Specific PCR markers for identification of persimmon varieties using genotyping-by-sequencing. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding. Sci Rep 2020; 10:16308. [PMID: 33004874 PMCID: PMC7530987 DOI: 10.1038/s41598-020-73321-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 09/11/2020] [Indexed: 11/17/2022] Open
Abstract
Genotyping-by-Sequencing (GBS) is a low-cost, high-throughput genotyping method that relies on restriction enzymes to reduce genome complexity. GBS is being widely used for various genetic and breeding applications. In the present study, 2240 individuals from eight maize populations, including two association populations (AM), backcross first generation (BC1), BC1F2, F2, double haploid (DH), intermated B73 × Mo17 (IBM), and a recombinant inbred line (RIL) population, were genotyped using GBS. A total of 955,120 of raw data for SNPs was obtained for each individual, with an average genotyping error of 0.70%. The rate of missing genotypic data for these SNPs was related to the level of multiplex sequencing: ~ 25% missing data for 96-plex and ~ 55% for 384-plex. Imputation can greatly reduce the rate of missing genotypes to 12.65% and 3.72% for AM populations and bi-parental populations, respectively, although it increases total genotyping error. For analysis of genetic diversity and linkage mapping, unimputed data with a low rate of genotyping error is beneficial, whereas, for association mapping, imputed data would result in higher marker density and would improve map resolution. Because imputation does not influence the prediction accuracy, both unimputed and imputed data can be used for genomic prediction. In summary, GBS is a versatile and efficient SNP discovery approach for homozygous materials and can be effectively applied for various purposes in maize genetics and breeding.
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20
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Zhang B, Zhao N, Peng K, He X, Chen CX, Liu H, Liu K, Jia L, Bao B. A combination of genome-wide association study screening and SNaPshot for detecting sex-related SNPs and genes in Cynoglossus semilaevis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100711. [PMID: 32683285 DOI: 10.1016/j.cbd.2020.100711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/16/2022]
Abstract
Chinese tongue sole (Cynoglossus semilaevis) males and females exhibit great differences in growth rate and appearance. The species is heterogametic (ZW/ZZ) and has sex-reversed "pseudomales" that are genetically female and physiologically male. In this study, we identified eight sex-specific single nucleotide polymorphism (SNP) markers for the sex identification of C. semilaevis by using a combination of genome-wide association study (GWAS) screening and SnaPshot validation. Candidate SNPs were screened using genotyping by sequencing to perform GWAS of the differential SNPs between the sexes of C. semilaevis. The SNP loci were amplified using a multiplex PCR system and detected via SNaPshot, which enables multiplexing of up to 30-40 SNPs in a single assay and ensures high accuracy of the results. The molecular markers detected in our study were used to successfully identify normal males and pseudomales from 45 caught and 40 cultured C. semilaevis specimens. Linkage disequilibrium analysis showed that the eight SNP loci were related to each other, with a strong linkage. Moreover, we investigated the expression of prdm6 mRNA containing a missense SNP and confirmed that the gene is differentially expressed in the gonads of the different sexes of C. semilaevis; the expression of prdm6 mRNA was significantly higher in the males than in the females and pseudomales. This means prdm6 may be related to sex differentiation in C. semilaevis.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Medicine Biotechnology Co, Ltd, Tianjin, China
| | - Kangkang Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Chun Xiu Chen
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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21
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Su K, Xing H, Guo Y, Zhao F, Liu Z, Li K, Li Y, Guo X. High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing. BMC Genomics 2020; 21:419. [PMID: 32571215 PMCID: PMC7310074 DOI: 10.1186/s12864-020-06836-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/16/2020] [Indexed: 11/28/2022] Open
Abstract
Background Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent ‘Cabernet sauvignon’ and paternal parent ‘Zuoyouhong’. A total of 181 hybrid offspring and their parents were used as samples for restriction-site associated DNA sequencing (RAD). Grapevine cane phloem and xylem cold hardiness of the experimental material was detected using the low-temperature exotherm method in 2016, 2017 and 2018. QTL mapping was then conducted based on the integrated map. Results We constructed a high-density genetic linkage map with 16,076, 11,643, and 25,917 single-nucleotide polymorphism (SNP) markers anchored in the maternal, paternal, and integrated maps, respectively. The average genetic distances of adjacent markers in the maps were 0.65 cM, 0.77 cM, and 0.41 cM, respectively. Colinearity analysis was conducted by comparison with the grape reference genome and showed good performance. Six QTLs were identified based on the phenotypic data of 3 years and they were mapped on linkage group (LG) 2, LG3, and LG15. Based on QTL results, candidate genes which may be involved in grapevine cold hardiness were selected. Conclusions High-density linkage maps can facilitate grapevine fine QTL mapping, genome comparison, and sequence assembly. The cold hardiness QTL mapping and candidate gene discovery performed in this study provide an important reference for molecular-assisted selection in grapevine cold hardiness breeding.
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Affiliation(s)
- Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China. .,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, P.R. China.
| | - Fangyuan Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China. .,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, P.R. China.
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22
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Mele MA, Kang HM, Lee YT, Islam MZ. Grape terpenoids: flavor importance, genetic regulation, and future potential. Crit Rev Food Sci Nutr 2020; 61:1429-1447. [PMID: 32401037 DOI: 10.1080/10408398.2020.1760203] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Terpenes significantly affect the flavor and quality of grapes and wine. This review summarizes recent research on terpenoids with regard to grape wine. Although, the grapevine terpene synthase gene family is the largest identified, genetic modifications involving terpenes to improve wine flavor have received little attention. Key enzyme modulation alters metabolite production. Over the last decade, the heterologous manipulation of grape glycosidase has been used to alter terpenoids, and cytochrome P450s may affect terpene synthesis. Metabolic and genetic engineering can further modify terpenoid metabolism, while using transgenic grapevines (trait transfer to the plant) could yield more flavorful wine. We also discuss traits involved in wine aroma quality, and the strategies that can be used to improve grapevine breeding technology.
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Affiliation(s)
- Mahmuda Akter Mele
- Department of Horticulture, Kangwon National University, Chuncheon, Republic of Korea
| | - Ho-Min Kang
- Department of Horticulture, Kangwon National University, Chuncheon, Republic of Korea
| | - Young-Tack Lee
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Republic of Korea
| | - Mohammad Zahirul Islam
- Department of Food Science and Biotechnology, Gachon University, Seongnam, Republic of Korea
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23
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Rubio B, Lalanne-Tisné G, Voisin R, Tandonnet JP, Portier U, Van Ghelder C, Lafargue M, Petit JP, Donnart M, Joubard B, Bert PF, Papura D, Le Cunff L, Ollat N, Esmenjaud D. Characterization of genetic determinants of the resistance to phylloxera, Daktulosphaira vitifoliae, and the dagger nematode Xiphinema index from muscadine background. BMC PLANT BIOLOGY 2020; 20:213. [PMID: 32398088 PMCID: PMC7218577 DOI: 10.1186/s12870-020-2310-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Muscadine (Muscadinia rotundifolia) is known as a resistance source to many pests and diseases in grapevine. The genetics of its resistance to two major grapevine pests, the phylloxera D. vitifoliae and the dagger nematode X. index, vector of the Grapevine fanleaf virus (GFLV), was investigated in a backcross progeny between the F1 resistant hybrid material VRH8771 (Vitis-Muscadinia) derived from the muscadine R source 'NC184-4' and V. vinifera cv. 'Cabernet-Sauvignon' (CS). RESULTS In this pseudo-testcross, parental maps were constructed using simple-sequence repeats markers and single nucleotide polymorphism markers from a GBS approach. For the VRH8771 map, 2271 SNP and 135 SSR markers were assembled, resulting in 19 linkage groups (LG) and an average distance between markers of 0.98 cM. Phylloxera resistance was assessed by monitoring root nodosity number in an in planta experiment and larval development in a root in vitro assay. Nematode resistance was studied using 10-12 month long tests for the selection of durable resistance and rating criteria based on nematode reproduction factor and gall index. A major QTL for phylloxera larval development, explaining more than 70% of the total variance and co-localizing with a QTL for nodosity number, was identified on LG 7 and designated RDV6. Additional QTLs were detected on LG 3 (RDV7) and LG 10 (RDV8), depending on the in planta or in vitro experiments, suggesting that various loci may influence or modulate nodosity formation and larval development. Using a Bulked Segregant Analysis approach and a proportion test, markers clustered in three regions on LG 9, LG 10 and LG 18 were shown to be associated to the nematode resistant phenotype. QTL analysis confirmed the results and QTLs were thus designated respectively XiR2, XiR3 and XiR4, although a LOD-score below the significant threshold value was obtained for the QTL on LG 18. CONCLUSIONS Based on a high-resolution linkage map and a segregating grapevine backcross progeny, the first QTLs for resistance to D. vitifoliae and to X. index were identified from a muscadine source. All together these results open the way to the development of marker-assisted selection in grapevine rootstock breeding programs based on muscadine derived resistance to phylloxera and to X. index in order to delay GFLV transmission.
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Affiliation(s)
- Bernadette Rubio
- INRAE, UMR EGFV, 33883, Villenave d'Ornon, France
- IFV, Domaine de l'Espiguette, 30240, Le Grau du Roi, France
| | - Guillaume Lalanne-Tisné
- INRAE, UMR EGFV, 33883, Villenave d'Ornon, France
- IFV, Domaine de l'Espiguette, 30240, Le Grau du Roi, France
| | - Roger Voisin
- INRAE, Université Nice Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | | | - Ulysse Portier
- INRAE, Université Nice Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Cyril Van Ghelder
- INRAE, Université Nice Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | | | | | | | | | | | | | - Loïc Le Cunff
- IFV, Domaine de l'Espiguette, 30240, Le Grau du Roi, France
| | | | - Daniel Esmenjaud
- INRAE, Université Nice Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
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24
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Holtgräwe D, Rosleff Soerensen T, Hausmann L, Pucker B, Viehöver P, Töpfer R, Weisshaar B. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' ( Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. FRONTIERS IN PLANT SCIENCE 2020; 11:156. [PMID: 32194587 PMCID: PMC7064618 DOI: 10.3389/fpls.2020.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar 'Börner,' carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of 'Börner' to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the 'Börner' genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.
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Affiliation(s)
- Daniela Holtgräwe
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Ludger Hausmann
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Boas Pucker
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöver
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Siebeldingen, Germany
| | - Bernd Weisshaar
- Faculty of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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25
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Zou C, Karn A, Reisch B, Nguyen A, Sun Y, Bao Y, Campbell MS, Church D, Williams S, Xu X, Ledbetter CA, Patel S, Fennell A, Glaubitz JC, Clark M, Ware D, Londo JP, Sun Q, Cadle-Davidson L. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun 2020; 11:413. [PMID: 31964885 PMCID: PMC6972940 DOI: 10.1038/s41467-019-14280-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Bruce Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Allen Nguyen
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yongming Sun
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yun Bao
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | | | | | | | - Xia Xu
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Craig A Ledbetter
- USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA
| | - Sagar Patel
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Jeffrey C Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Jason P Londo
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
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26
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Kaya HB, Akdemir D, Lozano R, Cetin O, Sozer Kaya H, Sahin M, Smith JL, Tanyolac B, Jannink JL. Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Sci Rep 2019; 9:18764. [PMID: 31822760 PMCID: PMC6904458 DOI: 10.1038/s41598-019-55338-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/05/2019] [Indexed: 01/08/2023] Open
Abstract
Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.
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Affiliation(s)
- Hilal Betul Kaya
- Department of Bioengineering, Faculty of Engineering, Manisa Celal Bayar University, Manisa, Turkey.
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
| | - Deniz Akdemir
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY, USA
| | - Roberto Lozano
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | | | | | | | - Jenny L Smith
- National Clonal Germplasm Repository, USDA-ARS, One Shields Avenue, Davis, CA, USA
| | - Bahattin Tanyolac
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Jean-Luc Jannink
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
- USDA ARS, Robert W. Holley Center for Agriculture & Health, Ithaca, NY, USA
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27
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Demmings EM, Williams BR, Lee CR, Barba P, Yang S, Hwang CF, Reisch BI, Chitwood DH, Londo JP. Quantitative Trait Locus Analysis of Leaf Morphology Indicates Conserved Shape Loci in Grapevine. FRONTIERS IN PLANT SCIENCE 2019; 10:1373. [PMID: 31803199 PMCID: PMC6873345 DOI: 10.3389/fpls.2019.01373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/04/2019] [Indexed: 05/02/2023]
Abstract
Leaf shape in plants plays important roles in water use, canopy structure, and physiological tolerances to abiotic stresses; all important traits for the future development and sustainability of grapevine cultivation. Historically, researchers have used ampelography, the study of leaf shape in grapevines, to differentiate Vitis species and cultivars based on finite leaf attributes. However, ampelographic measurements have limitations and new methods for quantifying shape are now available. We paired an analysis of finite trait attributes with a 17-point landmark survey and generalized Procrustes analysis (GPA) to reconstruct grapevine leaves digitally from five interspecific hybrid mapping families. Using the reconstructed leaves, we performed three types of quantitative trait loci (QTL) analyses to determine the genetic architecture that defines leaf shape. In the first analysis, we compared several important ampelographic measurements as finite trait QTL. In the second and third analyses, we identified significant shape variation via principal components analysis (PCA) and using a multivariate least squares interval mapping (MLSIM) approach. In total, we identified 271 significant QTL across the three measures of leaf shape and identified specific QTL hotspots in the grape genome which appear to drive major aspects of grapevine leaf shape.
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Affiliation(s)
- Elizabeth M. Demmings
- Department of Food Science, Cornell University, Geneva, NY, United States
- Horticulture Section, School of Integrative Plant Science, Cornell Agritech at the New York State Agricultural Experiment Station, Geneva, NY, United States
| | - Brigette R. Williams
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Mountain Grove, MO, United States
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei City, Taiwan
| | - Paola Barba
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
| | - Shanshan Yang
- Bioinformatics Core, Knowledge Enterprise Development, Arizona State University, Tempe, AZ, United States
| | - Chin-Feng Hwang
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Mountain Grove, MO, United States
| | - Bruce I. Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell Agritech at the New York State Agricultural Experiment Station, Geneva, NY, United States
| | - Daniel H. Chitwood
- Department of Horticulture, Michigan State University, Lansing, MI, United States
- Department of Computational Mathematics, Science and Engineering, Michigan State University, Lansing, MI, United States
| | - Jason P. Londo
- Horticulture Section, School of Integrative Plant Science, Cornell Agritech at the New York State Agricultural Experiment Station, Geneva, NY, United States
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY, United States
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28
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Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS. The population genetics of structural variants in grapevine domestication. NATURE PLANTS 2019; 5:965-979. [PMID: 31506640 DOI: 10.1038/s41477-019-0507-8] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/26/2019] [Indexed: 05/20/2023]
Abstract
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.
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Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA
| | | | - Edwin Solares
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Yuanda Lv
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, Tbilisi, Georgia
| | - Dario Cantu
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
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29
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Sapkota S, Chen L, Yang S, Hyma K, Cadle-Davidson L, Hwang C. Quantitative trait locus mapping of downy mildew and botrytis bunch rot resistance in a Vitis aestivalis-derived ‘Norton’-based population. ACTA HORTICULTURAE 2019:305-312. [PMID: 0 DOI: 10.17660/actahortic.2019.1248.44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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30
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Zheng C, Boer MP, van Eeuwijk FA. Construction of Genetic Linkage Maps in Multiparental Populations. Genetics 2019; 212:1031-1044. [PMID: 31182487 PMCID: PMC6707453 DOI: 10.1534/genetics.119.302229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/04/2019] [Indexed: 11/18/2022] Open
Abstract
Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages.
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Affiliation(s)
- Chaozhi Zheng
- Biometris, Wageningen University and Research, 6700 AA, The Netherlands
| | - Martin P Boer
- Biometris, Wageningen University and Research, 6700 AA, The Netherlands
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31
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Tello J, Roux C, Chouiki H, Laucou V, Sarah G, Weber A, Santoni S, Flutre T, Pons T, This P, Péros JP, Doligez A. A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2237-2252. [PMID: 31049634 DOI: 10.1007/s00122-019-03351-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/20/2019] [Indexed: 05/21/2023]
Abstract
A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.
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Affiliation(s)
- Javier Tello
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Catherine Roux
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Hajar Chouiki
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Valérie Laucou
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Audrey Weber
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Timothée Flutre
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Thierry Pons
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Patrice This
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Péros
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France.
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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32
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Barba P, Loughner R, Wentworth K, Nyrop JP, Loeb GM, Reisch BI. A QTL associated with leaf trichome traits has a major influence on the abundance of the predatory mite Typhlodromus pyri in a hybrid grapevine population. HORTICULTURE RESEARCH 2019; 6:87. [PMID: 31645947 PMCID: PMC6804712 DOI: 10.1038/s41438-019-0169-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/16/2019] [Accepted: 05/31/2019] [Indexed: 05/29/2023]
Abstract
The abundance of predatory phytoseiid mites, Typhlodromus pyri, important biological control agents of spider mite pests in numerous crops, is positively influenced by the density of leaf trichomes and tuft-form domatia in vein axils. Identification of the genetic regions controlling both trophic levels could facilitate the improvement of predatory mite habitat in breeding programs. The abundance of T. pyri and non-glandular trichomes was measured in a segregating F1 family derived from the cross of the complex Vitis hybrid, 'Horizon', with Illinois 547-1 (V. rupestris B38 × V. cinerea B9), finding positive correlation among traits. High density genetic maps were used to localize one major quantitative trait locus (QTL) on chromosome 1 of Illinois 547-1 associated with both predatory mite abundance and leaf trichomes. This QTL explained 23% of the variation in phytoseiid abundance and similar amounts of variance in domatia rating (21%), domatia size (16%), leaf bristle density (37% in veins and 33% in blades), and leaf hair density (20% in veins and 15% in blades). Another nine QTL distributed among chromosomes 1, 2, 5, 8, and 15 were associated solely with trichome density, and explained 7-17% of the phenotypic variation. Combined, our results provide evidence of the genetic architecture of non-glandular trichomes in Vitis, with a major locus influencing trichome densities, domatia size and predatory mite abundance. This information is relevant for breeding grapevines with a more favorable habitat for biological control agents.
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Affiliation(s)
- Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, 8831314 Chile
| | - Rebecca Loughner
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Karen Wentworth
- Department of Entomology, Cornell AgriTech, Geneva, NY 14456 USA
| | - Jan Peter Nyrop
- Department of Entomology, Cornell AgriTech, Geneva, NY 14456 USA
| | - Gregory M. Loeb
- Department of Entomology, Cornell AgriTech, Geneva, NY 14456 USA
| | - Bruce I. Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Geneva, NY 14456 USA
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Abstract
Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species. Design Type(s) | sequence assembly objective • genetic mapping and linkage analysis objective • sequence annotation objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | | Sample Characteristic(s) | Vitis riparia • leaf |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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De Ollas C, Morillón R, Fotopoulos V, Puértolas J, Ollitrault P, Gómez-Cadenas A, Arbona V. Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:427. [PMID: 31057569 PMCID: PMC6477659 DOI: 10.3389/fpls.2019.00427] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Raphaël Morillón
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, France
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Jaime Puértolas
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San-Giuliano, France
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
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Sapkota S, Chen LL, Yang S, Hyma KE, Cadle-Davidson L, Hwang CF. Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived 'Norton'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:137-147. [PMID: 30341491 DOI: 10.1007/s00122-018-3203-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/06/2018] [Indexed: 05/08/2023]
Abstract
A major QTL for downy mildew resistance was detected on chromosome 18 (Rpv27) in Vitis aestivalis-derived 'Norton' based on a high-resolution linkage map with SNP and SSR markers as well as 2 years of field and laboratory phenotyping data. Grapevine downy mildew caused by the oomycete Plasmopara viticola is one of the most widespread and destructive diseases, particularly in humid viticultural areas where it damages green tissues and defoliates vines. Traditional Vitis vinifera wine grape cultivars are susceptible to downy mildew whereas several North American and a few Asian cultivars possess various levels of resistance to this disease. To identify genetic determinants of downy mildew resistance in V. aestivalis-derived 'Norton,' a mapping population with 182 genotypes was developed from a cross between 'Norton' and V. vinifera 'Cabernet Sauvignon' from which a consensus map was constructed via 411 simple sequence repeat (SSR) markers. Using genotyping-by-sequencing, 3825 single nucleotide polymorphism (SNP) markers were also generated. Of these, 1665 SNP and 407 SSR markers were clustered into 19 linkage groups in 159 genotypes, spanning a genetic distance of 2203.5 cM. Disease progression in response to P. viticola was studied in this population for 2 years under both laboratory and field conditions, and strong correlations were observed among data sets (Spearman correlation coefficient = 0.57-0.79). A quantitative trait loci (QTL) analysis indicated a resistance locus on chromosome 18, here named Rpv27, explaining 33.8% of the total phenotypic variation. Flanking markers closely linked with the trait can be further used for marker-assisted selection in the development of new cultivars with resistance to downy mildew.
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Affiliation(s)
- Surya Sapkota
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Springfield, MO, 65897, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, NYS Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
| | - Li-Ling Chen
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Springfield, MO, 65897, USA
| | - Shanshan Yang
- Bioinformatics Core Facility, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Katie E Hyma
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Chin-Feng Hwang
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Springfield, MO, 65897, USA.
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Burzynski-Chang EA, Ryona I, Reisch BI, Gonda I, Foolad MR, Giovannoni JJ, Sacks GL. HS-SPME-GC-MS Analyses of Volatiles in Plant Populations-Quantitating Compound × Individual Matrix Effects. Molecules 2018; 23:E2436. [PMID: 30249067 PMCID: PMC6222754 DOI: 10.3390/molecules23102436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 11/17/2022] Open
Abstract
Headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography⁻mass spectrometry (GC-MS) is widely employed for volatile analyses of plants, including mapping populations used in plant breeding research. Studies often employ a single internal surrogate standard, even when multiple analytes are measured, with the assumption that any relative changes in matrix effects among individuals would be similar for all compounds, i.e., matrix effects do not show Compound × Individual interactions. We tested this assumption using individuals from two plant populations: an interspecific grape (Vitis spp.) mapping population (n = 140) and a tomato (Solanum spp.) recombinant inbred line (RIL) population (n = 148). Individual plants from the two populations were spiked with a cocktail of internal standards (n = 6, 9, respectively) prior to HS-SPME-GC-MS. Variation in the relative responses of internal standards indicated that Compound × Individual interactions exist but were different between the two populations. For the grape population, relative responses among pairs of internal standards varied considerably among individuals, with a maximum of 249% relative standard deviation (RSD) for the pair of [U13C]hexanal and [U13C]hexanol. However, in the tomato population, relative responses of internal standard pairs varied much less, with pairwise RSDs ranging from 8% to 56%. The approach described in this paper could be used to evaluate the suitability of using surrogate standards for HS-SPME-GC-MS studies in other plant populations.
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Affiliation(s)
| | - Imelda Ryona
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA.
| | - Bruce I Reisch
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA.
| | - Itay Gonda
- Boyce Thompson Institute for Plant Science, Ithaca, NY 14853, USA.
| | - Majid R Foolad
- Department of Plant Science, Pennsylvania State University, University Park, PA 16802, USA.
| | | | - Gavin L Sacks
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA.
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Ma GJ, Song QJ, Markell SG, Qi LL. High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1423-1432. [PMID: 29564500 DOI: 10.1007/s00122-018-3087-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
A novel rust resistance gene, R 15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R 15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F2 individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R 15 ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R 15 was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.
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Affiliation(s)
- G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Q J Song
- Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - L L Qi
- Red River Valley Agricultural Research Center, USDA-Agricultural Research Service, Fargo, ND, 58102-2765, USA.
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Barba P, Lillis J, Luce RS, Travadon R, Osier M, Baumgartner K, Wilcox WF, Reisch BI, Cadle-Davidson L. Two dominant loci determine resistance to Phomopsis cane lesions in F 1 families of hybrid grapevines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1173-1189. [PMID: 29468460 PMCID: PMC5895676 DOI: 10.1007/s00122-018-3070-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/15/2018] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Rapid characterization of novel NB-LRR-associated resistance to Phomopsis cane spot on grapevine using high-throughput sampling and low-coverage sequencing for genotyping, locus mapping and transcriptome analysis provides insights into genetic resistance to a hemibiotrophic fungus. Phomopsis cane and leaf spot, caused by the hemibiotrophic fungus Diaporthe ampelina (syn = Phomopsis viticola), reduces the productivity in grapevines. Host resistance was studied on three F1 families derived from crosses involving resistant genotypes 'Horizon', Illinois 547-1, Vitis cinerea B9 and V. vinifera 'Chardonnay'. All families had progeny with extremely susceptible phenotypes, developing lesions on both dormant canes and maturing fruit clusters. Segregation of symptoms was observed under natural levels of inoculum in the field, while phenotypes on green shoots were confirmed under controlled inoculations in greenhouse. High-density genetic maps were used to localize novel qualitative resistance loci named Rda1 and Rda2 from V. cinerea B9 and 'Horizon', respectively. Co-linearity between reference genetic and physical maps allowed localization of Rda2 locus between 1.5 and 2.4 Mbp on chromosome 7, and Rda1 locus between 19.3 and 19.6 Mbp of chromosome 15, which spans a cluster of five NB-LRR genes. Further dissection of this locus was obtained by QTL mapping of gene expression values 14 h after inoculation across a subset of the 'Chardonnay' × V. cinerea B9 progeny. This provided evidence for the association between transcript levels of two of these NB-LRR genes with Rda1, with increased NB-LRR expression among susceptible progeny. In resistant parent V. cinerea B9, inoculation with D. ampelina was characterized by up-regulation of SA-associated genes and down-regulation of ethylene pathways, suggesting an R-gene-mediated response. With dominant effects associated with disease-free berries and minimal symptoms on canes, Rda1 and Rda2 are promising loci for grapevine genetic improvement.
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Affiliation(s)
- Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santa Rosa, 11610, Santiago, Chile.
| | | | - R Stephen Luce
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Michael Osier
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Kendra Baumgartner
- USDA-Agricultural Research Service, Crops Pathology and Genetics Research Unit, Davis, CA, 95616, USA
| | - Wayne F Wilcox
- Plant Pathology Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
| | - Bruce I Reisch
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
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Divilov K, Barba P, Cadle-Davidson L, Reisch BI. Single and multiple phenotype QTL analyses of downy mildew resistance in interspecific grapevines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1133-1143. [PMID: 29417162 PMCID: PMC5895686 DOI: 10.1007/s00122-018-3065-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/26/2018] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Downy mildew resistance across days post-inoculation, experiments, and years in two interspecific grapevine F1 families was investigated using linear mixed models and Bayesian networks, and five new QTL were identified. Breeding grapevines for downy mildew disease resistance has traditionally relied on qualitative gene resistance, which can be overcome by pathogen evolution. Analyzing two interspecific F1 families, both having ancestry derived from Vitis vinifera and wild North American Vitis species, across 2 years and multiple experiments, we found multiple loci associated with downy mildew sporulation and hypersensitive response in both families using a single phenotype model. The loci explained between 7 and 17% of the variance for either phenotype, suggesting a complex genetic architecture for these traits in the two families studied. For two loci, we used RNA-Seq to detect differentially transcribed genes and found that the candidate genes at these loci were likely not NBS-LRR genes. Additionally, using a multiple phenotype Bayesian network analysis, we found effects between the leaf trichome density, hypersensitive response, and sporulation phenotypes. Moderate-high heritabilities were found for all three phenotypes, suggesting that selection for downy mildew resistance is an achievable goal by breeding for either physical- or non-physical-based resistance mechanisms, with the combination of the two possibly providing durable resistance.
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Affiliation(s)
- Konstantin Divilov
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, Chile
| | | | - Bruce I Reisch
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment Station, Cornell University, Geneva, NY, USA.
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Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Accounting for Errors in Low Coverage High-Throughput Sequencing Data When Constructing Genetic Maps Using Biparental Outcrossed Populations. Genetics 2018; 209:65-76. [PMID: 29487138 PMCID: PMC5937187 DOI: 10.1534/genetics.117.300627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/25/2018] [Indexed: 01/06/2023] Open
Abstract
Next-generation sequencing is an efficient method that allows for substantially more markers than previous technologies, providing opportunities for building high-density genetic linkage maps, which facilitate the development of nonmodel species' genomic assemblies and the investigation of their genes. However, constructing genetic maps using data generated via high-throughput sequencing technology (e.g., genotyping-by-sequencing) is complicated by the presence of sequencing errors and genotyping errors resulting from missing parental alleles due to low sequencing depth. If unaccounted for, these errors lead to inflated genetic maps. In addition, map construction in many species is performed using full-sibling family populations derived from the outcrossing of two individuals, where unknown parental phase and varying segregation types further complicate construction. We present a new methodology for modeling low coverage sequencing data in the construction of genetic linkage maps using full-sibling populations of diploid species, implemented in a package called GUSMap. Our model is based on the Lander-Green hidden Markov model but extended to account for errors present in sequencing data. We were able to obtain accurate estimates of the recombination fractions and overall map distance using GUSMap, while most existing mapping packages produced inflated genetic maps in the presence of errors. Our results demonstrate the feasibility of using low coverage sequencing data to produce genetic maps without requiring extensive filtering of potentially erroneous genotypes, provided that the associated errors are correctly accounted for in the model.
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Smith HM, Smith BP, Morales NB, Moskwa S, Clingeleffer PR, Thomas MR. SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation. PLoS One 2018; 13:e0193121. [PMID: 29462210 PMCID: PMC5819801 DOI: 10.1371/journal.pone.0193121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/05/2018] [Indexed: 11/17/2022] Open
Abstract
Plant parasitic nematodes, including root knot nematode Meloidogyne species, cause extensive damage to agriculture and horticultural crops. As Vitis vinifera cultivars are susceptible to root knot nematode parasitism, rootstocks resistant to these soil pests provide a sustainable approach to maintain grapevine production. Currently, most of the commercially available root knot nematode resistant rootstocks are highly vigorous and take up excess potassium, which reduces wine quality. As a result, there is a pressing need to breed new root knot nematode resistant rootstocks, which have no impact on wine quality. To develop molecular markers that predict root knot nematode resistance for marker assisted breeding, a genetic approach was employed to identify a root knot nematode resistance locus in grapevine. To this end, a Meloidogyne javanica resistant Vitis cinerea accession was crossed to a susceptible Vitis vinifera cultivar Riesling and results from screening the F1 individuals support a model that root knot nematode resistance, is conferred by a single dominant allele, referred as MELOIDOGYNE JAVANICA RESISTANCE1 (MJR1). Further, MJR1 resistance appears to be mediated by a hypersensitive response that occurs in the root apical meristem. Single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing and results from association and genetic mapping identified the MJR1 locus, which is located on chromosome 18 in the Vitis cinerea accession. Validation of the SNPs linked to the MJR1 locus using a Sequenom MassARRAY platform found that only 50% could be validated. The validated SNPs that flank and co-segregate with the MJR1 locus can be used for marker-assisted selection for Meloidogyne javanica resistance in grapevine.
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Affiliation(s)
- Harley M. Smith
- CSIRO Agriculture and Food, Glen Osmond, South Australia, Australia
| | - Brady P. Smith
- CSIRO Agriculture and Food, Glen Osmond, South Australia, Australia
| | - Norma B. Morales
- CSIRO Agriculture and Food, Glen Osmond, South Australia, Australia
| | - Sam Moskwa
- CSIRO Information Management & Technology, Clayton South, Victoria, Australia
| | | | - Mark R. Thomas
- CSIRO Agriculture and Food, Glen Osmond, South Australia, Australia
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Klein LL, Miller AJ, Ciotir C, Hyma K, Uribe-Convers S, Londo J. High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. AMERICAN JOURNAL OF BOTANY 2018; 105:215-226. [PMID: 29578297 DOI: 10.1002/ajb2.1033] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/04/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Grapes are one of the most economically important berry crops worldwide, with the vast majority of production derived from the domesticated Eurasian species Vitis vinifera. Expansion of production into new areas, development of new cultivars, and concerns about adapting grapevines for changing climates necessitate the use of wild grapevine species in breeding programs. Diversity within Vitis has long been a topic of study; however, questions remain regarding relationships between species. Furthermore, the identity of some living accessions is unclear. METHODS This study generated 11,020 single nucleotide polymorphism (SNP) markers for more than 300 accessions in the USDA-ARS grape germplasm repository using genotyping-by-sequencing. Resulting data sets were used to reconstruct evolutionary relationships among several North American and Eurasian Vitis species, and to suggest taxonomic labels for previously unidentified and misidentified germplasm accessions based on genetic distance. KEY RESULTS Maximum likelihood analyses of SNP data support the monophyly of Vitis, subg. Vitis, a Eurasian subg. Vitis clade, and a North American subg. Vitis clade. Data delineate species groups within North America. In addition, analysis of genetic distance suggested taxonomic identities for 20 previously unidentified Vitis accessions and for 28 putatively misidentified accessions. CONCLUSIONS This work advances understanding of Vitis evolutionary relationships and provides the foundation for ongoing germplasm enhancement. It supports conservation and breeding efforts by contributing to a growing genetic framework for identifying novel genetic variation and for incorporating new, unsampled populations into the germplasm repository system.
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Affiliation(s)
- Laura L Klein
- Department of Biology, Saint Louis University, St. Louis, MO, 63110, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, MO, 63110, USA
| | - Claudia Ciotir
- Department of Biology, Saint Louis University, St. Louis, MO, 63110, USA
| | - Katie Hyma
- Cornell University, Institute for Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Simon Uribe-Convers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason Londo
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, 14425, USA
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Patel S, Lu Z, Jin X, Swaminathan P, Zeng E, Fennell AY. Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly. BMC Genomics 2018; 19:57. [PMID: 29343235 PMCID: PMC5773036 DOI: 10.1186/s12864-018-4434-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/04/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). RESULTS The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from the MYB and ERF families. CONCLUSIONS The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.
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Affiliation(s)
- Sagar Patel
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Zhixiu Lu
- Department of Computer Science, University of South Dakota, Vermillion, SD, USA
| | - Xiaozhu Jin
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Padmapriya Swaminathan
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA
| | - Erliang Zeng
- Department of Computer Science, University of South Dakota, Vermillion, SD, USA.,Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Anne Y Fennell
- Agronomy, Horticulture and Plant Science Department and BioSNTR, 247 McFadden BioStress Laboratory, South Dakota State University, Brookings, SD, 57006, USA.
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Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design. G3-GENES GENOMES GENETICS 2018; 8:161-172. [PMID: 29141988 PMCID: PMC5765344 DOI: 10.1534/g3.117.300376] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.
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Yan M, Byrne DH, Klein PE, Yang J, Dong Q, Anderson N. Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. HORTICULTURE RESEARCH 2018; 5:17. [PMID: 29619228 PMCID: PMC5878828 DOI: 10.1038/s41438-018-0021-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/03/2017] [Accepted: 01/22/2018] [Indexed: 05/09/2023]
Abstract
Roses, which have been cultivated for at least 5000 years, are one of the most important ornamental crops in the world. Because of the interspecific nature and high heterozygosity in commercial roses, the genetic resources available for rose are limited. To effectively identify markers associated with QTL controlling important traits, such as disease resistance, abundant markers along the genome and careful phenotyping are required. Utilizing genotyping by sequencing technology and the strawberry genome (Fragaria vesca v2.0.a1) as a reference, we generated thousands of informative single nucleotide polymorphism (SNP) markers. These SNPs along with known bridge simple sequence repeat (SSR) markers allowed us to create the first high-density integrated consensus map for diploid roses. Individual maps were first created for populations J06-20-14-3×"Little Chief" (J14-3×LC), J06-20-14-3×"Vineyard Song" (J14-3×VS) and "Old Blush"×"Red Fairy" (OB×RF) and these maps were linked with 824 SNPs and 13 SSR bridge markers. The anchor SSR markers were used to determine the numbering of the rose linkage groups. The diploid consensus map has seven linkage groups (LGs), a total length of 892.2 cM, and an average distance of 0.25 cM between 3527 markers. By combining three individual populations, the marker density and the reliability of the marker order in the consensus map was improved over a single population map. Extensive synteny between the strawberry and diploid rose genomes was observed. This consensus map will serve as the tool for the discovery of marker-trait associations in rose breeding using pedigree-based analysis. The high level of conservation observed between the strawberry and rose genomes will help further comparative studies within the Rosaceae family and may aid in the identification of candidate genes within QTL regions.
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Affiliation(s)
- Muqing Yan
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Patricia E. Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
| | - Jizhou Yang
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
- Present Address: Department of Computer Science, San Francisco State University, San Francisco, CA 94132 USA
| | - Qianni Dong
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Present Address: Monsanto Company, 700 Chesterfield Parkway West, Chesterfield, MO 63017 USA
| | - Natalie Anderson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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Divilov K, Wiesner-Hanks T, Barba P, Cadle-Davidson L, Reisch BI. Computer Vision for High-Throughput Quantitative Phenotyping: A Case Study of Grapevine Downy Mildew Sporulation and Leaf Trichomes. PHYTOPATHOLOGY 2017; 107:1549-1555. [PMID: 28745103 DOI: 10.1094/phyto-04-17-0137-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Quantitative phenotyping of downy mildew sporulation is frequently used in plant breeding and genetic studies, as well as in studies focused on pathogen biology such as chemical efficacy trials. In these scenarios, phenotyping a large number of genotypes or treatments can be advantageous but is often limited by time and cost. We present a novel computational pipeline dedicated to estimating the percent area of downy mildew sporulation from images of inoculated grapevine leaf discs in a manner that is time and cost efficient. The pipeline was tested on images from leaf disc assay experiments involving two F1 grapevine families, one that had glabrous leaves (Vitis rupestris B38 × 'Horizon' [RH]) and another that had leaf trichomes (Horizon × V. cinerea B9 [HC]). Correlations between computer vision and manual visual ratings reached 0.89 in the RH family and 0.43 in the HC family. Additionally, we were able to use the computer vision system prior to sporulation to measure the percent leaf trichome area. We estimate that an experienced rater scoring sporulation would spend at least 90% less time using the computer vision system compared with the manual visual method. This will allow more treatments to be phenotyped in order to better understand the genetic architecture of downy mildew resistance and of leaf trichome density. We anticipate that this computer vision system will find applications in other pathosystems or traits where responses can be imaged with sufficient contrast from the background.
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Affiliation(s)
- Konstantin Divilov
- First, second, and third authors: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY; fourth author: United States Department of Agriculture-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY; and fifth author: Horticulture Section, School of Integrative Plant Science, Cornell University
| | - Tyr Wiesner-Hanks
- First, second, and third authors: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY; fourth author: United States Department of Agriculture-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY; and fifth author: Horticulture Section, School of Integrative Plant Science, Cornell University
| | - Paola Barba
- First, second, and third authors: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY; fourth author: United States Department of Agriculture-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY; and fifth author: Horticulture Section, School of Integrative Plant Science, Cornell University
| | - Lance Cadle-Davidson
- First, second, and third authors: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY; fourth author: United States Department of Agriculture-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY; and fifth author: Horticulture Section, School of Integrative Plant Science, Cornell University
| | - Bruce I Reisch
- First, second, and third authors: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY; fourth author: United States Department of Agriculture-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY; and fifth author: Horticulture Section, School of Integrative Plant Science, Cornell University
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Zhang D, Easterling KA, Pitra NJ, Coles MC, Buckler ES, Bass HW, Matthews PD. Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop. THE PLANT GENOME 2017; 10. [PMID: 29293819 DOI: 10.3835/plantgenome2017.04.0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Hop ( L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female-biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using a genotyping-by-sequencing (GBS) approach. From the resulting ∼1.2 million single-nucleotide polymorphisms (SNPs), prequalified GBS markers were validated by inferences in population structures and phylogeny. Analysis of pseudo-testcross (Pt) mapping data from F families revealed mixed patterns of Mendelian and non-Mendelian segregation. Three-dimensional (3D) cytogenetic analysis of late meiotic prophase nuclei from two wild and two cultivated hop revealed conspicuous and prevalent occurrences of multiple, atypical, nondisomic chromosome complexes including autosomes. We used genome-wide association studies (GWAS) and fixation index (F) analysis to demonstrate selection mapping of genetic loci for key traits including sex, bitter acids, and drought tolerance. Among the possible mechanisms underlying the observed segregation distortion from the genomic data analysis, the cytogenetic analysis points to meiotic chromosome behavior as one of the contributing factors. The findings shed light on long-standing questions on the unusual transmission genetics and phenotypic variation in hop, with major implications for breeding, cultivation, and the natural history of .
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Abstract
We generated genomic data to estimate the population history of grapes, the most economically important horticultural crop in the world. Domesticated grapes experienced a protracted, 22,000-y population decline prior to domestication; we hypothesize that this decline reflects low-intensity cultivation by humans prior to domestication. Domestication altered the mating system of grapes. The sex determination region is detectable as a region of heightened genetic divergence between wild and cultivated accessions. Based on gene expression analyses, we propose candidate genes that alter sex determination. Finally, grapes contain more deleterious mutations in heterozygous states than do their wild ancestors. The accumulation of deleterious mutations is due in part to clonal propagation, which shelters deleterious recessive mutations. We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
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Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize. G3-GENES GENOMES GENETICS 2017; 7:2161-2170. [PMID: 28526729 PMCID: PMC5499125 DOI: 10.1534/g3.117.042036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of issues encountered with GBS be considered, including the sequencing of nonoverlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation. We addressed these issues while developing and validating a new, comprehensive platform for GBS. This study supports the notion that GBS can be tailored to particular aims, and using Zea mays our results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. Optimizing size selection to sequence a high proportion of shared loci among individuals in different libraries and using simple in silico filters, a GBS procedure was established that produces high call rates per marker (>85%) with accuracy exceeding 99.4%. Furthermore, by capitalizing on the sequence-read structure of GBS data (stacks of reads), a new tool for resolving local haplotypes and scoring phased genotypes was developed, a feature that is not available in many GBS pipelines. Using local haplotypes reduces the marker dimensionality of the genotype matrix while increasing the informativeness of the data. Phased GBS in maize also revealed the existence of reproducibly inaccurate (apparent accuracy) genotypes that were due to divergent copy number variants (CNVs) unobservable in the underlying single nucleotide polymorphism (SNP) data.
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