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Gómez HAG, Niederauer GF, Minatel IO, Antunes ERM, Carneiro MJ, Sawaya ACHF, Zanus MC, Ritschel PS, Quecini V, Pereira Lima GP, Marques MOM. Wine metabolome and sensory analyses demonstrate the oenological potential of novel grapevine genotypes for sustainable viticulture in warm climates. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 39171419 DOI: 10.1002/jsfa.13832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Genetic breeding is essential to develop grapevine genotypes adapted to warm climates and resistant to pathogens. Traditionally cultivated Vitis vinifera is susceptible to biotic and abiotic stresses. Winemakers and consumers, however, perceive wines from non-vinifera or hybrid cultivars as inferior. In this study, sensory analyses and comprehensive metabolite profiling by targeted and untargeted approaches were used to investigate the oenological potential of wines from grapes of genotypes developed throughout four breeding cycles to improve climate adaptation, sugar contents and berry color. RESULTS Novel genotypes had higher yields and the wines exhibited increased contents of polyphenols, including anthocyanins. Volatile monoterpenes in the wines decreased throughout breeding cycles in the absence of selective pressure. Polyphenol contents were higher in intermediate wines, with hydroxytyrosol contents reaching up to three times reported values. Mouthfeel attributes astringency, leafy taste, flavor and body, and persistency showed significant correlation with untargeted features. Supervised model-based analyses of the metabolome effectively discriminate wines from distinct genetic origins. CONCLUSION Taken together, the results demonstrate the potential of novel grapevine genotypes to a more sustainable viticulture and quality wine production in warm climates. Comprehensive metabolite profiling of the wines reveals that genotype clustering is dependent on the chemical class and that traits not submitted to selective pressure are also altered by breeding. Supervised multivariate models were effective to predict the genetic origin of the wines based on the metabolic profile, indicating the potential of the technique to identify biomarkers for wines from sustainable genotypes. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Héctor Alonzo Gómez Gómez
- School of Agriculture, São Paulo State University (Unesp), Botucatu, São Paulo, Brazil
- Plant Genetic Resources Center, Agronomic Institute (IAC), Campinas, São Paulo, Brazil
- Academic Department of Food, Faculty of Technological Sciences, National University of Agriculture, Catacamas, Honduras
| | | | - Igor Otavio Minatel
- Institute of Biosciences, São Paulo State University (Unesp), Botucatu, São Paulo, Brazil
| | | | | | | | | | | | - Vera Quecini
- Embrapa Uva e Vinho, Bento Gonçalves, Rio Grande do Sul, Brazil
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Possamai T, Scota L, Velasco R, Migliaro D. A Sustainable Strategy for Marker-Assisted Selection (MAS) Applied in Grapevine ( Vitis spp.) Breeding for Resistance to Downy ( Plasmopara Viticola) and Powdery ( Erysiphe Necator) Mildews. PLANTS (BASEL, SWITZERLAND) 2024; 13:2001. [PMID: 39065527 PMCID: PMC11280485 DOI: 10.3390/plants13142001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/04/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
Plant breeders utilize marker-assisted selection (MAS) to identify favorable or unfavorable alleles in seedlings early. In this task, they need methods that provide maximum information with minimal input of time and economic resources. Grape breeding aimed at producing cultivars resistant to pathogens employs several resistance loci (Rpv, Ren, and Run) that are ideal for implementing MAS. In this work, a sustainable MAS protocol was developed based on non-purified DNA (crude), multiplex PCR of SSR markers, and capillary electrophoresis, and its application on grapevine seedlings to follow some main resistance loci was described. The optimized protocol was utilized on 8440 samples and showed high efficiency, reasonable throughput (2-3.2 min sample), easy handling, flexibility, and tolerable costs (reduced by at least 3.5 times compared to a standard protocol). The Rpv, Ren, and Run allelic data analysis did not show limitations to loci combination and pyramiding, but segregation distortions were frequent and displayed both low (undesired) and high rates of inheritance. The protocol and results presented are useful tools for grape breeders and beyond, and they can address sustainable changes in MAS. Several progenies generated have valuable pyramided resistance and will be the subject of new studies and implementation in the breeding program.
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Affiliation(s)
| | | | | | - Daniele Migliaro
- CREA—Research Center for Viticulture and Enology, 31015 Conegliano, Italy; (L.S.); (R.V.)
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3
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Cantu D, Massonnet M, Cochetel N. The wild side of grape genomics. Trends Genet 2024; 40:601-612. [PMID: 38777691 DOI: 10.1016/j.tig.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.
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Affiliation(s)
- Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
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4
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Wang Y, Ding K, Li H, Kuang Y, Liang Z. Biography of Vitis genomics: recent advances and prospective. HORTICULTURE RESEARCH 2024; 11:uhae128. [PMID: 38966864 PMCID: PMC11220177 DOI: 10.1093/hr/uhae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/25/2024] [Indexed: 07/06/2024]
Abstract
The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kangyi Ding
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayang Li
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangfu Kuang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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5
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Gomez HAG, Niederauer GF, Minatel IO, Antunes ERM, Carneiro MJ, Sawaya ACHF, Zanus MC, Ritschel PS, Quecini V, Pereira Lima GP, Marques MOM. Metabolite profiling reveals the influence of grapevine genetic distance on the chemical signature of juices. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:2383-2397. [PMID: 37961851 DOI: 10.1002/jsfa.13124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/28/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Yield, disease tolerance, and climate adaptation are important traits in grapevine genetic breeding programs. Selection for these characteristics causes unpredictable changes in primary and specialized metabolism, affecting the physicochemical properties and chemical composition of the berries and their processed products, juice, and wine. In this study, we investigated the influence of the genetic distance between grapevine genotypes on the chemical signatures of the juices, by integrating comprehensive metabolic profiling to genetic analyses. RESULTS The studied grapevine cultivars exhibited low genetic diversity. Breeding for agronomic traits promoted higher contents of soluble sugars, total phenolics, and anthocyanins in the juices. Untargeted juice metabolomics identified a total of 147 metabolites, consisting of 30 volatiles, 21 phenolics, and 96 ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) features. Juices from grapes of the most recent cultivars exhibited increased levels of trans-resveratrol, catechin, and luteolin. The blend of volatiles from juices of later cultivars was also more complex, consisting of 29 distinct metabolites in 'BRS Magna'. Grapes from 'BRS Carmem', an intermediate cultivar, gave the most divergent UHPLC-MS juice profile. CONCLUSION Contents of soluble solids, total phenolics, and anthocyanins in grape juices were increased by controlled crosses and hybrid selection. Integrative analyses demonstrated that the juices' metabolic profiles accurately represent the cultivars' genetic distances. Juices from 'BRS Violeta' and 'BRS Magna' show relevant positive association with health-related phenolics and a distinct set of odor volatiles, although these characteristics were specifically sought by breeding. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Hector Alonzo Gomez Gomez
- School of Agriculture, São Paulo State University (UNESP), São Paulo, Brazil
- Plant Genetic Resources Center, Agronomic Institute (IAC), São Paulo, Brazil
| | | | - Igor Otavio Minatel
- Institute of Biosciences, São Paulo State University (UNESP), São Paulo, Brazil
| | | | | | | | - Mauro Celso Zanus
- Embrapa, Embrapa Uva e Vinho, Bento Gonçalves, 95701-008, RS, Brazil
| | | | - Vera Quecini
- Embrapa, Embrapa Uva e Vinho, Bento Gonçalves, 95701-008, RS, Brazil
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6
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Cochetel N, Minio A, Guarracino A, Garcia JF, Figueroa-Balderas R, Massonnet M, Kasuga T, Londo JP, Garrison E, Gaut BS, Cantu D. A super-pangenome of the North American wild grape species. Genome Biol 2023; 24:290. [PMID: 38111050 PMCID: PMC10729490 DOI: 10.1186/s13059-023-03133-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. RESULTS Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. CONCLUSIONS This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.
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Affiliation(s)
- Noé Cochetel
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Jadran F Garcia
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | | | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA, USA
| | - Jason P Londo
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA.
- Genome Center, University of California Davis, Davis, CA, USA.
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7
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Zou C, Sapkota S, Figueroa-Balderas R, Glaubitz J, Cantu D, Kingham BF, Sun Q, Cadle-Davidson L. A multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus. PLANT PHYSIOLOGY 2023; 193:2321-2336. [PMID: 37706526 DOI: 10.1093/plphys/kiad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/10/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023]
Abstract
Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multitiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2,000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of 3 putative disease resistance RPP13-like protein 2 genes located tandemly in a nonsyntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana 'PI 588149' assembly, initially built solely from Pacific Biosciences (PacBio) high-fidelity (HiFi) reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs and will likely be widely adopted in highly heterozygous species.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Surya Sapkota
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Jeff Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Brewster F Kingham
- DNA Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY 14456, USA
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8
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Zhang Y, Liu C, Liu X, Wang Z, Wang Y, Zhong GY, Li S, Dai Z, Liang Z, Fan P. Basic leucine zipper gene VvbZIP61 is expressed at a quantitative trait locus for high monoterpene content in grape berries. HORTICULTURE RESEARCH 2023; 10:uhad151. [PMID: 37701455 PMCID: PMC10493639 DOI: 10.1093/hr/uhad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/26/2023] [Indexed: 09/14/2023]
Abstract
The widely appreciated muscat flavor of grapes and wine is mainly attributable to the monoterpenes that accumulate in ripe grape berries. To identify quantitative trait loci (QTL) for grape berry monoterpene content, an F1 mapping population was constructed by a cross between two grapevine genotypes, one with neutral aroma berries (cv. 'Beifeng') and the other with a pronounced muscat aroma (elite Vitis vinifera line '3-34'). A high-density genetic linkage map spanning 1563.7 cM was constructed using 3332 SNP markers that were assigned to 19 linkage groups. Monoterpenes were extracted from the berry of the F1 progeny, then identified and quantified by gas chromatography-mass spectrometry. Twelve stable QTLs associated with the amounts of 11 monoterpenes in berries were thus identified. In parallel, the levels of RNA in berries from 34 diverse cultivars were estimated by RNA sequencing and compared to the monoterpene content of the berries. The expression of five genes mapping to stable QTLs correlated well with the monoterpene content of berries. These genes, including the basic leucine zipper VvbZIP61 gene on chromosome 12, are therefore considered as potentially being involved in monoterpene metabolism. Overexpression of VvbZIP61 in Vitis amurensis callus through Agrobacterium-mediated transformation significantly increased the accumulation of several monoterpenes in the callus, including nerol, linalool, geranial, geraniol, β-myrcene, and D-limonene. It is hypothesized that VvbZIP61 expression acts to increase muscat flavor in grapes. These results advance our understanding of the genetic control of monoterpene biosynthesis in grapes and provide important information for the marker-assisted selection of aroma compounds in grape breeding.
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Affiliation(s)
- Yuyu Zhang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuixia Liu
- Centre for Special Economic Plant Studies, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, Guangxi, China
| | - Xianju Liu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zemin Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Gan-yuan Zhong
- Grape Genetics Research Unit, USDA-ARS, Geneva 14456, USA
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Li B, Gschwend AR. Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1234130. [PMID: 37719220 PMCID: PMC10501149 DOI: 10.3389/fpls.2023.1234130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.
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Affiliation(s)
| | - Andrea R. Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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10
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Morales-Cruz A, Aguirre-Liguori J, Massonnet M, Minio A, Zaccheo M, Cochetel N, Walker A, Riaz S, Zhou Y, Cantu D, Gaut BS. Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. Commun Biol 2023; 6:580. [PMID: 37253933 DOI: 10.1038/s42003-023-04938-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives. There is little understanding of the genes that contribute to plant resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (Vitis vinifera) are not resistant to the bacterium. Here we study a wild grapevine species, V. arizonica, that segregates for resistance. Using genome-wide association, we identify candidate resistance genes. Resistance-associated kmers are shared with a sister species of V. arizonica but not with more distant species, suggesting that resistance evolved more than once. Finally, resistance is climate dependent, because individuals from low ( < 10 °C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in colder climates. In fact, climate is as effective a predictor of resistance phenotypes as some genetic markers. We extend our climate observations to additional crops, predicting that increased pathogen pressure is more likely for grapevines and almonds than some other susceptible crops.
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Affiliation(s)
- Abraham Morales-Cruz
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Jonas Aguirre-Liguori
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Mélanie Massonnet
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Andrea Minio
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Mirella Zaccheo
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Noe Cochetel
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Andrew Walker
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA
| | - Summaira Riaz
- San Joaquin Valley Agricultural Center, United States Dept of Agriculture, Parlier, CA, USA
| | - Yongfeng Zhou
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Agricultural Genomics Institute at Shenzhen, The Chinese Academy of Agricultural Sciences, No. 7 Pengfei Road, Shenzen, 518120, China.
| | - Dario Cantu
- Dept. of Viticulture and Enology, University of California, Davis, CA, USA.
- Dept. of Viticulture and Enology, One Shields Avenue, University of California Davis, Davis, CA, 95616-5270, USA.
| | - Brandon S Gaut
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
- Dept. of Ecology and Evolutionary Biology, 321 Steinhaus Hall UC Irvine, Irvine, CA, 92617-2525, USA.
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11
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Sapkota S, Zou C, Ledbetter C, Underhill A, Sun Q, Gadoury D, Cadle-Davidson L. Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew. HORTICULTURE RESEARCH 2023; 10:uhad052. [PMID: 37213681 PMCID: PMC10194894 DOI: 10.1093/hr/uhad052] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/12/2023] [Indexed: 05/23/2023]
Abstract
Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis. Here, a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis 'PI 588631' that rapidly stopped over 97% of Erysiphe necator conidia, before or immediately after emergence of a secondary hypha from appressoria. This resistance was effective across multiple years of vineyard evaluation on leaves, stems, rachises, and fruit and against a diverse array of E. necator laboratory isolates. Using core genome rhAmpSeq markers, resistance mapped to a single dominant locus (here named REN12) on chromosome 13 near 22.8-27.0 Mb, irrespective of tissue type, explaining up to 86.9% of the phenotypic variation observed on leaves. Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region, from 25.15 to 25.93 Mb. RNASeq analysis indicated the allele-specific expression of four resistance genes (NLRs) from the resistant parent. REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented, and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms. While no virulent isolates were identified among the genetically diverse isolates and wild populations of E. necator tested here, NLR loci like REN12 are often race-specific. Thus, stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90% reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.
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Affiliation(s)
- Surya Sapkota
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Craig Ledbetter
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Crop Diseases, Pests and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Anna Underhill
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - David Gadoury
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
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12
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Alahakoon D, Fennell A. Genetic analysis of grapevine root system architecture and loci associated gene networks. FRONTIERS IN PLANT SCIENCE 2023; 13:1083374. [PMID: 36816477 PMCID: PMC9932984 DOI: 10.3389/fpls.2022.1083374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Own-rooted grapevines and grapevine rootstocks are vegetatively propagated from cuttings and have an adventitious root system. Unraveling the genetic underpinnings of the adventitious root system architecture (RSA) is important for improving own-rooted and grafted grapevine sustainability for a changing climate. Grapevine RSA genetic analysis was conducted in an Vitis sp. 'VRS-F2' population. Nine root morphology, three total root system morphology, and two biomass traits that contribute to root anchorage and water and nutrient uptake were phenotyped. Quantitative trait loci (QTL) analysis was performed using a high density integrated GBS and rhAmpSeq genetic map. Thirty-one QTL were detected for eleven of the RSA traits (surface area, root volume, total root length, fresh weight, number of tips, forks or links, longest root and average root diameter, link length, and link surface area) revealing many small effects. Several QTL were colocated on chromosomes 1, 9, 13, 18, and 19. QTL with identical peak positions on chromosomes 1 or 13 were enriched for AP2-EREBP, AS2, C2C2-CO, HMG, and MYB transcription factors, and QTL on chromosomes 9 or 13 were enriched for the ALFIN-LIKE transcription factor and regulation of autophagy pathways. QTL modeling for individual root traits identified eight models explaining 13.2 to 31.8% of the phenotypic variation. 'Seyval blanc' was the grandparent contributing to the allele models that included a greater surface area, total root length, and branching (number of forks and links) traits promoting a greater root density. In contrast, V. riparia 'Manitoba 37' contributed the allele for greater average branch length (link length) and diameter, promoting a less dense elongated root system with thicker roots. LATERAL ORGAN BOUNDARY DOMAIN (LBD or AS2/LOB) and the PROTODERMAL FACTOR (PFD2 and ANL2) were identified as important candidate genes in the enriched pathways underlying the hotspots for grapevine adventitious RSA. The combined QTL hotspot and trait modeling identified transcription factors, cell cycle and circadian rhythm genes with a known role in root cell and epidermal layer differentiation, lateral root development and cortex thickness. These genes are candidates for tailoring grapevine root system texture, density and length in breeding programs.
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Affiliation(s)
| | - Anne Fennell
- Agronomy, Horticulture, and Plant Science Department, South Dakota State University, Brookings, SD, United States
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13
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Kong Y, Liu C, Zhang X, Liu X, Li W, Li F, Wang X, Yue X. Characterization of fatty acid compositions in longissimus thoracis muscle and identification of candidate gene and SNPs related to polyunsaturated fatty acid in Hu sheep. J Anim Sci 2023; 101:skac382. [PMID: 36394948 PMCID: PMC9833039 DOI: 10.1093/jas/skac382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Fatty acid (FA) composition contributes greatly to the quality and nutritional value of lamb meat. In the present study, FA was measured in longissimus thoracis (LT) muscles of 1,085 Hu sheep using gas chromatography. Comparative transcriptomic analysis was conducted in LT muscles to identify differentially expressed genes (DEGs) between six individuals with high polyunsaturated fatty acids (H-PUFA, 15.27% ± 0.42%) and six with low PUFA (L-PUFA, 5.22% ± 0.25%). Subsequently, the single nucleotide polymorphisms (SNPs) in a candidate gene PLIN2 were correlated with FA traits. The results showed a total of 29 FA compositions and 8 FA groups were identified, with the highest content of monounsaturated fatty acids (MUFA, 46.54%, mainly C18:1n9c), followed by saturated fatty acids (SFA, 44.32%, mainly C16:0), and PUFA (8.72%, mainly C18:2n6c), and significant correlations were observed among the most of FA traits. Transcriptomic analyses identified 110 upregulated and 302 downregulated DEGs between H-PUFA and L-PUFA groups. The functional enrichment analysis revealed three significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 17 gene ontology (GO) terms, in which regulation of lipolysis in adipocytes, the AMPK signaling pathway, and the PPAR signaling pathway may play important roles in FA metabolism and biosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified 37 module genes associated with PUFA-related traits. In general, PLIN1, LIPE, FABP4, LEP, ACACA, ADIPOQ, SCD, PCK2, FASN, PLIN2, LPL, FABP3, THRSP, and ACADVL may have a great impact on PUFA metabolism and lipid deposition. Four SNPs within PLIN2 were significantly associated with FA. Of those, SNP1 (g.287 G>A) was significantly associated with C18:1n9c and MUFA, and SNP4 (g.7807 T>C) was significantly correlated with PUFA (C18:3n3). In addition, the combined genotype of SNP1 (g.287 G>A), SNP3 (g.7664 T>C), and SNP4 (g.7807 T>C) were significantly correlated with C16:1, C17:0, C18:1C6, PUFA (C18:3n3, C22:6n3), and n-6/n-3 PUFA. These results contribute to the knowledge of the biological mechanisms and genetic markers involved in the composition of FA in Hu sheep.
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Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chongyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xueying Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xing Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wenqiao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xinji Wang
- Extension Station of Animal Husbandry and Veterinary Medicine in Minqin, Minqin County 733300, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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14
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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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15
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HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt. Sci Data 2022; 9:660. [PMID: 36307491 PMCID: PMC9616894 DOI: 10.1038/s41597-022-01753-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/30/2022] [Indexed: 11/12/2022] Open
Abstract
Cultivated grapevines are commonly grafted on closely related species to cope with specific biotic and abiotic stress conditions. The three North American Vitis species V. riparia, V. rupestris, and V. berlandieri, are the main species used for breeding grape rootstocks. Here, we report the diploid chromosome-scale assembly of three widely used rootstocks derived from these species: Richter 110 (110R), Kober 5BB, and 101–14 Millardet et de Grasset (Mgt). Draft genomes of the three hybrids were assembled using PacBio HiFi sequences at an average coverage of 53.1 X-fold. Using the tool suite HaploSync, we reconstructed the two sets of nineteen chromosome-scale pseudomolecules for each genome with an average haploid genome size of 494.5 Mbp. Residual haplotype switches were resolved using shared-haplotype information. These three reference genomes represent a valuable resource for studying the genetic basis of grape adaption to biotic and abiotic stresses, and designing trait-associated markers for rootstock breeding programs. Measurement(s) | Genome Assembly Sequence | Technology Type(s) | PacBio Sequel System | Sample Characteristic - Organism | Vitis cinerea var. helleri x Vitis rupestris • Vitis riparia x Vitis rupestris • Vitis cinerea var. helleri x Vitis riparia | Sample Characteristic - Location | State of California |
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16
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Qiu T, Underhill A, Sapkota S, Cadle-Davidson L, Jiang Y. High throughput saliency-based quantification of grape powdery mildew at the microscopic level for disease resistance breeding. HORTICULTURE RESEARCH 2022; 9:uhac187. [PMID: 36338851 PMCID: PMC9630970 DOI: 10.1093/hr/uhac187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Imaging-based high throughput phenotyping (HTP) systems have demonstrated promising solutions to enhance genetic understanding of grapevine powdery mildew (PM) resistance and have accelerated PM-resistant cultivar breeding. The accuracy and throughput of extracting phenotypic traits from images are still the bottleneck of modern HTP systems, especially at the microscopic level. The goal of this study was to develop a saliency-based processing pipeline for the quantification of PM infection in microscopic images and comprehensively evaluate its performance for genetic analyses. An input image was segregated into subimages that were classified as infected or healthy by a pretrained CNN classifier. Saliency maps from the classification were generated post-hoc and used for the quantification of PM infection in the input image at the pixel level without the use of mask annotations. A total of seven phenotypic traits were extracted from images collected for a biparental population. Experimental results showed that optimal combinations of convolutional neural network and saliency methods achieved strong measurement correlations (r = 0.74 to 0.75) with human assessments at the image patch level, and the traits calculated by the saliency-based processing pipeline were highly correlated (r = 0.87 to 0.88) with reference PM infection ratings at the leaf image level. The high quantification accuracy of the saliency-based pipeline led to the increased explanation of phenotypic variance and reliable identification of quantitative trait loci. Therefore, the saliency-based processing pipeline can be used as an effective and efficient analysis tool for PM disease research and breeding programs in the future, especially agricultural and life science studies requiring microscopic image analysis.
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Affiliation(s)
- Tian Qiu
- School of Electrical and Computer Engineering, College of Engineering, Cornell University, Ithaca, NY 14850, United States of America
| | - Anna Underhill
- United States Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, United States of America
| | - Surya Sapkota
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, United States of America
| | - Lance Cadle-Davidson
- United States Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, United States of America
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, United States of America
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17
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Park M, Darwish AG, Elhag RI, Tsolova V, Soliman KFA, El-Sharkawy I. A multi-locus genome-wide association study reveals the genetics underlying muscadine antioxidant in berry skin. FRONTIERS IN PLANT SCIENCE 2022; 13:969301. [PMID: 35991419 PMCID: PMC9386419 DOI: 10.3389/fpls.2022.969301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Muscadine berries display enhanced nutraceutical value due to the accumulation of distinctive phytochemical constituents with great potential antioxidant activity. Such nutritional and health merits are not only restricted to muscadine, but muscadine berries accumulate higher amounts of bioactive polyphenolics compared with other grape species. For the genetic study of the antioxidant trait in muscadine, a multi-locus genome-wide association study (GWAS) with 350 muscadine genotypes and 1,283 RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) markers was performed. Phenotyping was conducted with several antioxidant-related traits, including total phenolic content (TPC), total flavonoid content (TFC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, and FRAP antioxidant assay in muscadine berry skin. The correlation coefficient analysis revealed that the TPC, and DPPH/FRAP activities were significantly correlated. Through the GWAS analysis, 12 QTNs were identified from the four traits, of which six were pleiotropic QTNs. Two pleiotropic QTNs, chr2_14464718 and chr4_16491374, were commonly identified from the TPC and DPPH/FRAP activities. Co-located genes with the two pleiotropic QTNs were isolated, and two candidate genes were identified with transcriptome analysis. UDP-glycosyltransferase and 4-hydroxy-4-methyl-2-oxoglutarate aldolase were the candidate genes that are positively and negatively correlated to the quantitative property of traits, respectively. These results are the first genetic evidence of the quantitative property of antioxidants in muscadine and provide genetic resources for breeding antioxidant-rich cultivars for both Muscadinia and Euvitis species.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Ahmed G. Darwish
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
- Department of Biochemistry, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Rashid I. Elhag
- College of Science and Technology, Florida A&M University, Tallahassee, FL, United States
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Karam F. A. Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
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18
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Minio A, Cochetel N, Vondras AM, Massonnet M, Cantu D. Assembly of complete diploid-phased chromosomes from draft genome sequences. G3 GENES|GENOMES|GENETICS 2022; 12:6605224. [PMID: 35686922 PMCID: PMC9339290 DOI: 10.1093/g3journal/jkac143] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023]
Abstract
De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosync’s correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
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Alahakoon D, Fennell A, Helget Z, Bates T, Karn A, Manns D, Mansfield AK, Reisch BI, Sacks G, Sun Q, Zou C, Cadle-Davidson L, Londo JP. Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map. PLANTS (BASEL, SWITZERLAND) 2022; 11:696. [PMID: 35270166 PMCID: PMC8912348 DOI: 10.3390/plants11050696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [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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Affiliation(s)
- Dilmini Alahakoon
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA; (D.A.); (Z.H.)
| | - Anne Fennell
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA; (D.A.); (Z.H.)
| | - Zachary Helget
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA; (D.A.); (Z.H.)
| | - Terry Bates
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; (T.B.); (G.S.)
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (B.I.R.); (J.P.L.)
| | - David Manns
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.M.); (A.K.M.)
| | - Anna Katharine Mansfield
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.M.); (A.K.M.)
| | - Bruce I. Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (B.I.R.); (J.P.L.)
| | - Gavin Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; (T.B.); (G.S.)
| | - Qi Sun
- Computational Biology Service Unit, Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY 14853, USA; (Q.S.); (C.Z.)
| | - Cheng Zou
- Computational Biology Service Unit, Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY 14853, USA; (Q.S.); (C.Z.)
| | | | - Jason P. Londo
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (B.I.R.); (J.P.L.)
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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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21
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Yin L, Karn A, Cadle-Davidson L, Zou C, Londo J, Sun Q, Clark MD. Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape. HORTICULTURE RESEARCH 2022; 9:uhac027. [PMID: 35184180 PMCID: PMC8976690 DOI: 10.1093/hr/uhac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/13/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The foliage of the native grape species Vitis riparia and certain cold-hardy hybrid grapes are particularly susceptible to the insect pest phylloxera, Daktulosphaira vitifoliae Fitch. A previous study using a cold-hardy hybrid grape biparental F1 population (N~125) detected the first quantitative trait locus (QTL) for foliar resistance on chromosome 14, designated as resistance to Daktulosphaira vitifoliae 3 (Rdv3). This locus spans a ~7-Mbp (10-20 cM) region and is too wide for effective marker-assisted selection or identification of candidate genes. Therefore, we fine mapped the QTL using a larger F1 population, GE1783 (N~1023), and genome-wide rhAmpSeq haplotype markers. Through three selective phenotyping experiments replicated in the greenhouse, we screened 184 potential recombinants of GE1783 using a 0 to 7 severity rating scale among other phylloxera severity traits. A 500-kb fine mapped region at 4.8 Mbp on chromosome 14 was identified. The tightly linked rhAmpSeq marker 14_4805213 and flanking markers can be used for future marker-assisted breeding. This region contains 36 candidate genes with predicted functions in disease resistance (R genes and Bonzai genes) and gall formation (bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase). Disease resistance genes suggest a traditional R-gene-mediated resistance mechanism often accompanied by a hypersensitive response, which has been widely studied in the plant pathology field. A novel resistance mechanism, non-responsiveness to phylloxera gall formation is proposed as a function of the bifunctional dehydratase gene, which plays a role in gallic acid biosynthesis and is important in gall formation. This study has implications for improvement of foliar phylloxera resistance in cold-hardy hybrid germplasm and is a starting place to understand the mechanism of resistance in crops to gall-forming insects.
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Affiliation(s)
- Lu Yin
- Department of Horticultural Science, University of Minnesota, Twin Cities, Minnesota 55018, USA
- School of Life Science, Arizona State University, Tempe, Arizona 85281, USA
| | - Avinash Karn
- AgReliant Genetics LLC, Lebanon, Indiana 46052, USA
- School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, New York 14456, USA
| | - Lance Cadle-Davidson
- School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, New York 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, New York 14456, USA
| | - Cheng Zou
- Institute of Biotechnology, BRC Bioinformatics Facility, Cornell University, Ithaca, New York 14853, USA
| | - Jason Londo
- School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, New York 14456, USA
- Grape Genetics Research Unit, USDA-ARS, Geneva, New York 14456, USA
| | - Qi Sun
- Institute of Biotechnology, BRC Bioinformatics Facility, Cornell University, Ithaca, New York 14853, USA
| | - Matthew D Clark
- Department of Horticultural Science, University of Minnesota, Twin Cities, Minnesota 55018, USA
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22
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Park M, Vera D, Kambrianda D, Gajjar P, Cadle-Davidson L, Tsolova V, El-Sharkawy I. Chromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits. HORTICULTURE RESEARCH 2022; 9:uhab011. [PMID: 35040982 PMCID: PMC8769032 DOI: 10.1093/hr/uhab011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/25/2021] [Indexed: 05/29/2023]
Abstract
Vitis has two subgenera: Euvitis, which includes commercially important Vitis vinifera and interspecific hybrid cultivars, and Muscadinia. Of note, the market for Muscadinia grapes remains small, and only Muscadinia rotundifolia is cultivated as a commercial crop. To establish a basis for the study of Muscadinia species, we generated chromosome-level whole-genome sequences of Muscadinia rotundifolia cv. Noble. A total of 393.8 Mb of sequences were assembled from 20 haploid chromosomes, and 26 394 coding genes were identified from the sequences. Comparative analysis with the genome sequence of V. vinifera revealed a smaller size of the M. rotundifolia genome but highly conserved gene synteny. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from breeding populations of M. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 52 quantitative trait nucleotides (QTNs) associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the QTNs with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
| | - Daniel Vera
- Silico LLC, 23 Essex Street #761119, Melrose, MA 02176, USA
| | - Devaiah Kambrianda
- Plant and Soil Sciences, Southern University Agricultural Research and Extension Center, 181 B. A. Little Dr., Baton Rouge, LA 70813, USA
| | - Pranavkumar Gajjar
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
| | - Lance Cadle-Davidson
- USDA-ARS, Grape Genetics Research Unit, 630 West W North St., Geneva, NY, 14456, USA
| | - Violeta Tsolova
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, 6361 Mahan Dr., Tallahassee, FL 32308, USA
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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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Wolfe MD, Chan AW, Kulakow P, Rabbi I, Jannink JL. Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices. Genetics 2021; 219:iyab122. [PMID: 34740244 PMCID: PMC8570794 DOI: 10.1093/genetics/iyab122] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 11/14/2022] Open
Abstract
Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).
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Affiliation(s)
- Marnin D Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences,
Cornell University, Ithaca, NY 14850, USA
| | - Ariel W Chan
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences,
Cornell University, Ithaca, NY 14850, USA
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan,
Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan,
Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences,
Cornell University, Ithaca, NY 14850, USA
- USDA-ARS, Ithaca, NY 14850, USA
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25
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Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021; 22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. RESULTS By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. CONCLUSIONS Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | | | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
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26
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Cochetel N, Minio A, Massonnet M, Vondras AM, Figueroa-Balderas R, Cantu D. Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. G3-GENES GENOMES GENETICS 2021; 11:6129119. [PMID: 33824960 PMCID: PMC8049426 DOI: 10.1093/g3journal/jkab033] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/22/2021] [Indexed: 12/11/2022]
Abstract
Muscadinia rotundifolia, the muscadine grape, has been cultivated for centuries in the southeastern United States. M. rotundifolia is resistant to many of the pathogens that detrimentally affect Vitis vinifera, the grape species commonly used for winemaking. For this reason, M. rotundifolia is a valuable genetic resource for breeding. Single-molecule real-time reads were combined with optical maps to reconstruct the two haplotypes of each of the 20 M. rotundifolia cv. Trayshed chromosomes. The completeness and accuracy of the assembly were confirmed using a high-density linkage map. Protein-coding genes were annotated using an integrated and comprehensive approach. This included using full-length cDNA sequencing (Iso-Seq) to improve gene structure and hypothetical spliced variant predictions. Our data strongly support that Muscadinia chromosomes 7 and 20 are fused in Vitis and pinpoint the location of the fusion in Cabernet Sauvignon and PN40024 chromosome 7. Disease-related gene numbers in Trayshed and Cabernet Sauvignon were similar, but their clustering locations were different. A dramatic expansion of the Toll/Interleukin-1 Receptor-like Nucleotide-Binding Site Leucine-Rich Repeat (TIR-NBS-LRR) class was detected on Trayshed chromosome 12 at the Resistance to Uncinula necator 1 (RUN1)/Resistance to Plasmopara viticola 1 (RPV1) locus, which confers strong dominant resistance to powdery and downy mildews. A genome browser, annotation, and Blast tool for Trayshed are available at www.grapegenomics.com.
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Affiliation(s)
- Noé Cochetel
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
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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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28
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Zhong H, Zhang F, Zhou X, Pan M, Xu J, Hao J, Han S, Mei C, Xian H, Wang M, Ji J, Shi W, Wu X. Genome-Wide Identification of Sequence Variations and SSR Marker Development in the Munake Grape Cultivar. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.664835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Munake grape cultivar produces uniquely flavored and high-quality fruits. Despite the numerous beneficial agronomic traits of Munake, there are few genetic resources available for this cultivar. To address this knowledge gap, the entire genome was sequenced using whole-genome sequencing approaches and compared with a Vitis vinifera L. reference genome. This study describes more than 3 million single nucleotide polymorphism (SNP), 300,000 insertion and deletion (InDel), 14,000 structural variation (SV), and 80,000 simple sequence repeat (SSR) markers (one SSR per 4.23 kb), as well as their primers. Among the SSRs, 44 SSR primer pairs were randomly selected and validated by polymerase chain reaction (PCR), allowing discrimination between the different Munake cultivar genotypes. The genetic data provided allow a deeper understanding of Munake cultivar genomic sequence and contribute to better knowledge of the genetic basis behind its key agronomic traits.
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29
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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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30
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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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Karn A, Zou C, Brooks S, Fresnedo-Ramírez J, Gabler F, Sun Q, Ramming D, Naegele R, Ledbetter C, Cadle-Davidson L. Discovery of the REN11 Locus From Vitis aestivalis for Stable Resistance to Grapevine Powdery Mildew in a Family Segregating for Several Unstable and Tissue-Specific Quantitative Resistance Loci. FRONTIERS IN PLANT SCIENCE 2021; 12:733899. [PMID: 34539723 PMCID: PMC8448101 DOI: 10.3389/fpls.2021.733899] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/09/2021] [Indexed: 05/05/2023]
Abstract
Race-specific resistance loci, whether having qualitative or quantitative effects, present plant-breeding challenges for phenotypic selection and deciding which loci to select or stack with other resistance loci for improved durability. Previously, resistance to grapevine powdery mildew (GPM, caused by Erysiphe necator) was predicted to be conferred by at least three race-specific loci in the mapping family B37-28 × C56-11 segregating for GPM resistance from Vitis aestivalis. In this study, 9 years of vineyard GPM disease severity ratings plus a greenhouse and laboratory assays were genetically mapped, using a rhAmpSeq core genome marker platform with 2,000 local haplotype markers. A new qualitative resistance locus, named REN11, on the chromosome (Chr) 15 was found to be effective in nearly all (11 of 12) vineyard environments on leaves, rachis, berries, and most of the time (7 of 12) stems. REN11 was independently validated in a pseudo-testcross with the grandparent source of resistance, "Tamiami." Five other loci significantly predicted GPM severity on leaves in only one or two environments, which could indicate race-specific resistance or their roles in different timepoints in epidemic progress. Loci on Chr 8 and 9 reproducibly predicted disease severity on stems but not on other tissues and had additive effects with REN11 on the stems. The rhAmpSeq local haplotype sequences published in this study for REN11 and Chr 8 and 9 stem quantitative trait locus (QTL) can be used directly for marker-assisted selection or converted to SNP assays. In screening for REN11 in a diversity panel of 20,651 vines representing the diversity of Vitis, this rhAmpSeq haplotype had a false positive rate of 0.034% or less. The effects of the other foliar resistance loci detected in this study seem too unstable for genetic improvement regardless of quantitative effect size, whether due to race specificity or other environmental variables.
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Affiliation(s)
- Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, United States
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Siraprapa Brooks
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Grape Genetics Research Unit, Geneva, NY, United States
| | - Jonathan Fresnedo-Ramírez
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Franka Gabler
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Commodity Protection and Quality Research, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Qi Sun
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Grape Genetics Research Unit, Geneva, NY, United States
| | - David Ramming
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Crop Diseases, Pests and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Rachel Naegele
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Crop Diseases, Pests and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Craig Ledbetter
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Crop Diseases, Pests and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, United States
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Grape Genetics Research Unit, Geneva, NY, United States
- *Correspondence: Lance Cadle-Davidson
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Weldon WA, Knaus BJ, Grünwald NJ, Havill JS, Block MH, Gent DH, Cadle-Davidson LE, Gadoury DM. Transcriptome-Derived Amplicon Sequencing Markers Elucidate the U.S. Podosphaera macularis Population Structure Across Feral and Commercial Plantings of Humulus lupulus. PHYTOPATHOLOGY 2021; 111:194-203. [PMID: 33044132 DOI: 10.1094/phyto-07-20-0299-fi] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Obligately biotrophic plant pathogens pose challenges in population genetic studies due to their genomic complexities and elaborate culturing requirements with limited biomass. Hop powdery mildew (Podosphaera macularis) is an obligately biotrophic ascomycete that threatens sustainable hop production. P. macularis populations of the Pacific Northwest (PNW) United States differ from those of the Midwest and Northeastern United States, lacking one of two mating types needed for sexual recombination and harboring two strains that are differentially aggressive on the cultivar Cascade and able to overcome the Humulus lupulus R-gene R6 (V6), respectively. To develop a high-throughput marker platform for tracking the flow of genotypes across the United States and internationally, we used an existing transcriptome of diverse P. macularis isolates to design a multiplex of 54 amplicon sequencing markers, validated across a panel of 391 U.S. samples and 123 international samples. The results suggest that P. macularis from U.S. commercial hop yards form one population closely related to P. macularis of the United Kingdom, while P. macularis from U.S. feral hop locations grouped with P. macularis of Eastern Europe. Included in this multiplex was a marker that successfully tracked V6-virulence in 65 of 66 samples with a confirmed V6-phenotype. A new qPCR assay for high-throughput genotyping of P. macularis mating type generated the highest resolution distribution map of P. macularis mating type to date. Together, these genotyping strategies enable the high-throughput and inexpensive tracking of pathogen spread among geographical regions from single-colony samples and provide a roadmap to develop markers for other obligate biotrophs.
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Affiliation(s)
- William A Weldon
- Section of Plant Pathology and Plant-Microbe Biology, Cornell AgriTech, Cornell University, Geneva, NY 14456
| | - Brian J Knaus
- Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service Horticultural Crops Research Unit, Corvallis, OR 97330
| | - Joshua S Havill
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Mary H Block
- Department of Botany and Plant Pathology, Corvallis, OR 97331
| | - David H Gent
- U.S. Department of Agriculture-Agricultural Research Service Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - Lance E Cadle-Davidson
- Section of Plant Pathology and Plant-Microbe Biology, Cornell AgriTech, Cornell University, Geneva, NY 14456
- U.S. Department of Agriculture-Agricultural Research Service Grape Genetics Research Unit, Geneva, NY 14456
| | - David M Gadoury
- Section of Plant Pathology and Plant-Microbe Biology, Cornell AgriTech, Cornell University, Geneva, NY 14456
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Everhart S, Gambhir N, Stam R. Population Genomics of Filamentous Plant Pathogens-A Brief Overview of Research Questions, Approaches, and Pitfalls. PHYTOPATHOLOGY 2021; 111:12-22. [PMID: 33337245 DOI: 10.1094/phyto-11-20-0527-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics-using dozens of genetic markers or polymorphism data of several genes-to population genomics-using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.
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Affiliation(s)
- Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Nikita Gambhir
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Remco Stam
- Phytopathology, School of Life Sciences Weihenstephan, Technical University Munich, Germany
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Patel S, Robben M, Fennell A, Londo JP, Alahakoon D, Villegas-Diaz R, Swaminathan P. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37'. HORTICULTURE RESEARCH 2020; 7:92. [PMID: 32528704 PMCID: PMC7261805 DOI: 10.1038/s41438-020-0316-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. 'Manitoba 37' with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera 'PN40024' CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia 'Manitoba 37' and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia's genetic contributions in grape breeding and research.
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Affiliation(s)
- Sagar Patel
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Michael Robben
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Jason P. Londo
- Grape Genetics Research Unit, USDA ARS, Geneva, NY 14456 USA
| | - Dilmini Alahakoon
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Roberto Villegas-Diaz
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
| | - Padmapriya Swaminathan
- Agronomy, Horticulture and Plant Science Department and BioSNTR, South Dakota State University, Brookings, SD 57006 USA
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