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Dixon CW, Gschwend AR. Trichomes and unique gene expression confer insect herbivory resistance in Vitis labrusca grapevines. BMC PLANT BIOLOGY 2024; 24:609. [PMID: 38926877 PMCID: PMC11209964 DOI: 10.1186/s12870-024-05260-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Grapevine (Vitis) is one of the world's most valuable fruit crops, but insect herbivory can decrease yields. Understanding insect herbivory resistance is critical to mitigating these losses. Vitis labrusca, a wild North American grapevine species, has been leveraged in breeding programs to generate hybrid grapevines with enhanced abiotic and biotic stress resistance, rendering it a valuable genetic resource for sustainable viticulture. This study assessed the resistance of V. labrusca acc. 'GREM4' and Vitis vinifera cv. 'PN40024' grapevines to Popillia japonica (Japanese beetle) herbivory and identified morphological and genetic adaptations underlying this putative resistance. RESULTS 'GREM4' displayed greater resistance to beetle herbivory compared to 'PN40024' in both choice and no-choice herbivory assays spanning periods of 30 min to 19 h. 'GREM4' had significantly higher average leaf trichome densities than 'PN40024' and beetles preferred to feed on the side of leaves with fewer trichomes. When leaves from each species that specifically did not differ in trichome densities were fed on by beetles, significantly less leaf area was damaged in 'GREM4' (3.29mm2) compared to 'PN40024' (9.80mm2), suggesting additional factors beyond trichomes contributed to insect herbivory resistance in 'GREM4'. Comparative transcriptomic analyses revealed 'GREM4' exhibited greater constitutive (0 h) expression of defense response and secondary metabolite biosynthesis genes compared to 'PN40024', indicative of heightened constitutive defenses. Upon herbivory, 'GREM4' displayed a greater number of differentially expressed genes (690) compared to 'PN40024' (502), suggesting a broader response. Genes up-regulated in 'GREM4' were enriched in terpene biosynthesis, flavonoid biosynthesis, phytohormone signaling, and disease defense-related functions, likely contributing to heighted insect herbivory defense, while genes differentially expressed in 'PN40024' under herbivory were enriched in xyloglucan, cell wall formation, and calcium ion binding. The majority of genes implicated in insect herbivory defense were orthologs with specific expression patterns in 'GREM4' and 'PN40024', but some paralogous and genome-specific genes also likely contributed to conferring resistance. CONCLUSIONS Our findings suggest that 'GREM4' insect herbivory resistance was attributed to a combination of factors, including trichomes and unique constitutive and inducible expression of genes implicated in terpene, flavonoid, and phenylpropanoid biosynthesis, as well as pathogen defense.
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Affiliation(s)
- Cullen W Dixon
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Andrea R Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA.
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2
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Mohanta TK, Mohanta YK, Kaushik P, Kumar J. Physiology, genomics, and evolutionary aspects of desert plants. J Adv Res 2024; 58:63-78. [PMID: 37160225 PMCID: PMC10982872 DOI: 10.1016/j.jare.2023.04.019] [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: 11/17/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture. AIM OF THE REVIEW The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture. KEY SCIENTIFIC CONCEPTS OF REVIEW This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 611, Oman.
| | - Yugal Kishore Mohanta
- Dept. of Applied Biology, University of Science and Technology Meghalaya, Baridua, Meghalaya 793101, India
| | - Prashant Kaushik
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Jitesh Kumar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, United States
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3
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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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4
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Chedid E, Avia K, Dumas V, Ley L, Reibel N, Butterlin G, Soma M, Lopez-Lozano R, Baret F, Merdinoglu D, Duchêne É. LiDAR Is Effective in Characterizing Vine Growth and Detecting Associated Genetic Loci. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0116. [PMID: 38026470 PMCID: PMC10655830 DOI: 10.34133/plantphenomics.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
The strong societal demand to reduce pesticide use and adaptation to climate change challenges the capacities of phenotyping new varieties in the vineyard. High-throughput phenotyping is a way to obtain meaningful and reliable information on hundreds of genotypes in a limited period. We evaluated traits related to growth in 209 genotypes from an interspecific grapevine biparental cross, between IJ119, a local genitor, and Divona, both in summer and in winter, using several methods: fresh pruning wood weight, exposed leaf area calculated from digital images, leaf chlorophyll concentration, and LiDAR-derived apparent volumes. Using high-density genetic information obtained by the genotyping by sequencing technology (GBS), we detected 6 regions of the grapevine genome [quantitative trait loci (QTL)] associated with the variations of the traits in the progeny. The detection of statistically significant QTLs, as well as correlations (R2) with traditional methods above 0.46, shows that LiDAR technology is effective in characterizing the growth features of the grapevine. Heritabilities calculated with LiDAR-derived total canopy and pruning wood volumes were high, above 0.66, and stable between growing seasons. These variables provided genetic models explaining up to 47% of the phenotypic variance, which were better than models obtained with the exposed leaf area estimated from images and the destructive pruning weight measurements. Our results highlight the relevance of LiDAR-derived traits for characterizing genetically induced differences in grapevine growth and open new perspectives for high-throughput phenotyping of grapevines in the vineyard.
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Affiliation(s)
- Elsa Chedid
- INRAE,
University of Strasbourg, UMR SVQV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Komlan Avia
- INRAE,
University of Strasbourg, UMR SVQV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Vincent Dumas
- INRAE,
University of Strasbourg, UMR SVQV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Lionel Ley
- INRAE, UEAV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Nicolas Reibel
- INRAE, UEAV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Gisèle Butterlin
- INRAE,
University of Strasbourg, UMR SVQV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Maxime Soma
- INRAE, Aix-Marseille Université, UMR RECOVER, 3275 Route de Cézanne, 13182 Aix-en-Provence, France
| | - Raul Lopez-Lozano
- INRAE,
Avignon Université, UMR EMMAH, UMT CAPTE, 228, route de l’aérodrome, 84914 Avignon, France
| | - Frédéric Baret
- INRAE,
Avignon Université, UMR EMMAH, UMT CAPTE, 228, route de l’aérodrome, 84914 Avignon, France
| | - Didier Merdinoglu
- INRAE,
University of Strasbourg, UMR SVQV, 28, rue de Herrlisheim, 68000 Colmar, France
| | - Éric Duchêne
- INRAE,
University of Strasbourg, UMR SVQV, 28, rue de Herrlisheim, 68000 Colmar, France
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5
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Tang N, Wu P, Cao Z, Liu Y, Zhang X, Lou J, Liu X, Hu Y, Sun X, Wang Q, Si S, Chen Z. A NAC transcription factor ZaNAC93 confers floral initiation, fruit development, and prickle formation in Zanthoxylum armatum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107813. [PMID: 37290134 DOI: 10.1016/j.plaphy.2023.107813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/27/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023]
Abstract
Zanthoxylum armatum is a dioecious prickly plant which developed apomictic reproduction. The increases in male flowers and prickle density in female plants lead to low yield and picking efficiency. However, little is known concerning the mechanisms of floral development and prickle formation. NAC is a well-known transcription factor that participates in multiple aspects of plant growth and development. Herein, we characterize the functions and regulatory mechanisms of candidate NACs controlling both traits in Z. armatum. A total of 159 ZaNACs were identified, and 16 of these were male-biased, represented by the NAP subfamily members ZaNAC93 and ZaNAC34, orthologs of AtNAC025 and AtNARS1/NAC2 respectively. Overexpression of ZaNAC93 in tomato led to modifications in flower and fruit development, including earlier flowering, increased numbers of lateral shoots and flowers, accelerated plant senescence, and reduced size and weight of fruits and seeds. In addition, the trichome density in leaves and inflorescences was dramatically reduced in ZaNAC93-OX lines. Overexpression of ZaNAC93 resulted in the up-/downregulation of genes associated with GA, ABA and JA signaling pathways, such as GAI, PYL and JAZ, as well as several TFs, including bZIP2, AGL11, FBP24 and MYB52. Yeast two-hybrid analysis revealed that ZaNAC93 protein could interact with AP1, GAI, bZIP2 and AGL11 in Z. armatum, which might contribute to floral induction, fruit growth, and trichome initiation. This work provides new insights into the molecular mechanisms of ZaNAC93 in reproductive development and prickle formation in Z. armatum.
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Affiliation(s)
- Ning Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Peiyin Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China.
| | - Zhengyan Cao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China.
| | - Yanni Liu
- College of Biology and Food Engineering, Chongqing Three Georges University, Chongqing, 404100, China.
| | - Xian Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China.
| | - Juan Lou
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Xia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Yang Hu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Xiaofan Sun
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Qiyao Wang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Shuo Si
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Zexiong Chen
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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6
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Su K, Sun J, Han J, Zheng T, Sun B, Liu S. Combined morphological and multi-omics analyses to reveal the developmental mechanism of Zanthoxylum bungeanum prickles. FRONTIERS IN PLANT SCIENCE 2022; 13:950084. [PMID: 36072325 PMCID: PMC9441855 DOI: 10.3389/fpls.2022.950084] [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: 06/01/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Zanthoxylum bungeanum Maxim. as an important economic forest, its epidermis bears prickles which complicate the harvesting process and increase the labor costs. To explore the developmental mechanism of prickles, three varieties of Zanthoxylum bungeanum (PZB, SZB, GSZB) were selected for morphological and multi-omics analyses. The absorption spectra of prickles and stems were detected using Fourier-transform infrared spectroscopy (FTIR), and they were found different at 1617, 1110, 3319, and 1999 cm-1. The morphology of prickles and stems were observed using light microscopy and transmission electron microscopy (TEM). The growth direction of cells on the prickle side and stem side were perpendicular to each other, and there was a resembling abscission zone (RAZ) between them. The vacuolar deposits of prickle cells were much more than stem cells, indicating that the lignification degree of prickles was higher than stems. In addition, 9 candidate genes (ZbYABBY2, ZbYABBY1, ZbYABBY5, ZbWRKY, ZbLOG5, ZbAZG2, ZbGh16, ZbIAA33, and ZbGh16X1) were screened out and validated base on transcriptome and qRT-PCA. As well as, 30 key metabolites were found related to prickle development base on metabolome analysis. Among them, 4-hydroxy-2-oxopentanoate, trans-2-hydroxy-cinnamate, trans-cinnamate, polyhydroxy-fatty acid, 10,16-dihydroxypalmitate, cinnamic acid were related to the biosynthesis of cutin, suberine and wax. Indole-3-acetate, tryptamine, anthranilate, fromylanthranilate, N6-(delta2-isopentenyl)-adenine were related to plant hormone signal transduction. Generally, this is the first study to reveal the developmental mechanism of prickles. The results of this study lay the foundation for the breeding of non-prickle Zanthoxylum bungeanum.
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Affiliation(s)
- Kexing Su
- College of Science, Northwest Agriculture and Forestry University, Xianyang, China
| | - Jiaqian Sun
- Powerchina Northwest Engineering Corporation Limited, Xi’an, China
- Shaanxi Union Research Center of University and Enterprise for River and Lake Ecosystems Protection and Restoration, Xi’an, China
| | - Jun Han
- Forestry and Grassland Bureau of Xunhua County, Qinghai, China
| | - Tao Zheng
- College of Science, Northwest Agriculture and Forestry University, Xianyang, China
| | - Bingyin Sun
- Department of Ecological Engineering, Yangling Vocational and Technical College, Xianyang, China
| | - Shuming Liu
- College of Science, Northwest Agriculture and Forestry University, Xianyang, China
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7
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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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8
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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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9
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LaPlante ER, Fleming MB, Migicovsky Z, Weber MG. Genome-Wide Association Study Reveals Genomic Region Associated with Mite-Recruitment Phenotypes in the Domesticated Grapevine ( Vitis vinifera). Genes (Basel) 2021; 12:1013. [PMID: 34208920 PMCID: PMC8307218 DOI: 10.3390/genes12071013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 01/25/2023] Open
Abstract
Indirect defenses are plant phenotypes that reduce damage by attracting natural enemies of plant pests and pathogens to leaves. Despite their economic and ecological importance, few studies have investigated the genetic underpinnings of indirect defense phenotypes. Here, we present a genome-wide association study of five phenotypes previously determined to increase populations of beneficial (fungivorous and predacious) mites on grape leaves (genus Vitis): leaf bristles, leaf hairs, and the size, density, and depth of leaf domatia. Using a common garden genetic panel of 399 V. vinifera cultivars, we tested for genetic associations of these phenotypes using previously obtained genotyping data from the Vitis9kSNP array. We found one single nucleotide polymorphism (SNP) significantly associated with domatia density. This SNP (Chr5:1160194) is near two genes of interest: Importin Alpha Isoform 1 (VIT_205s0077g01440), involved in downy mildew resistance, and GATA Transcription Factor 8 (VIT_205s0077g01450), involved in leaf shape development. Our findings are among the first to examine the genomic regions associated with ecologically important plant traits that facilitate interactions with beneficial mites, and suggest promising candidate genes for breeding and genetic editing to increase naturally occurring predator-based defenses in grapevines.
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Affiliation(s)
- Erika R. LaPlante
- Department of Plant Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI 48824, USA; (E.R.L.); (M.B.F.)
| | - Margaret B. Fleming
- Department of Plant Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI 48824, USA; (E.R.L.); (M.B.F.)
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada;
| | - Marjorie Gail Weber
- Department of Plant Biology, Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI 48824, USA; (E.R.L.); (M.B.F.)
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