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Perko A, Trapp O, Maul E, Röckel F, Piltaver A, Vršič S. Monitoring and Genotyping of Wild Grapevine ( Vitis vinifera L. subsp. sylvestris) in Slovenia. Plants (Basel) 2024; 13:1234. [PMID: 38732448 PMCID: PMC11085864 DOI: 10.3390/plants13091234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/20/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Vitis vinifera L. subsp. sylvestris (sylvestris) is the only native wild grapevine in Eurasia (Europe and western Asia) and is the existing ancestor of the grapevine varieties (for wine and table grape production) belonging to the subsp. sativa. In Slovenia, the prevailing opinion has been that there are no Slovenian sylvestris habitats. This study describes sylvestris in Slovenia for the first time and aims to present an overview of the locations of the wild grapevine in the country. In this project, a sample set of 89 accessions were examined using 24 SSR and 2 SSR markers plus APT3 markers to determine flower sex. The accessions were found in forests on the left bank of the Sava River in Slovenia, on the border between alluvial soils and limestone and dolomite soils, five different sites, some of which are described for the first time. The proportion of female to male accessions differed between sites. At two sites, female plants dominated; at others, the ratio was balanced. The plants' genetic diversity and structure were compared with autochthonous and unique varieties of subsp. sativa from old vineyards in Slovenia and with rootstocks escaped from nature from abandoned vineyards. Sylvestris was clearly distinguishable from vinifera and the rootstocks. Based on genetic analyses, it was confirmed that Slovenian sylvestris is closest to the Balkan and German sylvestris groups. Meanwhile, a safety duplication of the wild grapevine accessions has been established at the University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences at the University of Maribor.
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Affiliation(s)
- Andrej Perko
- University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia;
| | - Oliver Trapp
- Julius Kühn Institute (JKI)-Federal Research Centre of Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (O.T.); (F.R.)
| | - Erika Maul
- Julius Kühn Institute (JKI)-Federal Research Centre of Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (O.T.); (F.R.)
| | - Franco Röckel
- Julius Kühn Institute (JKI)-Federal Research Centre of Cultivated Plants, Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (O.T.); (F.R.)
| | - Andrej Piltaver
- Institute for the Systematics of Higher Fungi, Velika vas 17, 1262 Dol pri Ljubljani, Slovenia;
| | - Stanko Vršič
- University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia;
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Margaryan K, Töpfer R, Gasparyan B, Arakelyan A, Trapp O, Röckel F, Maul E. Wild grapes of Armenia: unexplored source of genetic diversity and disease resistance. Front Plant Sci 2023; 14:1276764. [PMID: 38143573 PMCID: PMC10739323 DOI: 10.3389/fpls.2023.1276764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023]
Abstract
The present study is the first in-depth research evaluating the genetic diversity and potential resistance of Armenian wild grapes utilizing DNA-based markers to understand the genetic signature of this unexplored germplasm. In the proposed research, five geographical regions with known viticultural history were explored. A total of 148 unique wild genotypes were collected and included in the study with 48 wild individuals previously collected as seed. A total of 24 nSSR markers were utilized to establish a fingerprint database to infer information on the population genetic diversity and structure. Three nSSR markers linked to the Ren1 locus were analyzed to identify potential resistance against powdery mildew. According to molecular fingerprinting data, the Armenian V. sylvestris gene pool conserves a high genetic diversity, displaying 292 different alleles with 12.167 allele per loci. The clustering analyses and diversity parameters supported eight genetic groups with 5.6% admixed proportion. The study of genetic polymorphism at the Ren1 locus revealed that 28 wild genotypes carried three R-alleles and 34 wild genotypes carried two R-alleles associated with PM resistance among analyzed 107 wild individuals. This gene pool richness represents an immense reservoir of under-explored genetic diversity and breeding potential. Therefore, continued survey and research efforts are crucial for the conservation, sustainable management, and utilization of Armenian wild grape resources in the face of emerging challenges in viticulture.
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Affiliation(s)
- Kristine Margaryan
- Research Group of Plant Genomics, Institute of Molecular Biology of National Academy of Sciences Republic of Armenia (RA), Yerevan, Armenia
- Department of Genetics and Cytology, Yerevan State University, Yerevan, Armenia
| | - Reinhard Töpfer
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences Republic of Armenia (RA), Yerevan, Armenia
| | - Arsen Arakelyan
- Research Group of Plant Genomics, Institute of Molecular Biology of National Academy of Sciences Republic of Armenia (RA), Yerevan, Armenia
| | - Oliver Trapp
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Franco Röckel
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Erika Maul
- Julius Kuehn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
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Guzmán-Ardiles RE, Pegoraro C, da Maia LC, Costa de Oliveira A. Genetic changes in the genus Vitis and the domestication of vine. Front Plant Sci 2023; 13:1019311. [PMID: 36926258 PMCID: PMC10011507 DOI: 10.3389/fpls.2022.1019311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/28/2022] [Indexed: 06/18/2023]
Abstract
The genus Vitis belongs to the Vitaceae family and is divided into two subgenera: Muscadinia and Vitis, the main difference between these subgenera being the number of chromosomes. There are many hypotheses about the origin of the genus, which have been formed with archaeological studies and lately with molecular analyses. Even though there is no consensus on the place of origin, these studies have shown that grapes have been used by man since ancient times, starting later on its domestication. Most studies point to the Near East and Greece as the beginning of domestication, current research suggests it took place in parallel in different sites, but in all cases Vitis vinifera (L.) subsp. sylvestris [Vitis vinifera (L.) subsp. sylvestris (Gmelin) Hagi] seems to be the species chosen by our ancestors to give rise to the now known Vitis vinifera (L.) subsp. vinifera [=sativa (Hegi)= caucasica (Vavilov)]. Its evolution and expansion into other territories followed the formation of new empires and their expansion, and this is where the historical importance of this crop lies. In this process, plants with hermaphrodite flowers were preferentially selected, with firmer, sweeter, larger fruits of different colors, thus favoring the selection of genes associated with these traits, also resulting in a change in seed morphology. Currently, genetic improvement programs have made use of wild species for the introgression of disease resistance genes and tolerance to diverse soil and climate environments. In addition, the mapping of genes of interest, both linked to agronomic and fruit quality traits, has allowed the use of molecular markers for assisted selection. Information on the domestication process and genetic resources help to understand the gene pool available for the development of cultivars that respond to producer and consumer requirements.
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Lukšić K, Zdunić G, Mucalo A, Marinov L, Ranković-vasić Z, Ivanović J, Nikolić D. Microstructure of Croatian Wild Grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) Pollen Grains Revealed by Scanning Electron Microscopy. Plants 2022; 11:1479. [PMID: 35684252 PMCID: PMC9182919 DOI: 10.3390/plants11111479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
Wild grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) is dioecious with male and female plants, whereas domesticated grapevine is mostly hermaphrodite with self-fertile hermaphrodite flowers. The pollen morphology of wild grapevine has been poorly studied. There is no detailed palynological study of V. sylvestris in Croatia and neighboring countries. Here, scanning electron microscopy (SEM) was used to analyze the pollen of V. sylvestris from male and female individuals growing at two natural sites in Croatia. The selective APT3 marker was used to confirm the flower phenotype with the genetic background. SEM analysis showed that the pollen grains of V. sylvestris were isopolar and radially symmetrical, with foveolate perforated ornamentation, regardless of the flower type of the individuals. All male flowers were 3-colporate and prolate in shape, whereas female individuals varied from subprolate to spheroidal and had inaperturate pollen grains. Pollen shape, dimensions and exine ornamentation proved very informative, and here we address the most polymorphic traits in the analyzed V. sylvestris individuals. Principal component analysis (PCA) and clustering based on pollen morphology variables clearly differentiated individuals by their flower type, and no grouping specific to population was observed, pointing to the conserved pollen structure of V. sylvestris. The results indicate the need to continue the palynological study of V. sylvestris and serve as a good phenotypic basis for functional genetic studies on genes involved in pollen morphology and function.
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Li N, Wang Y, Wang J, Zhang W, Meng Z, Wang Y, Zhang Y, Li S, Gao W, Deng C. Identification of Sex Differentiation-Related microRNAs in Spinach Female and Male Flower. Int J Mol Sci 2022; 23:4090. [PMID: 35456907 DOI: 10.3390/ijms23084090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023] Open
Abstract
Sex determination and differentiation is an important biological process for unisexual flower development. Spinach is a model plant to study the mechanism of sex determination and differentiation of dioecious plant. Till now, little is known about spinach sex determination and differentiation mechanism. MicroRNAs are key factors in flower development. Herein, small RNA sequencing was performed to explore the roles of microRNAs in spinach sex determination and differentiation. As a result, 92 known and 3402 novel microRNAs were identified in 18 spinach female and male flower samples. 74 differentially expressed microRNAs were identified between female and male flowers, including 20 female-biased and 48 male-biased expression microRNAs. Target prediction identified 22 sex-biased microRNA-target pairs, which may be involved in spinach sex determination or differentiation. Among the differentially expressed microRNAs between FNS and M03, 55 microRNAs were found to reside in sex chromosome; one of them, sol-miR2550n, was functionally studied via genetic transformation. Silencing of sol-miR2550n resulted in abnormal anther while overexpression of sol-miR2550n induced early flowering, indicating sol-miR2550n was a male-promoting factor and validating the reliability of our small RNA sequencing data. Conclusively, this work can supply valuable information for exploring spinach sex determination and differentiation and provide a new insight in studying unisexual flower development.
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Men Y, Li JR, Shen HL, Yang YM, Fan ST, Li K, Guo YS, Lin H, Liu ZD, Guo XW. VaAPRT3 Gene is Associated With Sex Determination in Vitis amurensis. Front Genet 2022; 12:727260. [PMID: 35003203 PMCID: PMC8733387 DOI: 10.3389/fgene.2021.727260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
In the past decade, progress has been made in sex determination mechanism in Vitis. However, genes responsible for sexual differentiation and its mechanism in V. amurensis remain unknown. Here, we identify a sex determination candidate gene coding adenine phosphoribosyl transferase 3 (VaAPRT3) in V. amurensis. Cloning and sequencing of the VaAPRT3 gene allowed us to develop a molecular marker able to discriminate female individuals from males or hermaphrodites based on a 22-bp InDel. Gene expression and endogenous cytokinin content analysis revealed that the VaAPRT3 gene is involved in sex determination or, to be precise, in female organ differentiation, through regulating cytokinin metabolism in V. amurensis. This study enlarged the understanding of sex determination mechanism in the genus Vitis, and the sex marker could be used as a helpful tool for sexual identification in breeding programs as well as in investigation and collection of V. amurensis germplasms.
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Affiliation(s)
- Yan Men
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Ji-Rui Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hai-Lin Shen
- Institute of Pomology, Jilin Academy of Agricultural Science, Gongzhuling, China
| | - Yi-Ming Yang
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shu-Tian Fan
- Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yin-Shan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhen-Dong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiu-Wu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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Margaryan K, Melyan G, Röckel F, Töpfer R, Maul E. Genetic Diversity of Armenian Grapevine ( Vitis vinifera L.) Germplasm: Molecular Characterization and Parentage Analysis. Biology (Basel) 2021; 10:1279. [PMID: 34943194 PMCID: PMC8698583 DOI: 10.3390/biology10121279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022]
Abstract
Armenia is an important country of origin of cultivated Vitis vinifera subsp. vinifera and wild Vitis vinifera subsp. sylvestris and has played a key role in the long history of grape cultivation in the Southern Caucasus. The existence of immense grapevine biodiversity in a small territory is strongly linked with unique relief and diverse climate conditions assembled with millennium-lasting cultural and historical context. In the present in-depth study using 25 nSSR markers, 492 samples collected in old vineyards, home gardens, and private collections were genotyped. For verification of cultivar identity, the symbiotic approach combining genotypic and phenotypic characterization for each genotype was carried out. The study provided 221 unique varieties, including 5 mutants, from which 66 were widely grown, neglected or minor autochthonous grapevine varieties, 49 turned out to be new bred cultivars created within the national breeding programs mainly during Soviet Era and 34 were non-Armenian varieties with different countries of origin. No references and corresponding genetic profiles existed for 67 genotypes. Parentage analysis was performed inferring 62 trios with 53 out of them having not been previously reported and 185 half-kinships. Instability of grapevine cultivars was detected, showing allelic variants, with three and in rare cases four alleles at one loci. Obtained results have great importance and revealed that Armenia conserved an extensive grape genetic diversity despite geographical isolation and low material exchange. This gene pool richness represents a huge reservoir of under-explored genetic diversity.
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Affiliation(s)
- Kristine Margaryan
- Research Group of Plant Genetics and Immunology, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
| | - Gagik Melyan
- Voskehat Educational and Research Center of Enology, Branch of Armenian National Agrarian University, Merdzavan 1139, Armavir Province, Armenia
| | - Franco Röckel
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (F.R.); (R.T.); (E.M.)
| | - Reinhard Töpfer
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (F.R.); (R.T.); (E.M.)
| | - Erika Maul
- Julius Kühn-Institute (JKI), Institute for Grapevine Breeding Geilweilerhof, 76833 Siebeldingen, Germany; (F.R.); (R.T.); (E.M.)
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Iocco-Corena P, Chaïb J, Torregrosa L, Mackenzie D, Thomas MR, Smith HM. VviPLATZ1 is a major factor that controls female flower morphology determination in grapevine. Nat Commun 2021; 12:6995. [PMID: 34848714 DOI: 10.1038/s41467-021-27259-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/10/2021] [Indexed: 12/26/2022] Open
Abstract
Plant genetic sex determinants that mediate the transition to dioecy are predicted to be diverse, as this type of mating system independently evolved multiple times in angiosperms. Wild Vitis species are dioecious with individuals producing morphologically distinct female or male flowers; whereas, modern domesticated Vitis vinifera cultivars form hermaphrodite flowers capable of self-pollination. Here, we identify the VviPLATZ1 transcription factor as a key candidate female flower morphology factor that localizes to the Vitis SEX-DETERMINING REGION. The expression pattern of this gene correlates with the formation reflex stamens, a prominent morphological phenotype of female flowers. After generating CRISPR/Cas9 gene-edited alleles in a hermaphrodite genotype, phenotype analysis shows that individual homozygous lines produce flowers with reflex stamens. Taken together, our results demonstrate that loss of VviPLATZ1 function is a major factor that controls female flower morphology in Vitis. Unlike wild Vitis species, which produce either female or male flowers, modern grapevine cultivars form hermaphrodite flowers for self-pollination. Here, the authors report that the VviPLATZ1 (plant AT-rich sequence-and zinc-binding protein1) transcription factor functions in controlling female flower morphology determination.
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Zou C, Massonnet M, Minio A, Patel S, Llaca V, Karn A, Gouker F, Cadle-Davidson L, Reisch B, Fennell A, Cantu D, Sun Q, Londo JP. Multiple independent recombinations led to hermaphroditism in grapevine. Proc Natl Acad Sci U S A 2021; 118:e2023548118. [PMID: 33837155 DOI: 10.1073/pnas.2023548118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We studied the grape sex-determining region (SDR) in 12 Vitis genomes and demonstrated its conservation across 556 genotypes including 193 accessions from 47 world-wide wild grapevine species and 363 accessions of cultivated grapevine. Although the grape SDR is recombination free in all wild species, we found two distinct hermaphrodite (H) haplotypes (H1 and H2) among the cultivated grapevines, both chimeras of male (M) and female (f) haplotypes. The two independent recombinations carry different genetic signatures which long predate the domestication of grapevine, suggesting independent evolutions of this trait in wild European grapevine gene pools prior to human domestication. Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.
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Su K, Guo Y, Zhong W, Lin H, Liu Z, Li K, Li Y, Guo X. High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing. Phytopathology 2021; 111:659-670. [PMID: 33635092 DOI: 10.1094/phyto-12-19-0480-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca 'Zhuosexiang') and white rot-susceptible cultivar (V. vinifera 'Victoria'). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.
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Affiliation(s)
- Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, People's Republic of China
| | - Weihao Zhong
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, People's Republic of China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, People's Republic of China
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Renner SS, Müller NA. Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration. Nat Plants 2021; 7:392-402. [PMID: 33782581 DOI: 10.1038/s41477-021-00884-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/18/2021] [Indexed: 05/17/2023]
Abstract
Hundreds of land plant lineages have independently evolved separate sexes in either gametophytes (dioicy) or sporophytes (dioecy), but 43% of all dioecious angiosperms are found in just 34 entirely dioecious clades, suggesting that their mode of sex determination evolved a long time ago. Here, we review recent insights on the molecular mechanisms that underlie the evolutionary change from individuals that each produce male and female gametes to individuals specializing in the production of just one type of gamete. The canonical model of sex chromosome evolution in plants predicts that two sex-determining genes will become linked in a sex-determining region (SDR), followed by expanding recombination suppression, chromosome differentiation and, ultimately, degeneration. Experimental work, however, is showing that single genes function as master regulators in model systems, such as the liverwort Marchantia and the angiosperms Diospyros and Populus. In Populus, this type of regulatory function has been demonstrated by genome editing. In other systems, including Actinidia, Asparagus and Vitis, two coinherited factors appear to independently regulate female and male function, yet sex chromosome differentiation has remained low. We discuss the best-understood systems and evolutionary pathways to dioecy, and present a meta-analysis of the sizes and ages of SDRs. We propose that limited sexual conflict explains why most SDRs are small and sex chromosomes remain homomorphic. It appears that models of increasing recombination suppression with age do not apply because selection favours mechanisms in which sex determination depends on minimal differences, keeping it surgically precise.
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Affiliation(s)
- Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany.
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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13
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Liu Z, Wang H, Xu Z, Zhang H, Li G, Wang X, Qian W. Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach ( Spinacia oleracea L.). Genome 2021; 64:777-788. [PMID: 33539259 DOI: 10.1139/gen-2020-0122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.
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Affiliation(s)
- Zhiyuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Haoying Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China.,Horticulture & landscape college, Hunan Agricultural University, Furong District, Changsha City, Hunan Province 410128, People's Republic of China
| | - Zhaosheng Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Helong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China
| | - Wei Qian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, People's Republic of China
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14
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Leite Montalvão AP, Kersten B, Fladung M, Müller NA. The Diversity and Dynamics of Sex Determination in Dioecious Plants. Front Plant Sci 2021; 11:580488. [PMID: 33519840 PMCID: PMC7843427 DOI: 10.3389/fpls.2020.580488] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/23/2020] [Indexed: 05/03/2023]
Abstract
The diversity of inflorescences among flowering plants is captivating. Such charm is not only due to the variety of sizes, shapes, colors, and flowers displayed, but also to the range of reproductive systems. For instance, hermaphrodites occur abundantly throughout the plant kingdom with both stamens and carpels within the same flower. Nevertheless, 10% of flowering plants have separate unisexual flowers, either in different locations of the same individual (monoecy) or on different individuals (dioecy). Despite their rarity, dioecious plants provide an excellent opportunity to investigate the mechanisms involved in sex expression and the evolution of sex-determining regions (SDRs) and sex chromosomes. The SDRs and the evolution of dioecy have been studied in many species ranging from Ginkgo to important fruit crops. Some of these studies, for example in asparagus or kiwifruit, identified two sex-determining genes within the non-recombining SDR and may thus be consistent with the classical model for the evolution of dioecy from hermaphroditism via gynodioecy, that predicts two successive mutations, the first one affecting male and the second one female function, becoming linked in a region of suppressed recombination. On the other hand, aided by genome sequencing and gene editing, single factor sex determination has emerged in other species, such as persimmon or poplar. Despite the diversity of sex-determining mechanisms, a tentative comparative analysis of the known sex-determining genes and candidates in different species suggests that similar genes and pathways may be employed repeatedly for the evolution of dioecy. The cytokinin signaling pathway appears important for sex determination in several species regardless of the underlying genetic system. Additionally, tapetum-related genes often seem to act as male-promoting factors when sex is determined via two genes. We present a unified model that synthesizes the genetic networks of sex determination in monoecious and dioecious plants and will support the generation of hypothesis regarding candidate sex determinants in future studies.
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Affiliation(s)
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, Großhansdorf, Germany
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15
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Li N, Meng Z, Tao M, Wang Y, Zhang Y, Li S, Gao W, Deng C. Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L. BMC Genomics 2020; 21:850. [PMID: 33256615 PMCID: PMC7708156 DOI: 10.1186/s12864-020-07277-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022] Open
Abstract
Background Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach. Results Compared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation. Conclusions In this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07277-4.
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Affiliation(s)
- Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Ziwei Meng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Minjie Tao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yueyuan Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yulan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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16
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Ramos MJN, Coito JL, Faísca-Silva D, Cunha J, Costa MMR, Amâncio S, Rocheta M. Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris). Sci Rep 2020; 10:18993. [PMID: 33149248 PMCID: PMC7642406 DOI: 10.1038/s41598-020-76012-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/06/2020] [Indexed: 12/30/2022] Open
Abstract
The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.
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Affiliation(s)
- Miguel J N Ramos
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
| | - João L Coito
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - David Faísca-Silva
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária E Veterinária, Quinta d'Almoinha, 2565-191, Dois Portos, Portugal
| | - M Manuela R Costa
- Plant Functional Biology Centre, Biosystems and Integrative Sciences Institute, University of Minho, 4710-057, Braga, Portugal
| | - Sara Amâncio
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Margarida Rocheta
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
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17
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Reynard JS, Brodard J, Remoliff E, Lefebvre M, Schumpp O, Candresse T. A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris). Arch Virol 2020; 165:2999-3002. [PMID: 32990843 PMCID: PMC7588375 DOI: 10.1007/s00705-020-04817-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 08/18/2020] [Indexed: 12/01/2022]
Abstract
We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named "grapevine foveavirus A" (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.
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Affiliation(s)
| | | | - Eric Remoliff
- Agroscope, route de Duiller 50, 1260, Nyon, Switzerland
| | - Marie Lefebvre
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | | | - Thierry Candresse
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon cedex, France
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18
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Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol 2020; 21:223. [PMID: 32892750 PMCID: PMC7487632 DOI: 10.1186/s13059-020-02131-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
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Affiliation(s)
- Hélène Badouin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| | - Amandine Velt
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - François Gindraud
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Timothée Flutre
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Vincent Dumas
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Jonathan Corbi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérémy Ganofsky
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Santoni
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Hélène Berges
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Eric Duchêne
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Raquel Tavares
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Roberto Bacilieri
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Camille Rustenholz
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France.
| | - Gabriel A B Marais
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
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19
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Su K, Xing H, Guo Y, Zhao F, Liu Z, Li K, Li Y, Guo X. High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing. BMC Genomics 2020; 21:419. [PMID: 32571215 PMCID: PMC7310074 DOI: 10.1186/s12864-020-06836-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/16/2020] [Indexed: 11/28/2022] Open
Abstract
Background Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In this study, grapevine interspecific hybridisation was carried out with the maternal parent ‘Cabernet sauvignon’ and paternal parent ‘Zuoyouhong’. A total of 181 hybrid offspring and their parents were used as samples for restriction-site associated DNA sequencing (RAD). Grapevine cane phloem and xylem cold hardiness of the experimental material was detected using the low-temperature exotherm method in 2016, 2017 and 2018. QTL mapping was then conducted based on the integrated map. Results We constructed a high-density genetic linkage map with 16,076, 11,643, and 25,917 single-nucleotide polymorphism (SNP) markers anchored in the maternal, paternal, and integrated maps, respectively. The average genetic distances of adjacent markers in the maps were 0.65 cM, 0.77 cM, and 0.41 cM, respectively. Colinearity analysis was conducted by comparison with the grape reference genome and showed good performance. Six QTLs were identified based on the phenotypic data of 3 years and they were mapped on linkage group (LG) 2, LG3, and LG15. Based on QTL results, candidate genes which may be involved in grapevine cold hardiness were selected. Conclusions High-density linkage maps can facilitate grapevine fine QTL mapping, genome comparison, and sequence assembly. The cold hardiness QTL mapping and candidate gene discovery performed in this study provide an important reference for molecular-assisted selection in grapevine cold hardiness breeding.
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Affiliation(s)
- Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China. .,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, P.R. China.
| | - Fangyuan Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, P.R. China. .,National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, P.R. China.
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20
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Massonnet M, Cochetel N, Minio A, Vondras AM, Lin J, Muyle A, Garcia JF, Zhou Y, Delledonne M, Riaz S, Figueroa-Balderas R, Gaut BS, Cantu D. The genetic basis of sex determination in grapes. Nat Commun 2020; 11:2902. [PMID: 32518223 DOI: 10.1038/s41467-020-16700-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
It remains a major challenge to identify the genes and mutations that lead to plant sexual differentiation. Here, we study the structure and evolution of the sex-determining region (SDR) in Vitis species. We report an improved, chromosome-scale Cabernet Sauvignon genome sequence and the phased assembly of nine wild and cultivated grape genomes. By resolving twenty Vitis SDR haplotypes, we compare male, female, and hermaphrodite haplotype structures and identify sex-linked regions. Coupled with gene expression data, we identify a candidate male-sterility mutation in the VviINP1 gene and potential female-sterility function associated with the transcription factor VviYABBY3. Our data suggest that dioecy has been lost during domestication through a rare recombination event between male and female haplotypes. This work significantly advances the understanding of the genetic basis of sex determination in Vitis and provides the information necessary to rapidly identify sex types in grape breeding programs. Grapevine is one of a few ancestrally dioecious crops that are reverted to hermaphroditism during domestication. Here, the authors identify candidate genes related to male- and female-sterility in grapes and describe the genetic process that led to hermaphroditism during domestication.
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21
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Feng G, Sanderson BJ, Keefover-Ring K, Liu J, Ma T, Yin T, Smart LB, DiFazio SP, Olson MS. Pathways to sex determination in plants: how many roads lead to Rome? Curr Opin Plant Biol 2020; 54:61-68. [PMID: 32106015 DOI: 10.1016/j.pbi.2020.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 05/20/2023]
Abstract
The presence of thousands of independent origins of dioecy in angiosperms provides a unique opportunity to address the parallel evolution of the molecular pathways underlying unisexual flowers. Recent progress towards identifying sex determination genes has identified hormone response pathways, mainly associated with cytokinin and ethylene response pathways, as having been recruited multiple times independently to control unisexuality. Moreover, transcriptomics has begun to identify commonalities among intermediate sections of signal transduction pathways. These recent advances set the stage for development of a comparative evolutionary development research program to identify the shared and unique aspects of the genetic pathways of unisexual flower development in angiosperms.
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Affiliation(s)
- Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin Madison, Madison, WI 53795, USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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22
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Luo Y, Pan BZ, Li L, Yang CX, Xu ZF. Developmental basis for flower sex determination and effects of cytokinin on sex determination in Plukenetia volubilis (Euphorbiaceae). Plant Reprod 2020; 33:21-34. [PMID: 31907610 PMCID: PMC7069929 DOI: 10.1007/s00497-019-00382-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/24/2019] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE Cytokinin might be an important factor to regulate floral sex at the very early stage of flower development in sacha inchi. Sacha inchi (Plukenetia volubilis, Euphorbiaceae) is characterized by having female and male flowers in a thyrse with particular differences. The mechanisms involved in the development of unisexual flowers are very poorly understood. In this study, the inflorescence and flower development of P. volubilis were investigated using light microscopy and scanning electron microscopy. We also investigated the effects of cytokinin on flower sex determination by exogenous application of 6-benzyladenine (BA) in P. volubilis. The floral development of P. volubilis was divided into eight stages, and the first morphological divergence between the male and female flowers was found to occur at stage 3. Both female and male flowers can be structurally distinguished by differences in the shape and size of the flower apex after sepal primordia initiation. There are no traces of gynoecia in male flowers or of androecia in female flowers. Exogenous application of BA effectively induced gynoecium primordia initiation and female flower development, especially at the early flower developmental stages. We propose that flower sex is determined earlier and probably occurs before flower initiation, either prior to or at inflorescence development due to the difference in the position of the female and male primordia in the inflorescence and in the time of the female and male primordia being initiated. The influence of cytokinin on female primordia during flower development in P. volubilis strongly suggests a feminization role for cytokinin in sex determination. These results indicate that cytokinin could modify the fate of the apical meristem of male flower and promote the formation of carpel primordia in P. volubilis.
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Affiliation(s)
- Yan Luo
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun Mengla, 666303, Yunnan, China
- Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Bang-Zhen Pan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun Mengla, 666303, Yunnan, China
| | - Lu Li
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, 650224, Yunnan, China
| | - Chen-Xuan Yang
- Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun Mengla, 666303, Yunnan, China.
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23
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Zou C, Karn A, Reisch B, Nguyen A, Sun Y, Bao Y, Campbell MS, Church D, Williams S, Xu X, Ledbetter CA, Patel S, Fennell A, Glaubitz JC, Clark M, Ware D, Londo JP, Sun Q, Cadle-Davidson L. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun 2020; 11:413. [PMID: 31964885 PMCID: PMC6972940 DOI: 10.1038/s41467-019-14280-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Bruce Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Allen Nguyen
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yongming Sun
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yun Bao
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | | | | | | | - Xia Xu
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Craig A Ledbetter
- USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA
| | - Sagar Patel
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Jeffrey C Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Jason P Londo
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
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24
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Kui L, Tang M, Duan S, Wang S, Dong X. Identification of Selective Sweeps in the Domesticated Table and Wine Grape ( Vitis vinifera L.). Front Plant Sci 2020; 11:572. [PMID: 32477387 PMCID: PMC7240110 DOI: 10.3389/fpls.2020.00572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/17/2020] [Indexed: 05/05/2023]
Abstract
Grapevine (Vitis vinifera) is one of the most important fruit species in the Classical Mediterranean world. It is thought to have been domesticated 6,000-8,000 years ago in the Near East. However, the domestication of its wild relative into wine grapes or table grapes remains largely unknown. In this study, we analyzed 30 table grapes, 30 wine grapes, 30 dual-purpose grape accessions, as well as 30 wild relatives (Vitis vinifera ssp. sylvestris). The phenotypic comparison showed striking differences in berry weight, acidity and the content of aroma. Based on a total of 7,522,958 single-nucleotide polymorphisms, we identified several significant selective sweep regions for table and wine grapes. Besides the well-known sex-determination locus on chromosome 2, the other four highest signals shared by table and wine grapes could not be linked to the known QTLs. The identification of these genomic regions under selection sweep may reveal agronomically important traits that have been selected during grape domestication. This information not only sheds light on the mechanisms of adaptions and diversification, but also guide the genetic improvement in breeding programs.
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Affiliation(s)
- Ling Kui
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Min Tang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Nowbio Biotechnology Company, Kunming, China
| | | | - Xiao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Nowbio Biotechnology Company, Kunming, China
- *Correspondence: Xiao Dong,
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25
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Coito JL, Silva HG, Ramos MJ, Cunha J, Eiras-Dias J, Amâncio S, Costa MM, Rocheta M. Vitis flower types: from the wild to crop plants. PeerJ 2019; 7:e7879. [PMID: 31737441 PMCID: PMC6855205 DOI: 10.7717/peerj.7879] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
Vitis vinifera can be divided into two subspecies, V. vinifera subsp. vinifera, one of the most important agricultural crops in the world, and its wild ancestor, V. vinifera subsp. sylvestris. Three flower types can be observed: hermaphrodite and female (on some varieties) in vinifera, and male or female flowers in sylvestris. It is assumed that the different flower types in the wild ancestor arose through specific floral patterns of organ abortion. A considerable amount of data about the diversity of sexual systems in grapevines has been collected over the past century. Several grapevine breeding studies led to the hypothesis that dioecy in vinifera is derived from a hermaphrodite ancestor and could be controlled by either, one or two linked genetic determinants following Mendelian inherence. More recently, experiments using molecular approaches suggested that these loci were located in a specific region of the chromosome 2 of vinifera. Based on the works published so far, its seems evident that a putative sex locus is present in chromosome 2. However, it is still not fully elucidated whether flower types are regulated by two linked loci or by one locus with three alleles. Nevertheless, several genes could contribute to sex determination in grapevine. This review presents the results from early studies, combined with the recent molecular approaches, which may contribute to the design of new experiments towards a better understanding of the sex inheritance in grapevine.
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Affiliation(s)
- João L. Coito
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Helena G. Silva
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Miguel J.N. Ramos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d’Almoinha, Dois Portos, Portugal
| | - José Eiras-Dias
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d’Almoinha, Dois Portos, Portugal
| | - Sara Amâncio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria M.R. Costa
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho - Campus de Gualtar, Braga, Portugal
| | - Margarida Rocheta
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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26
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Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS. The population genetics of structural variants in grapevine domestication. Nat Plants 2019; 5:965-979. [PMID: 31506640 DOI: 10.1038/s41477-019-0507-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/26/2019] [Indexed: 05/20/2023]
Abstract
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.
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Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA
| | | | - Edwin Solares
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Yuanda Lv
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, Tbilisi, Georgia
| | - Dario Cantu
- Department of Viticulture and Enology, UC Davis, Davis, CA, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
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27
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Barba P, Loughner R, Wentworth K, Nyrop JP, Loeb GM, Reisch BI. A QTL associated with leaf trichome traits has a major influence on the abundance of the predatory mite Typhlodromus pyri in a hybrid grapevine population. Hortic Res 2019; 6:87. [PMID: 31645947 PMCID: PMC6804712 DOI: 10.1038/s41438-019-0169-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/16/2019] [Accepted: 05/31/2019] [Indexed: 05/29/2023]
Abstract
The abundance of predatory phytoseiid mites, Typhlodromus pyri, important biological control agents of spider mite pests in numerous crops, is positively influenced by the density of leaf trichomes and tuft-form domatia in vein axils. Identification of the genetic regions controlling both trophic levels could facilitate the improvement of predatory mite habitat in breeding programs. The abundance of T. pyri and non-glandular trichomes was measured in a segregating F1 family derived from the cross of the complex Vitis hybrid, 'Horizon', with Illinois 547-1 (V. rupestris B38 × V. cinerea B9), finding positive correlation among traits. High density genetic maps were used to localize one major quantitative trait locus (QTL) on chromosome 1 of Illinois 547-1 associated with both predatory mite abundance and leaf trichomes. This QTL explained 23% of the variation in phytoseiid abundance and similar amounts of variance in domatia rating (21%), domatia size (16%), leaf bristle density (37% in veins and 33% in blades), and leaf hair density (20% in veins and 15% in blades). Another nine QTL distributed among chromosomes 1, 2, 5, 8, and 15 were associated solely with trichome density, and explained 7-17% of the phenotypic variation. Combined, our results provide evidence of the genetic architecture of non-glandular trichomes in Vitis, with a major locus influencing trichome densities, domatia size and predatory mite abundance. This information is relevant for breeding grapevines with a more favorable habitat for biological control agents.
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Affiliation(s)
- Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago, 8831314 Chile
| | - Rebecca Loughner
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Karen Wentworth
- Department of Entomology, Cornell AgriTech, Geneva, NY 14456 USA
| | - Jan Peter Nyrop
- Department of Entomology, Cornell AgriTech, Geneva, NY 14456 USA
| | - Gregory M. Loeb
- Department of Entomology, Cornell AgriTech, Geneva, NY 14456 USA
| | - Bruce I. Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Geneva, NY 14456 USA
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28
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Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua. Genetics 2019; 212:815-835. [PMID: 31113811 PMCID: PMC6614902 DOI: 10.1534/genetics.119.302045] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022] Open
Abstract
Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.
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Affiliation(s)
- Paris Veltsos
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
| | - Kate E Ridout
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
- Department of Plant Sciences, University of Oxford, OX1 3RB, United Kingdom
- Department of Oncology, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Melissa A Toups
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
- Department of Integrative Biology, University of Texas, Austin, 78712 Texas
| | | | - Aline Muyle
- Laboratoire Biométrie et Biologie Évolutive (UMR 5558), CNRS/Université Lyon 1, 69100 Villeurbanne, France
| | - Olivier Emery
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
| | - Pasi Rastas
- University of Helsinki, Institute of Biotechnology, 00014, Finland
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200 Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200 Brno, Czech Republic
| | | | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, OX1 3RB, United Kingdom
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Switzerland
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29
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Lewter J, Worthington ML, Clark JR, Varanasi AV, Nelson L, Owens CL, Conner P, Gunawan G. High-density linkage maps and loci for berry color and flower sex in muscadine grape (Vitis rotundifolia). Theor Appl Genet 2019; 132:1571-1585. [PMID: 30756127 DOI: 10.1007/s00122-019-03302-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Linkage maps of muscadine grape generated using genotyping-by-sequencing (GBS) provide insight into genome collinearity between Muscadinia and Euvitis subgenera and genetic control of flower sex and berry color. The muscadine grape, Vitis rotundifolia, is a specialty crop native to the southeastern USA. Muscadine vines can be male, female, or perfect-flowered, and berry color ranges from bronze to black. Genetic linkage maps were constructed using genotyping-by-sequencing in two F1 populations segregating for flower sex and berry color. The linkage maps consisted of 1244 and 2069 markers assigned to 20 linkage groups (LG) for the 'Black Beauty' × 'Nesbitt' and 'Supreme' × 'Nesbitt' populations, respectively. Data from both populations were used to generate a consensus map with 2346 markers across 20 LGs. A high degree of collinearity was observed between the genetic maps and the Vitis vinifera physical map. The higher chromosome number in muscadine (2n = 40) compared to V. vinifera (2n = 38) was accounted for by the behavior of V. vinifera chromosome 7 as two independently segregating LGs in muscadine. The muscadine sex locus mapped to an interval that aligned to 4.64-5.09 Mb on V. vinifera chromosome 2, a region which includes the previously described V. vinifera subsp. sylvestris sex locus. While the MYB transcription factor genes controlling fruit color in V. vinifera are located on chromosome 2, the muscadine berry color locus mapped to an interval aligning to 11.09-11.88 Mb on V. vinifera chromosome 4, suggesting that a mutation in a different gene in the anthocyanin biosynthesis pathway determines berry color in muscadine. These linkage maps lay the groundwork for marker-assisted breeding in muscadine and provide insight into the evolution of Vitis species.
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Affiliation(s)
- Jennifer Lewter
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Margaret L Worthington
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA.
| | - John R Clark
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Aruna V Varanasi
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Lacy Nelson
- Department of Horticulture, University of Arkansas, 316 Plant Sciences Bldg., Fayetteville, AR, 72701, USA
| | - Christopher L Owens
- USDA-ARS Grape Genetics Research Unit, Cornell University, 630 W. North St., Geneva, NY, 14456, USA
- IFG, 8224 Espresso Dr. Suite 200, Bakersfield, CA, 93312, USA
| | - Patrick Conner
- Department of Horticulture, University of Georgia, 4604 Research Way, Tifton, GA, 31793, USA
| | - Gunawati Gunawan
- Department of Horticulture, University of Georgia, 4604 Research Way, Tifton, GA, 31793, USA
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30
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Richter R, Gabriel D, Rist F, Töpfer R, Zyprian E. Identification of co-located QTLs and genomic regions affecting grapevine cluster architecture. Theor Appl Genet 2019; 132:1159-1177. [PMID: 30569367 DOI: 10.1007/s00122-018-3269-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/12/2018] [Indexed: 05/18/2023]
Abstract
Loose cluster architecture is an important aim in grapevine breeding since it has high impact on the phytosanitary status of grapes. This investigation analyzed the contributions of individual cluster sub-traits to the overall trait of cluster architecture. Six sub-traits showed large impact on cluster architecture as major determinants. They explained 57% of the OIV204 descriptor for cluster compactness rating in a highly diverse cross-population of 149 genotypes. Genetic analysis revealed several genomic regions involved in the expression of this trait. Based on the linkage of phenotypic features to molecular markers, QTL calculations shed new light on the genetic determinants of cluster architecture. Eight QTL clusters harbor overlapping confidence intervals of up to four co-located QTLs. A physical projection of the QTL clusters by confidence interval-flanking markers onto the PN40024 reference genome sequence revealed genes enriched in these regions.
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Affiliation(s)
- Robert Richter
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Doreen Gabriel
- Institute for Crop and Soil Science, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Bundesallee 58, 38116, Brunswick, Germany
| | - Florian Rist
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Eva Zyprian
- Institute for Grapevine Breeding Geilweilerhof, Julius Kuehn Institute, Federal Research Centre of Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany.
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31
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Liang Z, Duan S, Sheng J, Zhu S, Ni X, Shao J, Liu C, Nick P, Du F, Fan P, Mao R, Zhu Y, Deng W, Yang M, Huang H, Liu Y, Ding Y, Liu X, Jiang J, Zhu Y, Li S, He X, Chen W, Dong Y. Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. Nat Commun 2019; 10:1190. [PMID: 30867414 PMCID: PMC6416300 DOI: 10.1038/s41467-019-09135-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 02/21/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement. Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.
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Affiliation(s)
- Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shengchang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Nowbio Biotechnology Company, Kunming, 650201, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuemei Ni
- BGI, BGI-Shenzhen, Shenzhen, 518120, China.,BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jianhui Shao
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, 76128, Germany
| | - Fei Du
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ruzhi Mao
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yifan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Weiping Deng
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Yiqing Ding
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianju Liu
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, 650201, China.
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32
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Jia H, Jia H, Cai Q, Wang Y, Zhao H, Yang W, Wang G, Li Y, Zhan D, Shen Y, Niu Q, Chang L, Qiu J, Zhao L, Xie H, Fu W, Jin J, Li X, Jiao Y, Zhou C, Tu T, Chai C, Gao J, Fan L, van de Weg E, Wang J, Gao Z. The red bayberry genome and genetic basis of sex determination. Plant Biotechnol J 2019; 17:397-409. [PMID: 29992702 PMCID: PMC6335074 DOI: 10.1111/pbi.12985] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/01/2018] [Accepted: 07/04/2018] [Indexed: 05/12/2023]
Abstract
Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.
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Affiliation(s)
- Hui‐Min Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hui‐Juan Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | | | - Yan Wang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hai‐Bo Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wei‐Fei Yang
- Hangzhou 1 Gene LtdHangzhouChina
- Forestry Technology Extension CenterYuyaoNingboChina
- Present address:
Annoroad Gene Tech. Co., LtdBeijingChina
| | - Guo‐Yun Wang
- Forestry Technology Extension CenterYuyaoNingboChina
| | - Ying‐Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | - Yu‐Tong Shen
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qing‐Feng Niu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular GeneticsCenter of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Le Chang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jie Qiu
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Lan Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Han‐Bing Xie
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wan‐Yi Fu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jing Jin
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xiong‐Wei Li
- Forest & Fruit Tree InstituteShanghai Academy of Agricultural SciencesShanghaiChina
| | - Yun Jiao
- Institute of ForestryNingbo Academy of Agricultural ScienceNingboChina
| | | | - Ting Tu
- Shunmei Breeding and Propagation Centre for Chinese BayberryYuyaoChina
| | | | | | - Long‐Jiang Fan
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Eric van de Weg
- Plant Breeding‐Wageningen University and ResearchWageningenThe Netherlands
| | | | - Zhong‐Shan Gao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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Torres MF, Mathew LS, Ahmed I, Al-Azwani IK, Krueger R, Rivera-Nuñez D, Mohamoud YA, Clark AG, Suhre K, Malek JA. Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix. Nat Commun 2018; 9:3969. [PMID: 30266991 DOI: 10.1038/s41467-018-06375-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
The date palm tree is a commercially important member of the genus Phoenix whose 14 species are dioecious with separate male and female individuals. To identify sex determining genes we sequenced the genomes of 15 female and 13 male Phoenix trees representing all 14 species. We identified male-specific sequences and extended them using phased single-molecule sequencing or BAC clones. We observed that only four genes contained sequences conserved in all analyzed Phoenix males. Most of these sequences showed similarity to a single genomic locus in the closely related monoecious oil palm. CYP703 and GPAT3, two single copy genes present in males and critical for male flower development in other monocots, were absent in females. A LOG-like gene appears translocated into the Y-linked region and is suggested to play a role in suppressing female flowers. Our data are consistent with a two-mutation model for the evolution of dioecy in Phoenix. The origin and evolution of separate sexes in plants are long-standing questions. Here, the authors use genus-wide sequencing to identify sex determining candidate genes in the genus Phoenix and demonstrate the consistence with the previously proposed two-mutation model.
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34
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Coito JL, Silva H, Ramos MJN, Montez M, Cunha J, Amâncio S, Costa MMR, Rocheta M. Vitis Flower Sex Specification Acts Downstream and Independently of the ABCDE Model Genes. Front Plant Sci 2018; 9:1029. [PMID: 30061913 PMCID: PMC6055017 DOI: 10.3389/fpls.2018.01029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/25/2018] [Indexed: 05/20/2023]
Abstract
The most discriminating characteristic between the cultivated Vitis vinifera subsp. vinifera and the wild-form Vitis vinifera subsp. sylvestris is their sexual system. Flowers of cultivars are mainly hermaphroditic, whereas wild plants have female and male individuals whose flowers follow a hermaphroditic pattern during early stages of development and later develop non-functional reproductive organs. In angiosperms, the basic developmental system for floral organ identity is explained by the ABCDE model. This model postulates that regulatory gene functions work in a combinatorial way to confer organ identity in each whorl. In wild Vitis nothing is known about the function and expression profile of these genes. Here we show an overall view of the temporal and spatial expression pattern of the ABCDE genes as well as the pattern of VviSUPERMAN that establishes a boundary between the stamen and the carpel whorls, in the male, female and complete flower types. The results show a similar pattern in Vitis species suggesting that the pathway leading to unisexuality acts independently and/or downstream of B- and C- function genes.
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Affiliation(s)
- João L. Coito
- Linking Landscape, Environment, Agriculture and Food (LEAF), School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Helena Silva
- Plant Functional Biology Centre, Biosystems and Integrative Sciences Institute, University of Minho, Braga, Portugal
| | - Miguel J. N. Ramos
- Linking Landscape, Environment, Agriculture and Food (LEAF), School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Miguel Montez
- Linking Landscape, Environment, Agriculture and Food (LEAF), School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - Sara Amâncio
- Linking Landscape, Environment, Agriculture and Food (LEAF), School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Maria M. R. Costa
- Plant Functional Biology Centre, Biosystems and Integrative Sciences Institute, University of Minho, Braga, Portugal
| | - Margarida Rocheta
- Linking Landscape, Environment, Agriculture and Food (LEAF), School of Agriculture, University of Lisbon, Lisbon, Portugal
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35
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Marrano A, Micheletti D, Lorenzi S, Neale D, Grando MS. Genomic signatures of different adaptations to environmental stimuli between wild and cultivated Vitis vinifera L. Hortic Res 2018; 5:34. [PMID: 29977570 PMCID: PMC6026492 DOI: 10.1038/s41438-018-0041-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/23/2018] [Accepted: 04/06/2018] [Indexed: 05/03/2023]
Abstract
The application of population genetic methods in combination with gene mapping strategies can help to identify genes and mutations selected during the evolution from wild plants to crops and to explore the considerable genetic variation still maintained in natural populations. We genotyped a grapevine germplasm collection of 44 wild (Vitis vinifera subsp. sylvestris) and 48 cultivated (V. vinifera subsp. sativa) accessions at 54 K single-nucleotide polymorphisms (SNPs) to perform a whole-genome comparison of the main population genetic statistics. The analysis of Wright Fixation Index (FST) along the whole genome allowed us to identify several putative "signatures of selection" spanning over two thousand SNPs significantly differentiated between sativa and sylvestris. Many of these genomic regions included genes involved in the adaptation to environmental changes. An overall reduction of nucleotide diversity was observed across the whole genome within sylvestris, supporting a small effective population size of the wild grapevine. Tajima's D resulted positive in both wild and cultivated subgroups, which may indicate an ongoing balancing selection. Association mapping for six domestication-related traits was performed in combination with population genetics, providing further evidence of different perception and response to environmental stresses between sativa and sylvestris.
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Affiliation(s)
- Annarita Marrano
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - Diego Micheletti
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - David Neale
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - M. Stella Grando
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all ‘Adige (TN), Italy
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36
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Veltsos P, Cossard G, Beaudoing E, Beydon G, Savova Bianchi D, Roux C, C González-Martínez S, R Pannell J. Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. Genes (Basel) 2018; 9:E277. [PMID: 29844299 PMCID: PMC6027223 DOI: 10.3390/genes9060277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
Dioecious plants vary in whether their sex chromosomes are heteromorphic or homomorphic, but even homomorphic sex chromosomes may show divergence between homologues in the non-recombining, sex-determining region (SDR). Very little is known about the SDR of these species, which might represent particularly early stages of sex-chromosome evolution. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, a species with homomorphic sex chromosomes and mild Y-chromosome degeneration. We used RNA sequencing (RNAseq) to identify new Y-linked markers for M. annua. Twelve of 24 transcripts showing male-specific expression in a previous experiment could be amplified by polymerase chain reaction (PCR) only from males, and are thus likely to be Y-linked. Analysis of genome-capture data from multiple populations of M. annua pointed to an additional six male-limited (and thus Y-linked) sequences. We used these markers to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequences, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests that it is enriched for repeats, has low gene density, and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which we estimate to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, both in absolute terms and relative to their genome sizes. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Department of Biology, Jordan Hall, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA.
| | - Guillaume Cossard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel Beaudoing
- Faculty of Biology and Medicine, University of Lausanne, Bâtiment Génopode, 1014 Lausanne, Switzerland.
| | - Genséric Beydon
- National Centre for Genomic Resources (CNRGV), 24 Chemin de Borde Rouge-Auzeville-CS52627, 31326 Castanet Tolosan Cedex, France.
| | | | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Santiago C González-Martínez
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- BIOGECO, INRA, University of Bordeaux, 33610 Cestas, France.
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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37
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Laucou V, Launay A, Bacilieri R, Lacombe T, Adam-Blondon AF, Bérard A, Chauveau A, de Andrés MT, Hausmann L, Ibáñez J, Le Paslier MC, Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M, Töpfer R, Péros JP, Boursiquot JM. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLoS One 2018; 13:e0192540. [PMID: 29420602 PMCID: PMC5805323 DOI: 10.1371/journal.pone.0192540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/25/2018] [Indexed: 12/18/2022] Open
Abstract
Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
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Affiliation(s)
- Valérie Laucou
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Amandine Launay
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Thierry Lacombe
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
| | | | - Aurélie Bérard
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France
| | | | | | - Ludger Hausmann
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Javier Ibáñez
- ICVV, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain
| | | | | | | | - Erika Maul
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Maharajah Ponnaiah
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France.,LBD, Univ UPMC, CNRS, INSERM, Paris, France
| | - Reinhard Töpfer
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
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38
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Abstract
We generated genomic data to estimate the population history of grapes, the most economically important horticultural crop in the world. Domesticated grapes experienced a protracted, 22,000-y population decline prior to domestication; we hypothesize that this decline reflects low-intensity cultivation by humans prior to domestication. Domestication altered the mating system of grapes. The sex determination region is detectable as a region of heightened genetic divergence between wild and cultivated accessions. Based on gene expression analyses, we propose candidate genes that alter sex determination. Finally, grapes contain more deleterious mutations in heterozygous states than do their wild ancestors. The accumulation of deleterious mutations is due in part to clonal propagation, which shelters deleterious recessive mutations. We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
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Sousa A, Fuchs J, Renner SS. Cytogenetic comparison of heteromorphic and homomorphic sex chromosomes in Coccinia (Cucurbitaceae) points to sex chromosome turnover. Chromosome Res 2017; 25:191-200. [PMID: 28343268 DOI: 10.1007/s10577-017-9555-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/17/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022]
Abstract
Our understanding of the evolution of plant sex chromosomes is increasing rapidly due to high-throughput sequencing data and phylogenetic and molecular-cytogenetic approaches that make it possible to infer the evolutionary direction and steps leading from homomorphic to heteromorphic sex chromosomes. Here, we focus on four species of Coccinia, a genus of 25 dioecious species, including Coccinia grandis, the species with the largest known plant Y chromosome. Based on a phylogeny for the genus, we selected three species close to C. grandis to test the distribution of eight repetitive elements including two satellites, and several plastid and mitochondrial probes, that we had previously found to have distinct accumulation patterns in the C. grandis genome. Additionally, we determined C-values and performed immunostaining experiments with (peri-)centromere-specific antibodies on two species (for comparison with C. grandis). In spite of no microscopic chromosomal heteromorphism, single pairs of chromosomes in male cells of all three species accumulate some of the very same repeats that are enriched on the C. grandis Y chromosome, pointing to either old (previous) sex chromosomes or incipient (newly arising) ones, that is, to sex chromosome turnover. A 144-bp centromeric satellite repeat (CgCent) that characterizes all C. grandis chromosomes except the Y is highly abundant in all centromeric regions of the other species, indicating that the centromeric sequence of the Y chromosome diverged very recently.
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Affiliation(s)
- Aretuza Sousa
- Department of Biology, University of Munich (LMU), 80638, Munich, Germany.
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Susanne S Renner
- Department of Biology, University of Munich (LMU), 80638, Munich, Germany.
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40
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Migicovsky Z, Sawler J, Gardner KM, Aradhya MK, Prins BH, Schwaninger HR, Bustamante CD, Buckler ES, Zhong GY, Brown PJ, Myles S. Patterns of genomic and phenomic diversity in wine and table grapes. Hortic Res 2017; 4:17035. [PMID: 28791127 PMCID: PMC5539807 DOI: 10.1038/hortres.2017.35] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/16/2017] [Indexed: 05/18/2023]
Abstract
Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
| | - Jason Sawler
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
- Anandia Labs, Vancouver,
BC
V6T 1Z4, Canada
| | - Kyle M Gardner
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
- Agriculture and Agri-Food Canada, Fredericton
Research and Development Centre, Fredericton, NB,
Canada
E3B 4Z7
| | - Mallikarjuna K Aradhya
- National Clonal Germplasm Repository, United
States Department of Agriculture-Agricultural Research Service, University of
California, Davis, CA
95616, USA
| | - Bernard H Prins
- National Clonal Germplasm Repository, United
States Department of Agriculture-Agricultural Research Service, University of
California, Davis, CA
95616, USA
| | - Heidi R Schwaninger
- United States Department of Agriculture,
Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
| | | | - Edward S Buckler
- Department of Plant Breeding and Genetics,
Cornell University, Ithaca, NY
14853, USA
| | - Gan-Yuan Zhong
- United States Department of Agriculture,
Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
- United States Department of Agriculture,
Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
| | - Patrick J Brown
- Department of Crop Science, University of
Illinois, Urbana, IL
61801, USA
| | - Sean Myles
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
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41
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Coito JL, Ramos MJN, Cunha J, Silva HG, Amâncio S, Costa MMR, Rocheta M. VviAPRT3 and VviFSEX: Two Genes Involved in Sex Specification Able to Distinguish Different Flower Types in Vitis. Front Plant Sci 2017; 8:98. [PMID: 28197167 PMCID: PMC5281589 DOI: 10.3389/fpls.2017.00098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/17/2017] [Indexed: 05/06/2023]
Abstract
Vitis vinifera vinifera is a hermaphrodite subspecies, while its ancestor, Vitis vinifera sylvestris, is dioecious. We have identified two genes that together allow the discrimination between male, female and hermaphrodite Vitis plants. The sex locus region on chromosome 2 was screened resulting in the discovery of a new gene, VviFSEX. The same screening revealed another gene, VviAPRT3, located in the sex region, that be used as a sex marker. Both genes are good candidates to be involved in flower sex differentiation in grapevine. To assess their role in sex specification, spatial and temporal expression analysis was performed. The expression of VviFSEX is detected in petals, stamens and carpel primordia of all flower types, making its putative function unclear; however, female plants display a single allele for this gene, while male and hermaphrodites display two alleles. On the other hand, the specific expression of VviAPRT3 in the carpel primordial of male plants suggests a possible role in the abortion of pistil structures. We propose a model to explain the carpel abortion in male flowers and the absence of stamen viability in female flowers. In addition, this work reinforces the presence of a sex locus on Vitis chromosome 2.
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Affiliation(s)
- João L. Coito
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Miguel J. N. Ramos
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e VeterináriaTorres Vedras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de LisboaOeiras, Portugal
| | - Helena G. Silva
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Sara Amâncio
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Maria M. R. Costa
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Margarida Rocheta
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
- *Correspondence: Margarida Rocheta,
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Ramos MJN, Coito JL, Fino J, Cunha J, Silva H, de Almeida PG, Costa MMR, Amâncio S, Paulo OS, Rocheta M. Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification. Plant Mol Biol 2017; 93:151-170. [PMID: 27778293 DOI: 10.1007/s11103-016-0553-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/15/2016] [Indexed: 06/06/2023]
Abstract
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development.
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Affiliation(s)
- Miguel Jesus Nunes Ramos
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - João Lucas Coito
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - Joana Fino
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d'Almoinha, Dois Portos, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Silva
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Patrícia Gomes de Almeida
- Development and Evolutionary Morphogenesis, Centre for Ecology, Evolution and Environmental Change, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Maria Manuela Ribeiro Costa
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara Amâncio
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Margarida Rocheta
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal.
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Tennessen JA, Govindarajulu R, Liston A, Ashman T. Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region. New Phytol 2016; 211:1412-23. [PMID: 27102236 PMCID: PMC5074332 DOI: 10.1111/nph.13983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
Recombination in ancient, heteromorphic sex chromosomes is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the pseudoautosomal region (PAR). However, little is known about recombination dynamics of young, homomorphic plant sex chromosomes. We examine male and female function in crosses and unrelated samples of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the incipient ZW chromosome. The SDR of this ZW system is located within a 280 kb window, in which the maternal recombination rate is lower than the paternal one. In contrast to the SDR, the maternal PAR recombination rate is much higher than the rates of the paternal PAR or autosomes, culminating in an elevated chromosome-wide rate. W-specific divergence is elevated within the SDR and a single polymorphism is observed in high species-wide linkage disequilibrium with sex. Selection for recombination suppression within the small SDR may be weak, but fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutations on the W. The recombination dynamics of this nascent sex chromosome with a modestly diverged SDR may be typical of other dioecious plants.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative BiologyOregon State UniversityCorvallisOR97331USA
| | | | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331USA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260‐3929USA
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Pap D, Riaz S, Dry IB, Jermakow A, Tenscher AC, Cantu D, Oláh R, Walker MA. Identification of two novel powdery mildew resistance loci, Ren6 and Ren7, from the wild Chinese grape species Vitis piasezkii. BMC Plant Biol 2016; 16:170. [PMID: 27473850 PMCID: PMC4966781 DOI: 10.1186/s12870-016-0855-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 07/14/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Grapevine powdery mildew Erysiphe necator is a major fungal disease in all grape growing countries worldwide. Breeding for resistance to this disease is crucial to avoid extensive fungicide applications that are costly, labor intensive and may have detrimental effects on the environment. In the past decade, Chinese Vitis species have attracted attention from grape breeders because of their strong resistance to powdery mildew and their lack of negative fruit quality attributes that are often present in resistant North American species. In this study, we investigated powdery mildew resistance in multiple accessions of the Chinese species Vitis piasezkii that were collected during the 1980 Sino-American botanical expedition to the western Hubei province of China. RESULTS A framework genetic map was developed using simple sequence repeat markers in 277 seedlings of an F1 mapping population arising from a cross of the powdery mildew susceptible Vitis vinifera selection F2-35 and a resistant accession of V. piasezkii DVIT2027. Quantitative trait locus analyses identified two major powdery mildew resistance loci on chromosome 9 (Ren6) and chromosome 19 (Ren7) explaining 74.8 % of the cumulative phenotypic variation. The quantitative trait locus analysis for each locus, in the absence of the other, explained 95.4 % phenotypic variation for Ren6, while Ren7 accounted for 71.9 % of the phenotypic variation. Screening of an additional 259 seedlings of the F1 population and 910 seedlings from four pseudo-backcross populations with SSR markers defined regions of 22 kb and 330 kb for Ren6 and Ren7 in the V. vinifera PN40024 (12X) genome sequence, respectively. Both R loci operate post-penetration through the induction of programmed cell death, but vary significantly in the speed of response and degree of resistance; Ren6 confers complete resistance whereas Ren7 confers partial resistance to the disease with reduced colony size. A comparison of the kinetics of induction of powdery mildew resistance mediated by Ren6, Ren7 and the Run1 locus from Muscadinia rotundifolia, indicated that the speed and strength of resistance conferred by Ren6 is greater than that of Run1 which, in turn, is superior to that conferred by Ren7. CONCLUSIONS This is the first report of mapping powdery mildew resistance in the Chinese species V. piasezkii. Two distinct powdery mildew R loci designated Ren6 and Ren7 were found in multiple accessions of this Chinese grape species. Their location on different chromosomes to previously reported powdery mildew resistance R loci offers the potential for grape breeders to combine these R genes with existing powdery mildew R loci to produce grape germplasm with more durable resistance against this rapidly evolving fungal pathogen.
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Affiliation(s)
- Dániel Pap
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
- Department of Genetics and Plant Breeding, Corvinus University of Budapest, Villányi út 29-34, 1118 Budapest, Hungary
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Ian B. Dry
- CSIRO Agriculture, Glen Osmond, SA Australia
| | | | - Alan C. Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Róbert Oláh
- Department of Genetics and Plant Breeding, Corvinus University of Budapest, Villányi út 29-34, 1118 Budapest, Hungary
| | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
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Abstract
Although individuals in most flowering plant species, and in many haploid plants, have both sex functions, dioecious species-in which individuals have either male or female functions only-are scattered across many taxonomic groups, and many species have genetic sex determination. Among these, some have visibly heteromorphic sex chromosomes, and molecular genetic studies are starting to uncover sex-linked markers in others, showing that they too have fully sex-linked regions that are either too small or are located in chromosomes that are too small to be cytologically detectable from lack of pairing, lack of visible crossovers, or accumulation of heterochromatin. Detailed study is revealing that, like animal sex chromosomes, plant sex-linked regions show evidence for accumulation of repetitive sequences and genetic degeneration. Estimating when recombination stopped confirms the view that many plants have young sex-linked regions, making plants of great interest for studying the timescale of these changes.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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46
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Zyprian E, Ochßner I, Schwander F, Šimon S, Hausmann L, Bonow-Rex M, Moreno-Sanz P, Grando MS, Wiedemann-Merdinoglu S, Merdinoglu D, Eibach R, Töpfer R. Quantitative trait loci affecting pathogen resistance and ripening of grapevines. Mol Genet Genomics 2016; 291:1573-94. [PMID: 27038830 DOI: 10.1007/s00438-016-1200-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/12/2016] [Indexed: 10/22/2022]
Abstract
Grapevines (Vitis vinifera L.) form the basis of viticulture, and are susceptible to diseases such as downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator). Therefore, successful viticulture programs require the use of pesticides. Breeding for resistance is the only eco-friendly solution. Marker-assisted selection is currently widely used for grapevine breeding. Consequently, traits of interest must be tagged with molecular markers linked to quantitative trait loci (QTL). We herein present our findings regarding genetic mapping and QTL analysis of resistance to downy and powdery mildew diseases in the progenies of the GF.GA-47-42 ('Bacchus' × 'Seyval') × 'Villard blanc' cross. Simple sequence repeats and single nucleotide polymorphisms of 151 individuals were analyzed. A map consisting of 543 loci was screened for QTL analyses based on phenotypic variations observed in plants grown in the field or under controlled conditions. A major QTL for downy mildew resistance was detected on chromosome 18. For powdery mildew resistance, a QTL was identified on chromosome 15. This QTL was replaced by a novel QTL on chromosome 18 in 2003 (abnormally high temperatures) and 2004. Subsequently, both QTLs functioned together. Additionally, variations in the timing of the onset of veraison, which is a crucial step during grape ripening, were studied to identify genomic regions affecting this trait. A major QTL was detected on linkage group 16, which was supplemented by a minor QTL on linkage group 18. This study provides useful information regarding novel QTL-linked markers relevant for the breeding of disease-resistant grapevines adapted to current climatic conditions.
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47
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Yang S, Fresnedo-Ramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark M, Luby J, Manns DC, Sacks G, Mansfield AK, Londo J, Fennell A, Gadoury D, Reisch B, Cadle-Davidson L, Sun Q. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. Hortic Res 2016; 3:16002. [PMID: 27257505 PMCID: PMC4879517 DOI: 10.1038/hortres.2016.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 05/07/2023]
Abstract
Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.
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Affiliation(s)
- Shanshan Yang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Minghui Wang
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Linda Cote
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Schweitzer
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth M Takacs
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - James Luby
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - David C Manns
- Department of Food Science, Cornell University, Geneva, NY 14456, USA
| | - Gavin Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Jason Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anne Fennell
- Plant Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - David Gadoury
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
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Dangl GS, Mendum ML, Yang J, Walker MA, Preece JE. Hybridization of cultivated Vitis vinifera with wild V. californica and V. girdiana in California. Ecol Evol 2015; 5:5671-84. [PMID: 27069616 PMCID: PMC4813103 DOI: 10.1002/ece3.1797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/02/2015] [Indexed: 01/20/2023] Open
Abstract
Hybridization of introduced domesticates and closely related natives is well documented in annual crops. The widespread introduction of the domesticated grapevine, Vitis vinifera, into California where it overlaps with two native congenerics, with which it is interfertile, provides opportunity to investigate hybridization between woody perennials. Although geographically widespread, the introduction over the past two centuries has been limited to a few elite clonal cultivars, providing a unique opportunity to study the effects of hybridization on the native species. The amount of hybridization with V. vinifera and the genetic diversity of wild-growing Vitis californica and Vitis girdiana were examined using nineteen microsatellite markers. STRUCTURE analysis was used to define hybrid and introgressed individuals and to analyze genetic structure of the native species. FAMOZ software was used to identify which V. vinifera cultivars served as parents of F 1 hybrids. The three species were clearly distinguished by STRUCTURE analysis. Thirty percent of 119 V. californica vines were hybrids. The domesticated parent was identified for 16 F 1 hybrid vines; the original California cultivar, 'Mission', was the parent of eight. Backcrosses were also found, showing introgression into subsequent generations. Similar results were obtained for a small sample of V. girdiana. Removing hybrids greatly reduced the genetic variation of the presumed pure species, among which there was essentially no genetic structure. Limited genetic variability indicates the California natives may be threatened by genetic erosion. The discovery of F 1 hybrids of 'Mission', a cultivar not grown in the areas for ~100 years, suggests long generation times for wild vines that, often, grow into expansive liana and propagate by layering, all factors that limit recruitment in populations already disjunct by habitat lose. Hermaphroditic flowers and fruit that is more attractive to birds may favor the production of backcross seed and establishment of introgressed individuals.
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Affiliation(s)
- Gerald S. Dangl
- Foundation Plant ServicesUniversity of California DavisOne Shields Ave.DavisCalifornia95616
| | - Mary Lou Mendum
- Department of Plant SciencesUniversity of California DavisOne Shields Ave.DavisCalifornia95616
| | - Judy Yang
- Foundation Plant ServicesUniversity of California DavisOne Shields Ave.DavisCalifornia95616
| | - M. Andrew Walker
- Department of Viticulture and EnologyUniversity of California DavisOne Shields Ave.DavisCalifornia95616
| | - John E. Preece
- National Clonal Germplasm RepositoryUSDA‐ARSUniversity of California DavisOne Shields AveDavisCalifornia95616
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49
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Abstract
Sex chromosomes are a very peculiar part of the genome that have evolved independently in many groups of animals and plants (Bull ). Major research efforts have so far been focused on large heteromorphic sex chromosomes in a few animal and plant species (Chibalina & Filatov ; Zhou & Bachtrog ; Bellott et al. ; Hough et al. ; Zhou et al. ), while homomorphic (cytologically indistinguishable) sex chromosomes have largely been neglected. However, this situation is starting to change. In this issue, Geraldes et al. () describe a small (~100 kb long) sex-determining region on the homomorphic sex chromosomes of poplars (Populus trichocarpa and related species, Fig. ). All species in Populus and its sister genus Salix are dioecious, suggesting that dioecy and the sex chromosomes, if any, should be relatively old. Contrary to this expectation, Geraldes et al. () demonstrate that the sex-determining region in poplars is of very recent origin and probably evolved within the genus Populus only a few million years ago.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, OX1 3RB, UK
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Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L. Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLoS One 2015; 10:e0134880. [PMID: 26244767 PMCID: PMC4526651 DOI: 10.1371/journal.pone.0134880] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.
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Affiliation(s)
- Katie E. Hyma
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
| | - Minghui Wang
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Jason P. Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Charlotte B. Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
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