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Blois L, de Miguel M, Bert PF, Ollat N, Rubio B, Voss-Fels KP, Schmid J, Marguerit E. Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:223. [PMID: 37838631 PMCID: PMC10576685 DOI: 10.1007/s00122-023-04472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023]
Abstract
In woody perennial plants, quantitative genetics and association studies remain scarce for root-related traits, due to the time required to obtain mature plants and the complexity of phenotyping. In grapevine, a grafted cultivated plant, most of the rootstocks used are hybrids between American Vitis species (V. rupestris, V. riparia, and V. berlandieri). In this study, we used a wild population of an American Vitis species (V. berlandieri) to analyze the genetic architecture of the root-related traits of rootstocks in a grafted context. We studied a population consisting of 211 genotypes, with one to five replicates each (n = 846 individuals), plus four commercial rootstocks as control genotypes (110R, 5BB, Börner, and SO4). After two independent years of experimentation, the best linear unbiased estimates method revealed root-related traits with a moderate-to-high heritability (0.36-0.82) and coefficient of genetic variation (0.15-0.45). A genome-wide association study was performed with the BLINK model, leading to the detection of 11 QTL associated with four root-related traits (one QTL was associated with the total number of roots, four were associated with the number of small roots (< 1 mm in diameter), two were associated with the number of medium-sized roots (1 mm < diameter < 2 mm), and four were associated with mean diameter) accounting for up to 25.1% of the variance. Three genotypes were found to have better root-related trait performances than the commercial rootstocks and therefore constitute possible new candidates for use in grapevine rootstock breeding programs.
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Affiliation(s)
- Louis Blois
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France.
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany.
| | - Marina de Miguel
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Pierre-François Bert
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Bernadette Rubio
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
| | - Kai P Voss-Fels
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany
| | - Joachim Schmid
- Department of Grapevine Breeding, Geisenheim University, Von Lade Str. 1, 65366, Geisenheim, Germany
| | - Elisa Marguerit
- EGFV, Bordeaux Sciences Agro, INRAE, ISVV, Univ. Bordeaux, 33882, Villenave d'Ornon, France
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Polyploid SNP Genotyping Using the MassARRAY System. Methods Mol Biol 2023; 2638:93-113. [PMID: 36781637 DOI: 10.1007/978-1-0716-3024-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Molecular marker discovery and genotyping are major challenges in polyploid breeding programs incorporating molecular biology tools. In this context, this work describes a method for single nucleotide polymorphism (SNP) genotyping in polyploid crops using matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry, the MassARRAY System.
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Bali S, Brown C, Majtahedi H, Yilma S, Ingham RE, Cimrhakl L, Quick R, Sathuvalli V. Genomic markers linked to Meloidogyne chitwoodi resistance introgressed from Solanum bulbocastanum to cultivated potato and their utility in marker-assisted selection. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:12. [PMID: 37309410 PMCID: PMC10248663 DOI: 10.1007/s11032-022-01285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Meloidogyne chitwoodi is a major threat to potato production in the Pacific Northwest region of the United States. Infected tubers are rendered unmarketable; hence, growers' profitability is adversely affected. Breeding for nematode resistance is a long-term process and phenotyping the segregating populations for nematode resistance is the most time-consuming and laborious part of the process. Using DNA-based markers closely linked to the nematode resistance trait for marker-assisted selection (MAS) could enhance breeding efficiency and accuracy. In the present study, a pool of phenotyped progenies segregating for nematode resistance and susceptibility were fingerprinted using a 21 K single-nucleotide polymorphism (SNP) array. Eight candidate SNPs located on potato Chromosome 11, segregating with the nematode resistance trait, were identified and used as landmarks for discovery of other marker types such as simple sequence repeat (SSR) and insertion-deletion (INDEL) markers. Subsequently, a total of eight SNPs, 30 SSRs, and four INDELS located on scaffold 11 of Solanum bulbocastanum were used to design primers; markers were validated in a panel of resistant and susceptible clones. Two SNPs (SB_MC1Chr11-PotVar0066518 and SB_MC1Chr11-PotVar0064140), five SSRs (SB_MC1Chr11-SSR04, SB_MC1Chr11-SSR08, SB_MC1Chr11-SSR10, SB_MC1Chr11-SSR13, and SB_MC1Chr11-SSR20), and one INDEL (SB_MC1Chr11-INDEL4) markers showed polymorphism between the resistant and susceptible clones in the test panel and in other segregating progenies. These markers are robust, highly reproducible, and easy to use for MAS of nematode-resistant potato clones to enhance the breeding program. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01285-w.
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Affiliation(s)
- Sapinder Bali
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston-97838, OR USA
- Department of Plant Pathology, Washington State University, Pullman-99164, WA USA
| | - Charles Brown
- Temperate Tree Fruit and Vegetable Research Unit, USDA-Agricultural Research Service, Prosser-99350, WA USA
| | - Hassan Majtahedi
- Temperate Tree Fruit and Vegetable Research Unit, USDA-Agricultural Research Service, Prosser-99350, WA USA
| | - Solomon Yilma
- Department of Crop and Soil Sciences, Oregon State University, Corvallis-97331, OR USA
| | - Russell E. Ingham
- Department of Botany and Plant Pathology, Oregon State University, Corvallis-97333, OR USA
| | - Launa Cimrhakl
- Temperate Tree Fruit and Vegetable Research Unit, USDA-Agricultural Research Service, Prosser-99350, WA USA
| | - Rich Quick
- Temperate Tree Fruit and Vegetable Research Unit, USDA-Agricultural Research Service, Prosser-99350, WA USA
| | - Vidyasagar Sathuvalli
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston-97838, OR USA
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Babineau M, Collis E, Ruffell A, Bunch R, McNally J, Lyons RE, Kotze AC, Hunt PW. Selection of genome-wide SNPs for pooled allelotyping assays useful for population monitoring. Genome Biol Evol 2022; 14:6531970. [PMID: 35179579 PMCID: PMC8911822 DOI: 10.1093/gbe/evac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2022] [Indexed: 11/13/2022] Open
Abstract
Parasitic worms are serious pests of humans, livestock and crops worldwide. Multiple management strategies are employed in order to reduce their impact, and some of these may affect their genome and population allelic frequency distribution. The evolution of chemical resistance, ecological changes, and pest dispersal have allowed an increasing number of pests to become difficult to control with current management methods. Their lifestyle limits the use of ecological and individual-based management of populations. There is a need to develop rapid, affordable, and simple diagnostics to assess the efficacy of management strategies and delay the evolution of resistance to these strategies. This study presents a multi-locus, equal-representation, whole genome pooled SNPs selection approach as a monitoring tool for the ovine nematode parasite Haemonchus contortus. The SNP selection method used two reference genomes of different quality, then validated these SNPs against a high-quality recent genome assembly. From over 11 million high-quality SNPs identified, 334 SNPs were selected, of which 262 were species-specific, yielded similar allele frequencies when assessed as multiple individuals or as pools of individuals, and suitable to distinguish mixed nematode isolate pools from single isolate pools. As a proof-of-concept, 21 Australian H. contortus populations with various phenotypes and genotypes were screened. This analysis confirmed the overall low-level of genetic differentiation between populations collected from the field, but clearly identifying highly inbred populations, and populations showing genetic signatures associated with chemical resistance. The analysis showed that 66% of the SNPs were necessary for stability in assessing population genetic patterns, and SNP pairs did not show linkage according to allelic frequencies across the 21 populations. This method demonstrates that ongoing monitoring of parasite allelic frequencies and genetic changes can be achieved as a management assessment tool to identify drug-treatment failure, population incursions, and inbreeding signatures due to selection. The SNP selection method could also be applied to other parasite species.
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Affiliation(s)
- M Babineau
- CSIRO Agriculture and Food, Armidale, Australia
| | - E Collis
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - A Ruffell
- CSIRO Agriculture and Food, St-Lucia, Australia
| | - R Bunch
- CSIRO Agriculture and Food, Armidale, Australia
| | - J McNally
- CSIRO Agriculture and Food, Armidale, Australia
| | - R E Lyons
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - A C Kotze
- CSIRO Agriculture and Food, St-Lucia, Australia
| | - P W Hunt
- CSIRO Agriculture and Food, Armidale, Australia
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Yang Y, Hu X, Liu P, Chen L, Peng H, Wang Q, Zhang Q. A new root-knot nematode, Meloidogyne vitis sp. nov. (Nematoda: Meloidogynidae), parasitizing grape in Yunnan. PLoS One 2021; 16:e0245201. [PMID: 33534787 PMCID: PMC7857618 DOI: 10.1371/journal.pone.0245201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/19/2020] [Indexed: 11/19/2022] Open
Abstract
An unknown root-knot nematode was found at high density on grape roots collected from Yunnan Province. Morphometric traits and measurements, isozyme phenotypes, and molecular analysis clearly differentiated this nematode from previously described root-knot nematodes. This new species is described, illustrated and named Meloidogyne vitis sp. nov. The new species can be distinguished from other Meloidogyne spp. by a unique combination of characters. Females display a prominent neck, an excretory pore is located on the ventral region between 23rd and 25th annule behind lips, an EP/ST ratio of approximately 2.5 (1.98-2.96), a perineal pattern with two large and prominent phasmids, and a labial disc fused with the medial lips to form a dumbbell-shaped structure. Males display an obvious head region, a labial disc fused with the medial lips to form a dumbbell-shaped structure, no lateral lips, a prominent slit-like opening between the labial disc and medial lips, a distinct sunken appearance of the middle of the medial lips, and four incisures in the lateral field. Second-stage juveniles are characterized by a head region with slightly wrinkled mark, a labial disc fused with the medial lips to form a dumbbell-shaped structure, a slightly sunken appearance of the middle of the medial lips, a slit-like amphidial openings between the labial disc and lateral lips, and four incisures in the lateral field. The new species has rare Mdh (N3d) and Est phenotypes (VF1). Phylogenetic analysis based on ITS1-5.8S-ITS2, D2D3 fragments of rDNA, and coxI and coxII fragments of mtDNA sequences clearly separated the new species from other root-knot nematodes, and the closest relative was Meloidogyne mali. Meloidogyne mali was collected for amplifying these sequences as mentioned above, which were compared with the corresponding sequences of new species, the result showed that all of these sequences with highly base divergence (48-210 base divergence). Moreover, sequence characterized amplified region (SCAR) primers for rapid identification of this new species were designed.
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Affiliation(s)
- Yanmei Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Xianqi Hu
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Pei Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Li Chen
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi Province, China
| | - Huan Peng
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing, China
| | - Qiaomei Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Qi Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan Province, China
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Association between Neuron-Specific Enolase Gene Polymorphism and Delayed Encephalopathy after Acute Carbon Monoxide Poisoning. Behav Neurol 2020; 2020:8819210. [PMID: 33123300 PMCID: PMC7584970 DOI: 10.1155/2020/8819210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/11/2020] [Accepted: 09/30/2020] [Indexed: 11/18/2022] Open
Abstract
Objective The aim of this study is to explore the relationship between neuron-specific enolase (NSE) gene polymorphism and delayed encephalopathy after acute carbon monoxide poisoning (DEACMP) and provide a theoretical basis for DEACMP pathogenesis, diagnosis, and prognosis. Methods To investigate this relationship, we screened 6 NSE single nucleotide polymorphisms (SNPs), based on the results of the previous genome-wide association studies (GWAS). A total of 1,201 patients, including 416 in the DEACMP group and 785 in the acute carbon monoxide poisoning (ACMP) group, were detected by the Sequenom MassARRAY® method. The genotype frequencies and alleles of the 6 NSE SNPs (rs2071074, rs2071417, rs2071419, rs11064464, rs11064465, and rs3213434) were compared using different genetic models. Results In the SNPs rs2071419 and rs3213434, we found that the genotypes and allele frequencies in the two groups significantly correlated with the grouping of patients (χ 2 = 6.596, p = 0.037; χ 2 = 8.769, p = 0.012). The haplotypes GGTTTC and CCTTTC of ACMP and DEACMP were different (χ 2 = 6.563, p = 0.010; χ 2 = 4.151, p = 0.042). We also observed that rs2071419 and rs3213434 significantly correlated with DEACMP-increased risk in the dominant, codominant, and overdominant genetic models. In addition, we speculated that the C allele of the rs2071419 polymorphism and the T allele of the rs3213434 polymorphism in NSE may increase the DEACMP risk (p = 0.011, p = 0.006). Conclusions The results show that rs2071419 and rs3213434 are susceptible sites of DEACMP. The NSE C allele of rs2071419 and T allele of rs3213434 and the haplotypes GGTTTC and CCTTTC may be risk factors for DEACMP.
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Wallis CM. Grapevine (Vitis spp.) rootstock stilbenoid associations with host resistance to and induction by root knot nematodes, Meloidogyne incognita. BMC Res Notes 2020; 13:360. [PMID: 32727572 PMCID: PMC7392673 DOI: 10.1186/s13104-020-05201-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 11/21/2022] Open
Abstract
Objective The root knot nematodes (RKN) Meloidogyne incognita can severely reduce grapevine yields over time. Grapevine rootstocks have been developed from wild Vitis species that provide resistance to nematode infections. However, the potential biochemical or mechanical mechanisms of resistance have not been thoroughly explored. Therefore, this study measured levels of stilbenoids in roots of non-infected and RKN-infected grapevines with Cabernet Sauvignon scion grafted to susceptible (O39-16) or resistant (Freedom) rootstocks. This was part of a larger effort to assess phenolic compound levels within grapevine rootstocks to determine roles of stilbenoid compounds in improving nematode resistance and overall plant health. Results None of the assessed compounds were consistently greater in RKN infected plants versus healthy controls. Stilbenoids putatively identified as pallidol, ɑ-viniferin, miyabenol C, and hopeaphenol were overall much greater in Freedom than O39-16 rootstocks. By contrast, the stilbenoids ampelopsin A, ω-viniferin, and vitisin B were greater in O39-16 than Freedom. O39-16 and Freedom had similar levels of other stilbenoids especially monomers and dimers. Potentially the greater levels of specific stilbenoids present in Freedom than O39-16 provided RKN resistance. If validated, breeding programs could utilize the increased presence of these compounds as a marker for increased resistance to nematodes.
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Affiliation(s)
- Christopher M Wallis
- USDA-ARS San Joaquin Valley Agricultural Sciences Center, Crop Diseases, Pests and Genetics Research Unit, 9611 S. Riverbend Ave, Parlier, CA, 93648, USA.
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Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes ( Vitis vinifera L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2020; 21:ijms21030797. [PMID: 31991832 PMCID: PMC7037167 DOI: 10.3390/ijms21030797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.
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Gu J, Zeng J, Wang X, Gu X, Zhang X, Zhang P, Zhang F, Han Y, Han Y, Zhang H, Li W, Gu R. LRCH1 polymorphisms linked to delayed encephalopathy after acute carbon monoxide poisoning identified by GWAS analysis followed by Sequenom MassARRAY® validation. BMC MEDICAL GENETICS 2019; 20:197. [PMID: 31842790 PMCID: PMC6916040 DOI: 10.1186/s12881-019-0931-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 11/28/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND We explored the association of leucine-rich repeats and calponin homology domain containing 1 (LRCH1) gene polymorphisms with genetic susceptibility to delayed encephalopathy after acute carbon monoxide poisoning (DEACMP), which might provide a theoretical basis for the pathogenesis, diagnosis, and prognosis research of DEACMP. METHODS Four single nucleotide polymorphisms, rs1539177 (G/A), rs17068697 (G/A), rs9534475 (A/C), and rs2236592 (T/C), of LRCH1, selected as candidate genes through genome-wide association analysis, were genotyped in 661 patients (DEACMP group: 235 cases; ACMP group: 426 cases) using Sequenom Massarray®. The association analysis of four SNPs and LRCH1 was performed under different genetic models. RESULTS LRCH1 polymorphisms (rs1539177, rs17068697, rs9534475) under additive and dominant genetic models were significantly associated with an increased risk of DEACMP, but no significant association under allele and recessive models was found. The LRCH1 rs2236592 polymorphism was susceptible to DEACMP only under the dominant model (TT/TC + CC, OR = 1.616, 95% CI: 1.092-2.390, P = 0.015784). In addition, the A allele gene of rs9534475 polymorphism in LRCH1 might increase the risk for DEACMP (OR = 1.273, 95% CI: 1.013-1.601, P = 0.038445). CONCLUSIONS We found a significant association between the four LRCH1 polymorphisms and DEACMP. The allelic A of rs9534475 polymorphism in LRCH1 might be a risk factor for DEACMP.
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Affiliation(s)
- Jiapeng Gu
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Jiao Zeng
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Xi Wang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Xin Gu
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Xiaoli Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Ping Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Fan Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Yongkai Han
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China
| | - Yazhou Han
- Qinyang People's Hospital, Jiaozuo City, 454550, Henan Province, China
| | - Hongxing Zhang
- The Psychology College of Xinxiang Medical University, Xinxiang City, 453002, Henan Province, China
| | - Wenqiang Li
- International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Henan Key Lab of Biological Psychiatry of Xinxiang Medical University, Xinxiang City, 453002, Henan Province, China.
| | - Renjun Gu
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, No. 388 Jianshe Middle Road, Muye District, Xinxiang City, 453002, Henan Province, China.
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Tello J, Roux C, Chouiki H, Laucou V, Sarah G, Weber A, Santoni S, Flutre T, Pons T, This P, Péros JP, Doligez A. A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2237-2252. [PMID: 31049634 DOI: 10.1007/s00122-019-03351-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/20/2019] [Indexed: 05/21/2023]
Abstract
A half-diallel population involving five elite grapevine cultivars was generated and genotyped by GBS, and highly-informative segregation data was used to construct a high-density genetic map for Vitis vinifera L. Grapevine is one of the most relevant fruit crops in the world. Deeper genetic knowledge could assist modern grapevine breeding programs to develop new wine grape varieties able to face climate change effects. To assist in the rapid identification of markers for crop yield components, grape quality traits and adaptation potential, we generated a large Vitis vinifera L. population (N = 624) by crossing five red wine cultivars in a half-diallel scheme, which was subsequently sequenced by an efficient GBS procedure. A high number of fully informative genetic variants was detected using a novel mapping approach capable of reconstructing local haplotypes from adjacent biallelic SNPs, which were subsequently used to construct the densest consensus genetic map available for the cultivated grapevine to date. This 1378.3-cM map integrates 10 bi-parental consensus maps and orders 4437 markers in 3353 unique positions on 19 chromosomes. Markers are well distributed all along the grapevine reference genome, covering up to 98.8% of its genomic sequence. Additionally, a good agreement was observed between genetic and physical orders, adding confidence in the quality of this map. Collectively, our results pave the way for future genetic studies (such as fine QTL mapping) aimed to understand the complex relationship between genotypic and phenotypic variation in the cultivated grapevine. In addition, the method used (which efficiently delivers a high number of fully informative markers) could be of interest to other outbred organisms, notably perennial fruit crops.
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Affiliation(s)
- Javier Tello
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Catherine Roux
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Hajar Chouiki
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Valérie Laucou
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Audrey Weber
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
| | - Timothée Flutre
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Thierry Pons
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Patrice This
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Péros
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- UMR AGAP, University of Montpellier-CIRAD-INRA-Montpellier SupAgro, Montpellier, France.
- UMT Geno-Vigne®, IFV-INRA-Montpellier SupAgro, Montpellier, France.
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Smith HM, Clarke CW, Smith BP, Carmody BM, Thomas MR, Clingeleffer PR, Powell KS. Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in Vitis cinerea for marker-assisted selection. BMC PLANT BIOLOGY 2018; 18:360. [PMID: 30563461 PMCID: PMC6299647 DOI: 10.1186/s12870-018-1590-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 12/05/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Grape phylloxera (Daktulosphaira vitifoliae Fitch) is a major insect pest that negatively impacts commercial grapevine performance worldwide. Consequently, the use of phylloxera resistant rootstocks is an essential component of vineyard management. However, the majority of commercially available rootstocks used in viticulture production provide limited levels of grape phylloxera resistance, in part due to the adaptation of phylloxera biotypes to different Vitis species. Therefore, there is pressing need to develop new rootstocks better adapted to specific grape growing regions with complete resistance to grape phylloxera biotypes. RESULTS Grapevine rootstock breeding material, including an accession of Vitis cinerea and V. aestivalis, DRX55 ([M. rotundifolia x V. vinifera] x open pollinated) and MS27-31 (M. rotundifolia specific hybrid), provided complete resistance to grape phylloxera in potted plant assays. To map the genetic factor(s) of grape phylloxera resistance, a F1 V. cinerea x V. vinifera Riesling population was screened for resistance. Heritability analysis indicates that the V. cinerea accession contained a single allele referred as RESISTANCE TO DAKTULOSPHAIRA VITIFOLIAE 2 (RDV2) that confers grape phylloxera resistance. Using genetic maps constructed with pseudo-testcross markers for V. cinerea and Riesling, a single phylloxera resistance locus was identified in V. cinerea. After validating SNPs at the RDV2 locus, interval and linkage mapping showed that grape phylloxera resistance mapped to linkage group 14 at position 16.7 cM. CONCLUSION The mapping of RDV2 and the validation of markers linked to grape phylloxera resistance provides the basis to breed new rootstocks via marker-assisted selection that improve vineyard performance.
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Affiliation(s)
| | - Catherine W. Clarke
- Agriculture Victoria, Biosciences Research Division, 124 Chiltern Valley Road, Rutherglen, Melbourne, Victoria 3685 Australia
| | - Brady P. Smith
- CSIRO Agriculture and Food, Glen Osmond, SA 5064 Australia
| | - Bernadette M. Carmody
- Agriculture Victoria, Biosciences Research Division, 124 Chiltern Valley Road, Rutherglen, Melbourne, Victoria 3685 Australia
| | - Mark R. Thomas
- CSIRO Agriculture and Food, Glen Osmond, SA 5064 Australia
| | | | - Kevin S. Powell
- Agriculture Victoria, Biosciences Research Division, 124 Chiltern Valley Road, Rutherglen, Melbourne, Victoria 3685 Australia
- Sugar Research Australia, PO Box 122, Gordonvale, QLD 4865 Australia
- The Australian Wine Research Institute, Box 197, Glen Osmond, SA 5064 Australia
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