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Dong X, Wang Z, Tian L, Zhang Y, Qi D, Huo H, Xu J, Li Z, Liao R, Shi M, Wahocho SA, Liu C, Zhang S, Tian Z, Cao Y. De novo assembly of a wild pear (Pyrus betuleafolia) genome. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:581-595. [PMID: 31368610 PMCID: PMC6953202 DOI: 10.1111/pbi.13226] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/25/2019] [Accepted: 07/23/2019] [Indexed: 05/18/2023]
Abstract
China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.
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Affiliation(s)
- Xingguang Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Luming Tian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Dan Qi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Hongliang Huo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Jiayu Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zhe Li
- Berry Genomics CorporationBeijingChina
| | - Rui Liao
- Berry Genomics CorporationBeijingChina
| | - Miao Shi
- Berry Genomics CorporationBeijingChina
| | - Safdar Ali Wahocho
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Chao Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Simeng Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yufen Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
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Erfani-Moghadam J, Zarei A. Assessment of genetic structure among different pear species (Pyrus spp.) using apple-derived SSR and evidence of duplications in the pear genome. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1447398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Javad Erfani-Moghadam
- Department of Horticulture Science, College of Agriculture, Ilam University, Ilam, Iran
| | - Abdolkarim Zarei
- Department of Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran
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Montanari S, Brewer L, Lamberts R, Velasco R, Malnoy M, Perchepied L, Guérif P, Durel CE, Bus VGM, Gardiner SE, Chagné D. Genome mapping of postzygotic hybrid necrosis in an interspecific pear population. HORTICULTURE RESEARCH 2016; 3:15064. [PMID: 26770810 PMCID: PMC4702180 DOI: 10.1038/hortres.2015.64] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 05/22/2023]
Abstract
Deleterious epistatic interactions in plant inter- and intraspecific hybrids can cause a phenomenon known as hybrid necrosis, characterized by a typical seedling phenotype whose main distinguishing features are dwarfism, tissue necrosis and in some cases lethality. Identification of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding purposes. Development of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these genes. Although hybrid necrosis has been reported in several plant taxa, including Rosaceae species, this phenomenon has not been described previously in pear. In the interspecific pear population resulting from a cross between PEAR3 (Pyrus bretschneideri × Pyrus communis) and 'Moonglow' (P. communis), we observed two types of hybrid necrosis, expressed at different stages of plant development. Using a combination of previously mapped and newly developed genetic markers, we identified three chromosome regions associated with these two types of lethality, which were genetically independent. One type resulted from a negative epistatic interaction between a locus on linkage group 5 (LG5) of PEAR3 and a locus on LG1 of 'Moonglow', while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from 'Moonglow'.
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Affiliation(s)
- Sara Montanari
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Lester Brewer
- The New Zealand Institute for Plant & Food Research Limited, Motueka Research Centre, Motueka, New Zealand
| | - Robert Lamberts
- The New Zealand Institute for Plant & Food Research Limited, Motueka Research Centre, Motueka, New Zealand
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - Laure Perchepied
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Philippe Guérif
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
- Institut de Recherche en Horticulture et Semences - UMR1345, Université d’Angers, F-49045 Angers, France
| | - Vincent G M Bus
- The New Zealand Institute for Plant & Food Research Limited, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
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Urrestarazu J, Royo JB, Santesteban LG, Miranda C. Evaluating the Influence of the Microsatellite Marker Set on the Genetic Structure Inferred in Pyrus communis L. PLoS One 2015; 10:e0138417. [PMID: 26382618 PMCID: PMC4575082 DOI: 10.1371/journal.pone.0138417] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/29/2015] [Indexed: 12/19/2022] Open
Abstract
Fingerprinting information can be used to elucidate in a robust manner the genetic structure of germplasm collections, allowing a more rational and fine assessment of genetic resources. Bayesian model-based approaches are nowadays majorly preferred to infer genetic structure, but it is still largely unresolved how marker sets should be built in order to obtain a robust inference. The objective was to evaluate, in Pyrus germplasm collections, the influence of the SSR marker set size on the genetic structure inferred, also evaluating the influence of the criterion used to select those markers. Inferences were performed considering an increasing number of SSR markers that ranged from just two up to 25, incorporated one at a time into the analysis. The influence of the number of SSR markers used was evaluated comparing the number of populations and the strength of the signal detected, and also the similarity of the genotype assignments to populations between analyses. In order to test if those results were influenced by the criterion used to select the SSRs, several choosing scenarios based on the discrimination power or the fixation index values of the SSRs were tested. Our results indicate that population structure could be inferred accurately once a certain SSR number threshold was reached, which depended on the underlying structure within the genotypes, but the method used to select the markers included on each set appeared not to be very relevant. The minimum number of SSRs required to provide robust structure inferences and adequate measurements of the differentiation, even when low differentiation levels exist within populations, was proved similar to that of the complete list of recommended markers for fingerprinting. When a SSR set size similar to the minimum marker sets recommended for fingerprinting it is used, only major divisions or moderate (FST>0.05) differentiation of the germplasm are detected.
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Affiliation(s)
- Jorge Urrestarazu
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - José B Royo
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - Luis G Santesteban
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - Carlos Miranda
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
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Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV. A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1631-46. [PMID: 26037086 PMCID: PMC4477079 DOI: 10.1007/s00122-015-2541-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/18/2015] [Indexed: 05/07/2023]
Abstract
We have constructed a densely populated, saturated genetic linkage map of black raspberry and successfully placed a locus for aphid resistance. Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3-4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly.
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Affiliation(s)
- Jill M Bushakra
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd., Corvallis, OR, 97333, USA,
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Adal AM, Demissie ZA, Mahmoud SS. Identification, validation and cross-species transferability of novel Lavandula EST-SSRs. PLANTA 2015; 241:987-1004. [PMID: 25534945 DOI: 10.1007/s00425-014-2226-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
We identified and characterized EST-SSRs with strong discrimination power against Lavandula angustifolia and Lavandula x intermedia . The markers also showed considerable cross-species transferability rate into six related Lavandula species. Lavenders (Lavandula) are important economical crops grown around the globe for essential oil production. In an attempt to develop genetic markers for these plants, we analyzed over 13,000 unigenes developed from L. angustifolia and L. x intermedia EST databases, and identified 3,459 simple sequence repeats (SSR), which were dominated by trinucleotides (41.2 %) and dinucleotides (31.45 %). Approximately, 19 % of the unigenes contained at least one SSR marker, over 60 % of which were localized in the UTRs. Only 252 EST-SSRs were 18 bp or longer from which 31 loci were validated, and 24 amplified discrete fragments with 85 % polymorphism in L. x intermedia and L. angustifolia. The average number of alleles in L. x intermedia and L. angustifolia were 3.42 and 3.71 per marker with average PIC values of 0.47 and 0.52, respectively. These values suggest a moderate to strong level of informativeness for the markers, with some loci producing unique fingerprints. The cross-species transferability rate of the markers ranges 50-100 % across eight species. The utility of these markers was assessed in eight Lavandula species and 15 L. angustifolia and L. x intermedia cultivars, and the dendrogram deduced from their similarity indexes successfully delineated the species into their respective sections and the cultivars into their respective species. These markers have potential for application in fingerprinting, diversity studies and marker-assisted breeding of Lavandula.
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Affiliation(s)
- Ayelign M Adal
- Department of Biology, University of British Columbia, 1177 Research Rd, Kelowna, BC, V1V 1V7, Canada
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7
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Yamamoto T, Terakami S, Takada N, Nishio S, Onoue N, Nishitani C, Kunihisa M, Inoue E, Iwata H, Hayashi T, Itai A, Saito T. Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). BREEDING SCIENCE 2014; 64:351-61. [PMID: 25914590 PMCID: PMC4267310 DOI: 10.1270/jsbbs.64.351] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/05/2014] [Indexed: 05/19/2023]
Abstract
Using an F1 population from a cross between Japanese pear (Pyrus pyrifolia Nakai) cultivars 'Akiakari' and 'Taihaku', we performed quantitative trait locus (QTL) analysis of seven fruit traits (harvest time, fruit skin color, flesh firmness, fruit weight, acid content, total soluble solids content, and preharvest fruit drop). The constructed simple sequence repeat-based genetic linkage map of 'Akiakari' consisted of 208 loci and spanned 799 cM; that of 'Taihaku' consisted of 275 loci and spanned 1039 cM. Out of significant QTLs, two QTLs for harvest time, one for fruit skin color, and one for flesh firmness were stably detected in two successive years. The QTLs for harvest time were located at the bottom of linkage group (LG) Tai3 (nearest marker: BGA35) and at the top of LG Tai15 (nearest markers: PPACS2 and MEST050), in good accordance with results of genome-wide association study. The PPACS2 gene, a member of the ACC synthase gene family, may control harvest time, preharvest fruit drop, and fruit storage potential. One major QTL associated with fruit skin color was identified at the top of LG 8. QTLs identified in this study would be useful for marker-assisted selection in Japanese pear breeding programs.
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Affiliation(s)
- Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
- Corresponding author (e-mail: )
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Norio Takada
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Sogo Nishio
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Noriyuki Onoue
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Chikako Nishitani
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Miyuki Kunihisa
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Eiichi Inoue
- College of Agriculture, Ibaraki University,
3-21-1 Chuou, Ami-machi, Ibaraki 300-0393,
Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Takeshi Hayashi
- NARO Agricultural Research Center,
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
| | - Akihiro Itai
- Tottori University,
Koyamacho-minami, Tottori 680-8550,
Japan
| | - Toshihiro Saito
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
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Wu J, Li LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5771-81. [PMID: 25129128 PMCID: PMC4203118 DOI: 10.1093/jxb/eru311] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Pear (Pyrus spp) is an important fruit crop, grown in all temperate regions of the world, with global production ranked after grape and apples among deciduous tree crops. A high-density linkage map is a valuable tool for fine mapping quantitative trait loci (QTL) and map-based gene cloning. In this study, we firstly constructed a high-density linkage map of pear using SNPs integrated with SSRs, developed by the rapid and robust technology of restriction-associated DNA sequencing (RADseq). The linkage map consists of 3143 SNP markers and 98 SSRs, 3241 markers in total, spanning 2243.4 cM, with an average marker distance of 0.70 cM. Anchoring SSRs were able to anchor seventeen linkage groups to their corresponding chromosomes. Based on this high-density integrated pear linkage map and two years of fruit phenotyping, a total of 32 potential QTLs for 11 traits, including length of pedicel (LFP), single fruit weight (SFW), soluble solid content (SSC), transverse diameter (TD), vertical diameter (VD), calyx status (CS), flesh colour (FC), juice content (JC), number of seeds (NS), skin colour (SC), and skin smooth (SS), were identified and positioned on the genetic map. Among them, some important fruit-related traits have for the first time been identified, such as calyx status, length of pedicel, and flesh colour, and reliable localization of QTLs were verified repeatable. This high-density linkage map of pear is a worthy reference for mapping important fruit traits, QTL identification, and comparison and combination of different genetic maps.
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Affiliation(s)
- Jun Wu
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei-Ting Li
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Meng Li
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - M Awais Khan
- International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Xiu-Gen Li
- Zhengzhou Fruit Research Institute, Zhengzhou 450009, China
| | - Hui Chen
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Shao-Ling Zhang
- Center of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
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Wolko Ł, Bocianowski J, Antkowiak W, Słomski R. Genetic diversity and population structure of wild pear (Pyrus pyraster (L.) Burgsd.) in Poland. Open Life Sci 2014. [DOI: 10.1515/biol-2015-0003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractIn order to provide molecular characteristics
of wild pear (P. pyraster) resources, six populations
(192 accessions) from different regions of Poland were
investigated with 17 SSR loci. Each of the SSR loci used
was polymorphic, with a mean of 19.5 alleles per locus
and a mean PIC of 0.806. Both the high heterozygosity (Ho
= 0.751) and low Fis (0.007) indicated that the wild pear
populations maintain a relatively high level of diversity,
while the mean Findex of 0.039 and the number of migrants
per generation (Nm = 6.996) revealed a high gene flow and
weak inter-population differentiation. AMOVA analysis
located polymorphisms mainly within populations (96%).
Genetic relations between populations did not show
correlations with geographical distances. The dispersal
influence of gene flow could be the reason of the disrupted
relationship within populations and the low interpopulation
differentiation. We did not find any evidence
to support the hypothesis about influence of interspecies
hybridization with pear cultivars on the level of wild pear
population diversity.
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Affiliation(s)
- Łukasz Wolko
- 1Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Jan Bocianowski
- 2Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 60-637 Poznan, Poland
| | - Wojciech Antkowiak
- 3Department of Botany, Poznan University of Life Sciences, 60-625 Poznan, Poland
| | - Ryszard Słomski
- 1Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, 60-637 Poznan, Poland
- 4Institute of Human Genetics, Polish Academy of Sciences, 60-493 Poznań, Poland
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Saeed M, Brewer L, Johnston J, McGhie TK, Gardiner SE, Heyes JA, Chagné D. Genetic, metabolite and developmental determinism of fruit friction discolouration in pear. BMC PLANT BIOLOGY 2014; 14:241. [PMID: 25224302 PMCID: PMC4177423 DOI: 10.1186/s12870-014-0241-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/05/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The unattractive appearance of the surface of pear fruit caused by the postharvest disorder friction discolouration (FD) is responsible for significant consumer dissatisfaction in markets, leading to lower returns to growers. Developing an understanding of the genetic control of FD is essential to enable the full application of genomics-informed breeding for the development of new pear cultivars. Biochemical constituents [phenolic compounds and ascorbic acid (AsA)], polyphenol oxidase (PPO) activity, as well as skin anatomy, have been proposed to play important roles in FD susceptibility in studies on a limited number of cultivars. However, to date there has been no investigation on the biochemical and genetic control of FD, employing segregating populations. In this study, we used 250 seedlings from two segregating populations (POP369 and POP356) derived from interspecific crosses between Asian (Pyrus pyrifolia Nakai and P. bretschneideri Rehd.) and European (P. communis) pears to identify genetic factors associated with susceptibility to FD. RESULTS Single nucleotide polymorphism (SNP)-based linkage maps suitable for QTL analysis were developed for the parents of both populations. The maps for population POP369 comprised 174 and 265 SNP markers for the male and female parent, respectively, while POP356 maps comprised 353 and 398 SNP markers for the male and female parent, respectively. Phenotypic data for 22 variables were measured over two successive years (2011 and 2012) for POP369 and one year (2011) only for POP356. A total of 221 QTLs were identified that were linked to 22 phenotyped variables, including QTLs associated with FD for both populations that were stable over the successive years. In addition, clear evidence of the influence of developmental factors (fruit maturity) on FD and other variables was also recorded. CONCLUSIONS The QTLs associated with fruit firmness, PPO activity, AsA concentration and concentration of polyphenol compounds as well as FD are the first reported for pear. We conclude that the postharvest disorder FD is controlled by multiple small effect QTLs and that it will be very challenging to apply marker-assisted selection based on these QTLs. However, genomic selection could be employed to select elite genotypes with lower or no susceptibility to FD early in the breeding cycle.
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Affiliation(s)
- Munazza Saeed
- />Centre for Postharvest & Refrigeration Research, Massey University, Private Bag 11 222, Palmerston North, 4442 New Zealand
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
| | - Lester Brewer
- />Plant & Food Research, Motueka Research Centre, Old Mill Road, Motueka, 7198 New Zealand
| | - Jason Johnston
- />Plant & Food Research, Hawkes Bay Research Centre, Private Bag 1401, Havelock North, New Zealand
| | - Tony K McGhie
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
| | - Susan E Gardiner
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
| | - Julian A Heyes
- />Centre for Postharvest & Refrigeration Research, Massey University, Private Bag 11 222, Palmerston North, 4442 New Zealand
| | - David Chagné
- />The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Private Bag 11600, Palmerston North, 4442 New Zealand
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Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 2013; 8:e77022. [PMID: 24155917 PMCID: PMC3796552 DOI: 10.1371/journal.pone.0077022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022] Open
Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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Affiliation(s)
- Sara Montanari
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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Fan L, Zhang MY, Liu QZ, Li LT, Song Y, Wang LF, Zhang SL, Wu J. Transferability of Newly Developed Pear SSR Markers to Other Rosaceae Species. PLANT MOLECULAR BIOLOGY REPORTER 2013; 31:1271-1282. [PMID: 24415844 PMCID: PMC3881569 DOI: 10.1007/s11105-013-0586-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A set of 120 simple sequence repeats (SSRs) was developed from the newly assembled pear sequence and evaluated for polymorphisms in seven genotypes of pear from different genetic backgrounds. Of these, 67 (55.8 %) primer pairs produced polymorphic amplifications. Together, the 67 SSRs detected 277 alleles with an average of 4.13 per locus. Sequencing of the amplification products from randomly picked loci NAUPy31a and NAUpy53a verified the presence of the SSR loci. When the 67 primer pairs were tested on 96 individual members of eight species in the Rosaceae family, 61.2 % (41/67) of the tested SSRs successfully amplified a PCR product in at least one of the Rosaceae genera. The transferability from pear to different species varied from 58.2 % (apple) to 11.9 % (cherry). The ratio of transferability also reflected the closer relationships within Maloideae over Prunoideae. Two pear SSR markers, NAUpy43c and NAUpy55k, could distinguish the 20 different apple genotypes thoroughly, and UPGMA cluster analysis grouped them into three groups at the similarity level of 0.56. The high level of polymorphism and good transferability of pear SSRs to Rosaceae species indicate their promise for application to future molecular screening, map construction, and comparative genomic studies among pears and other Rosaceae species.
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Affiliation(s)
- L. Fan
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - M.-Y. Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Q.-Z. Liu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong, Pomological Institute of Shandong, Taian, Shandong 271000 China
| | - L.-T. Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Y. Song
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - L.-F. Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - S.-L. Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - J. Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Urbanovich OY, Kazlouvskaya ZA, Yakimovich OA, Kartel NA. Polymorphism of SSR alleles in pear cultivars grown in Belarus. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411030173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Feng S, Chen X, Zhang Y, Wang Y, Song Y, Chen XL, Li X, Li M, Liu J, Wang Q, Liu M. Differential Expression of Proteins in Red Pear Following Fruit Bagging Treatment. Protein J 2011; 30:194-200. [DOI: 10.1007/s10930-011-9320-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Pierantoni L, Dondini L, De Franceschi P, Musacchi S, Winkel BSJ, Sansavini S. Mapping of an anthocyanin-regulating MYB transcription factor and its expression in red and green pear, Pyrus communis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:1020-6. [PMID: 20951056 DOI: 10.1016/j.plaphy.2010.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 09/06/2010] [Accepted: 09/09/2010] [Indexed: 05/08/2023]
Abstract
'Max Red Bartlett' is a red bud mutation of the yellow pear (Pyrus communis L.) cultivar 'Williams' (known as 'Bartlett' in North America). Anthocyanins are the most important pigments for red colour in fruits. Synthesis of anthocyanins is mediated by a number of well-characterized enzymes that include chalcone synthase (CHS), flavanone-3-hydroxylase (F3H), dihydroflavonol-4-reductase (DFR), anthocyanidin synthase (ANS), and UDP-glucose:flavonoid-3-O-glucosyltransferase (UFGT). Expression of the genes encoding these five enzymes was examined in pear fruit skin in order to elucidate the molecular mechanism for red coloration. In addition, the gene PcMYB10, encoding an R2R3 MYB transcription factor involved in anthocyanin biosynthetic pathway regulation, was isolated from both 'Williams' and 'Max Red Bartlett'. Analysis of the deduced amino acid sequence suggests that this gene is an ortholog of anthocyanin regulators known in other plant species. Its expression level was significantly higher in 'Max Red Bartlett' (red pear) compared with the original yellow variety 'Williams'. Although the map position of PcMYB10 corresponds to that of MdMYBa and MdMYB10, which control pigmentation of apple fruit skin, PcMYB10 is not directly responsible for red versus yellow colour in the two pear varieties, as the mutation underlying this difference maps to a different region of the pear genome.
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Affiliation(s)
- Luca Pierantoni
- Department of Fruit Tree and Woody Plant Sciences (DCA), University of Bologna, viale Fanin 46, 40127 Bologna, Italy
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Koppolu R, Upadhyaya HD, Dwivedi SL, Hoisington DA, Varshney RK. Genetic relationships among seven sections of genus Arachis studied by using SSR markers. BMC PLANT BIOLOGY 2010; 10:15. [PMID: 20089171 PMCID: PMC2826335 DOI: 10.1186/1471-2229-10-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Accepted: 01/20/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis. RESULTS The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea. CONCLUSION A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.
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Affiliation(s)
- Ravi Koppolu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
| | - Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
| | - David A Hoisington
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, AP, India
- Genomics towards Gene Discovery Sub Programme, Generation Challenge Programme (GCP), c/o CIMMYT, Int APDO Postal 6-641, 06600 Mexico DF, Mexico
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Celton JM, Chagné D, Tustin SD, Terakami S, Nishitani C, Yamamoto T, Gardiner SE. Update on comparative genome mapping between Malus and Pyrus. BMC Res Notes 2009; 2:182. [PMID: 19747407 PMCID: PMC2749866 DOI: 10.1186/1756-0500-2-182] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 09/14/2009] [Indexed: 11/13/2022] Open
Abstract
Background Comparative genome mapping determines the linkage between homologous genes of related taxa. It has already been used in plants to characterize agronomically important genes in lesser studied species, using information from better studied species. In the Maloideae sub-family, which includes fruit species such as apple, pear, loquat and quince, genome co-linearity has been suggested between the genera Malus and Pyrus; however map comparisons are incomplete to date. Findings Genetic maps for the apple rootstocks 'Malling 9' ('M.9') (Malus × domestica) and 'Robusta 5' ('R5') (Malus × robusta), and pear cultivars 'Bartlett' and 'La France' (Pyrus communis) were constructed using Simple Sequence Repeat (SSR) markers developed from both species, including a new set of 73 pear Expressed Sequence Tag (EST) SSR markers. Integrated genetic maps for apple and pear were then constructed using 87 and 131 SSR markers in common, respectively. The genetic maps were aligned using 102 markers in common, including 64 pear SSR markers and 38 apple SSR markers. Of these 102 markers, 90 anchor markers showed complete co-linearity between the two genomes. Conclusion Our alignment of the genetic maps of two Malus cultivars of differing species origin with two Pyrus communis cultivars confirms the ready transferability of SSR markers from one genus to the other and supports a high level of co-linearity within the sub-family Maloideae between the genomes of Malus and Pyrus.
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Affiliation(s)
- Jean-Marc Celton
- University of Western Cape, Biotechnology Department, Modderdam Road, Bellville, Cape Town, 7535, South Africa.
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First report on the presence of fire blight resistance in linkage group 11 of Pyrus ussuriensis Maxim. J Appl Genet 2009; 50:99-103. [PMID: 19433906 DOI: 10.1007/bf03195660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Fire blight, caused by the gram-negative bacterium Erwinia amylovora (Burrill) Winslow et al., is a dangerous disease of pome fruits, including pear. A pear breeding program for fire blight resistance was initiated in 2003 at the Department of Pomology, Warsaw University of Life Sciences, Poland. Since several Asian species are considered to be potential sources of resistance to fire blight, the susceptible Pyrus communis 'Doyenne du Comice' was crossed with the resistant P. ussuriensis. The F1 full-sib progeny composed of 155 seedlings was tested for susceptibility to fire blight by artificial shoot inoculation. A framework linkage map of both parents was constructed based on 48 AFLP and 32 SSR markers and covered a length of 595 cM and 680 cM in 'Doyenne du Comice' and P. ussuriensis, respectively. For the first time a putative QTL for fire blight resistance in P. ussuriensis linkage group 11 was identified. Another putative QTL in linkage group 4 of 'Doyenne du Comice' seems to indicate that sources of fire blight resistance can be identified also in the susceptible cultivars.
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Vilanova S, Sargent DJ, Arús P, Monfort A. Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC PLANT BIOLOGY 2008. [PMID: 18564412 DOI: 10.1186/1471-22229-8-67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are x = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between Malus (subfamily Maloideae) and Prunus (subfamily Prunoideae); however no data has been published to date comparing Malus or Prunus to a member of the subfamily Rosoideae. In this paper we compare the genome of Fragaria, a member of the Rosoideae, to Prunus, a member of the Prunoideae. RESULTS The diploid genomes of Prunus (2n = 2x = 16) and Fragaria (2n = 2x = 14) were compared through the mapping of 71 anchor markers - 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) - on the reference maps of both genera. These markers provided good coverage of the Prunus (78%) and Fragaria (78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker in Prunus and 32 cM and 8.0 cM/marker in Fragaria. CONCLUSION Our results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.
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Affiliation(s)
- Santiago Vilanova
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain.
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Vilanova S, Sargent DJ, Arús P, Monfort A. Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC PLANT BIOLOGY 2008; 8:67. [PMID: 18564412 PMCID: PMC2442709 DOI: 10.1186/1471-2229-8-67] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 06/18/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are x = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between Malus (subfamily Maloideae) and Prunus (subfamily Prunoideae); however no data has been published to date comparing Malus or Prunus to a member of the subfamily Rosoideae. In this paper we compare the genome of Fragaria, a member of the Rosoideae, to Prunus, a member of the Prunoideae. RESULTS The diploid genomes of Prunus (2n = 2x = 16) and Fragaria (2n = 2x = 14) were compared through the mapping of 71 anchor markers - 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) - on the reference maps of both genera. These markers provided good coverage of the Prunus (78%) and Fragaria (78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker in Prunus and 32 cM and 8.0 cM/marker in Fragaria. CONCLUSION Our results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.
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Affiliation(s)
- Santiago Vilanova
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain
- Universidad Politécnica de Valencia, Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Spain
| | | | - Pere Arús
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain
| | - Amparo Monfort
- IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, 08348 Cabrils, Spain
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Li G, Hu W, Qin R, Jin H, Tan G, Zhu L, He G. Simple sequence repeat analyses of interspecific hybrids and MAALs of Oryza officinalis and Oryza sativa. Genetica 2007; 134:169-80. [PMID: 17978880 DOI: 10.1007/s10709-007-9222-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Accepted: 10/23/2007] [Indexed: 12/20/2022]
Abstract
Wild rice is a valuable resource for the genetic improvement of cultivated rice (Oryza sativa L., AA genome). Molecular markers are important tools for monitoring gene introgression from wild rice into cultivated rice. In this study, Simple sequence repeat (SSR) markers were used to analyze interspecific hybrids of O. sativa-O. officinalis (CC genome), the backcrossing progenies and the parent plants. Results showed that most of the SSR primers (335 out of 396, 84.6%) developed in cultivated rice successfully amplified products from DNA samples of wild rice O. officinalis. The polymorphism ratio of SSR bands between O. sativa and O. officinalis was as high as 93.9%, indicating differences between the two species with respect to SSRs. When the SSR markers were applied in the interspecific hybrids, only a portion of SSR primers amplified O. officinalis-specific bands in the F(1) hybrid (52.5%), BC(1) (52.5%), and MAALs (37.0%); a number of the bands disappeared. Of the 124 SSR loci that detected officinalis-specific bands in MAAL plants, 96 (77.4%) showed synteny between the A and C-genomes, and 20 (16.1%) showed duplication in the C-genome. Sequencing analysis revealed that indels, substitution and duplication contribute to the diversity of SSR loci between the genomes of O. sativa and O. officinalis.
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Affiliation(s)
- Gang Li
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Fraser LG, McNeilage MA, Tsang GK, Harvey CF, De Silva HN. Cross-species amplification of microsatellite loci within the dioecious, polyploid genus Actinidia (Actinidiaceae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 112:149-57. [PMID: 16211378 DOI: 10.1007/s00122-005-0117-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 09/14/2005] [Indexed: 05/04/2023]
Abstract
Microsatellite marker transfer across species in the dioecious genus Actinidia (kiwifruit) could offer an efficient and time-effective technique for use during trait transfer for vine and fruit improvement in breeding programmes. We evaluated the cross-species amplification of 20 EST-derived microsatellite markers that were fully informative in an Actinidia chinensis mapping family. We tested all 20 markers on 120 genotypes belonging to 21 species, 5 with varieties and/or chromosome races. These 26 taxa included 16 diploids, 7 tetraploids, 2 hexaploids and 1 octaploid, and represented all four taxonomic sections in the genus. All 20 markers showed some level of cross-species amplification. The most successful marker amplified in all genotypes from all species from all sections of the genus, the least successful amplified fragments only in A. chinensis and A. deliciosa. One species, A. glaucophylla, failed to amplify with all but 2 markers. PIC (Polymorphism information content) values were high, with 14 of 17 markers recording values of 0.90 and above. Sequence data demonstrated the presence of the microsatellite in all the amplified products. Sequence homology was less 5' of the microsatellite and increased toward the start codon of the translated region of the EST from which the marker was derived. The data confirm that EST-derived microsatellite markers from Actinidia species show cross-species amplification with high levels of polymorphism which could make them useful markers in breeding programmes.
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Affiliation(s)
- L G Fraser
- The Horticulture and Food Research Institute of New Zealand Ltd, Private Bag 92 169, Auckland, New Zealand.
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