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Noda T, Daiou K, Mihara T, Nagano Y. Potential application of simple easy-to-use insertion-deletion (InDel) markers in citrus cultivar identification. BREEDING SCIENCE 2021; 71:601-608. [PMID: 35087324 PMCID: PMC8784345 DOI: 10.1270/jsbbs.21021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/09/2021] [Indexed: 05/27/2023]
Abstract
We previously developed insertion-deletion (InDel) markers that distinguish three genotypes (two homozygous and one heterozygous) of diverse citrus cultivars. These InDel markers were codominant and could be clearly detected by using simple agarose gel electrophoresis. We sought to establish a method for cultivar identification using these 28 InDel markers to genotype 31 citrus cultivars. The results revealed that a minimum of 6 markers were required to identify individuals using the three-genotype classification method. Furthermore, we found that a simple method for distinguishing between two genotypes (homozygous and heterozygous) could be used to identify individuals using a minimum of 7 markers. Our findings provide a basis for the development of simple and rapid citrus cultivar identification methods.
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Affiliation(s)
- Takahiro Noda
- Kumamoto Prefectural Agricultural Research Center, 3801 Sakae, Koshi, Kumamoto 861-1113, Japan
| | - Kaoru Daiou
- Kumamoto Prefectural Agricultural Research Center, 3801 Sakae, Koshi, Kumamoto 861-1113, Japan
| | - Takashi Mihara
- Kumamoto Prefectural Fruit Tree Research Institute, 2566 Toyofuku Matsubase-machi, Uki, Kumamoto 869-0524, Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
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Curtolo M, Cristofani-Yaly M, Gazaffi R, Takita MA, Figueira A, Machado MA. QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genomics 2017; 18:289. [PMID: 28403819 PMCID: PMC5389163 DOI: 10.1186/s12864-017-3629-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/14/2017] [Indexed: 11/24/2022] Open
Abstract
Background Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits. A controlled Murcott x Pera crossing was conducted at the Citrus Germplasm Repository at the Sylvio Moreira Citrus Centre of the Agronomic Institute (IAC) located in Cordeirópolis, SP, in 1997. In 2012, 278 F1 individuals out of a family of 312 confirmed hybrid individuals were analyzed for fruit traits and genotyped using the DArTseq markers. Using OneMap software to obtain the integrated genetic map, we considered only the DArT loci that showed no segregation deviation. The likelihood ratio and the genomic information from the available Citrus sinensis L. Osbeck genome were used to determine the linkage groups (LGs). Results The resulting integrated map contained 661 markers in 13 LGs, with a genomic coverage of 2,774 cM and a mean density of 0.23 markers/cM. The groups were assigned to the nine Citrus haploid chromosomes; however, some of the chromosomes were represented by two LGs due the lack of information for a single integration, as in cases where markers segregated in a 3:1 fashion. A total of 19 QTLs were identified through composite interval mapping (CIM) of the 12 analyzed fruit characteristics: fruit diameter (cm), height (cm), height/diameter ratio, weight (g), rind thickness (cm), segments per fruit, total soluble solids (TSS, %), total titratable acidity (TTA, %), juice content (%), number of seeds, TSS/TTA ratio and number of fruits per box. The genomic sequence (pseudochromosomes) of C. sinensis was compared to the genetic map, and synteny was clearly identified. Further analysis of the map regions with the highest LOD scores enabled the identification of putative genes that could be associated with the fruit quality characteristics. Conclusion An integrated linkage map of Murcott tangor and Pera sweet orange using DArTseq™ molecular markers was established and it was useful to perform QTL mapping of twelve fruit quality traits. The next generation sequences data allowed the comparison between the linkage map and the genomic sequence (pseudochromosomes) of C. sinensis and the identification of genes that may be responsible for phenotypic traits in Citrus. The obtained linkage map was used to assign sequences that had not been previously assigned to a position in the reference genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3629-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maiara Curtolo
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil.,Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Mariângela Cristofani-Yaly
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil.
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos (UFSCar) - Centro de Ciências Agrárias, Rodovia Anhanguera, km 174, 13600-970, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - Marcos Antonio Machado
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
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Omura M, Shimada T. Citrus breeding, genetics and genomics in Japan. BREEDING SCIENCE 2016; 66:3-17. [PMID: 27069387 PMCID: PMC4780800 DOI: 10.1270/jsbbs.66.3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/09/2015] [Indexed: 05/03/2023]
Abstract
Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering.
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Affiliation(s)
- Mitsuo Omura
- Faculty of Agriculture, Shizuoka University,
836 Ohya, Suruga, Shizuoka, Shizuoka 422-8529,
Japan
| | - Takehiko Shimada
- Citrus Research Division, NARO Institute of Fruit Tree Science,
485-6 Okitsunakacho, Shimizu, Shizuoka, Shizuoka 424-0292,
Japan
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Rivard SR, Cappadocia M, Landry BS. A comparison of RFLP maps based on anther culture derived, selfed, and hybrid progenies of Solanum chacoense. Genome 2012; 39:611-21. [PMID: 18469920 DOI: 10.1139/g96-078] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Comparative RFLP linkage maps were constructed using five segregating populations derived from two self-incompatible lines (termed PI 230582 and PI 458314) of diploid tuber-bearing Solanum chacoense Bitt. The analysis was based on 84 RFLP loci identified by 73 different cDNA clones. Distortion of expected Mendelian segregation ratios was observed; less than 10% of the markers showed a skewed segregation in the gametes forming the F1, hybrid population compared with 30% in the selfed population and 46 and 70% in the two populations produced by anther culture. For the anther culture derived populations, most of the skewed loci were scattered throughout the genome, whereas in the populations derived from selfing, they were found primarily in linkage group 1, around the S locus. In this study, we also found that the rate of meiotic recombination could differ between the male and female gametes produced by our parental lines. Thus, male gametes of line PI 458314 showed significantly less recombination as assessed by the total length of the map (206 cM for male gametes vs. 375 cM for female gametes) and the phenomenon was genome-wide. In contrast, the maps from the gametes of PI 230582 had about the same length, but some linkage groups were longer in the female gametes, while others were longer in the male gametes. Key words : Solanum chacoense, RFLP, anther culture, skewed segregation, self-incompatibility, sex differences in recombination.
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Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus. Mol Biol Rep 2011; 39:5373-86. [PMID: 22170603 DOI: 10.1007/s11033-011-1338-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 12/03/2011] [Indexed: 10/14/2022]
Abstract
The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.
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Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla JF, Amaya I. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:755-78. [PMID: 21667037 DOI: 10.1007/s00122-011-1624-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/14/2011] [Indexed: 05/04/2023]
Abstract
Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.
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Hippolyte I, Bakry F, Seguin M, Gardes L, Rivallan R, Risterucci AM, Jenny C, Perrier X, Carreel F, Argout X, Piffanelli P, Khan IA, Miller RNG, Pappas GJ, Mbéguié-A-Mbéguié D, Matsumoto T, De Bernardinis V, Huttner E, Kilian A, Baurens FC, D'Hont A, Cote F, Courtois B, Glaszmann JC. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas. BMC PLANT BIOLOGY 2010; 10:65. [PMID: 20388207 PMCID: PMC2923539 DOI: 10.1186/1471-2229-10-65] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 04/13/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. RESULTS An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p < 0.05) from the expected Mendelian ratios. These skewed markers were distributed in different linkage groups for each parent. To solve some complex ordering of the markers on linkage groups, we associated tools such as tree-like graphic representations, recombination frequency statistics and cytogenetical studies to identify structural rearrangements and build parsimonious linkage group order. An illustration of such an approach is given for the P. Lilin parent. CONCLUSIONS We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.
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Affiliation(s)
- Isabelle Hippolyte
- CIRAD, UR Multiplication Végétative, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | - Frederic Bakry
- CIRAD, UR Multiplication Végétative, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | - Marc Seguin
- CIRAD, UMR DAP, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | - Laetitia Gardes
- CIRAD, UMR DAP, Av. Agropolis, 34398 Montpellier Cedex 5, France
- Current address: CIRAD, UMR Contrôle des maladies, Campus Baillarguet, 34398 Montpellier Cedex 5, France
| | - Ronan Rivallan
- CIRAD, UMR DAP, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | | | - Christophe Jenny
- CIRAD, UR Multiplication Végétative, Station de Neufchâteau, Sainte-Marie, 97130 Capesterre Belle-Eau, Guadeloupe FWI
| | - Xavier Perrier
- CIRAD, UR Multiplication Végétative, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | - Françoise Carreel
- Current address: CIRAD, UMR BGPI, Campus international de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Xavier Argout
- CIRAD, UMR DAP, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | - Pietro Piffanelli
- CIRAD, UMR DAP, Av. Agropolis, 34398 Montpellier Cedex 5, France
- Current address: Genomics Platform, Parco Tecnologico Padano, Via Einstein, Lodi, Italy
| | - Imtiaz A Khan
- Nuclear Institute of Agriculture, Tando Jam, Sindh, Pakistan
| | - Robert NG Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, CEP 70.910-900, Brasília, Brazil
| | | | | | - Takashi Matsumoto
- NIAS, Plant Genome Research Unit, Division of Genome and Biodiversity Research, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | | | - Eric Huttner
- Diversity Arrays Technology, PO Box 7141, Yarralumla, ACT 2600, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, PO Box 7141, Yarralumla, ACT 2600, Australia
| | | | - Angélique D'Hont
- CIRAD, UMR DAP, Av. Agropolis, 34398 Montpellier Cedex 5, France
| | - François Cote
- CIRAD, UPR Systèmes bananes et ananas, Boulevard de la Lironde, 34398 Montpellier Cedex 5, France
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Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R. Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 2008; 9:287. [PMID: 18558001 PMCID: PMC2435559 DOI: 10.1186/1471-2164-9-287] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 06/16/2008] [Indexed: 11/16/2022] Open
Abstract
Background During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences. Results Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis. Conclusion Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus.
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Affiliation(s)
- François L Luro
- INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao, France.
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Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum TG, Gmitter FG. EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. TREE GENETICS & GENOMES 2008; 4:1-10. [PMID: 0 DOI: 10.1007/s11295-007-0083-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Talon M, Gmitter Jr. FG. Citrus genomics. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:528361. [PMID: 18509486 PMCID: PMC2396216 DOI: 10.1155/2008/528361] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 03/15/2008] [Indexed: 05/18/2023]
Abstract
Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop.
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Affiliation(s)
- Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain
| | - Fred G. Gmitter Jr.
- Citrus Research and Education Center (CREC), University of Florida, IFAS, Lake Alfred, FL 33850, USA
- *Fred G. Gmitter Jr.:
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Carlos de Oliveira A, Bastianel M, Cristofani-Yaly M, Morais do Amaral A, Machado MA. Development of genetic maps of the citrus varieties ‘Murcott’ tangor and ‘Pêra’ sweet orange by using fluorescent AFLP markers. J Appl Genet 2007; 48:219-31. [PMID: 17666774 DOI: 10.1007/bf03195216] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The progeny of 87 BC(1) hybrids of 'Murcott' tangor and 'Pera' sweet orange, genotyped with fluorescent amplified fragment length polymorphism (fAFLP) markers, was used for the construction of genetic maps for both citrus varieties. Mapping strategies, considering the progeny as a result of backcrossing and cross-pollination, were exploited in Mapmaker 2.0 (LOD score >or= 3.0 and <or= 0.40) and JoinMap 3.0 software (LOD score >or= 3.0 and theta <or = 0.25), respectively. Genetic map distances (in cM) between the linked fAFLPs were estimated, in both packages, by the Kosambi's function. Maps of both parents were constructed in Mapmaker with 121 of the 202 fAFLP markers showing 1:1 Mendelian segregation rates ('Murcott' map: 65 fAFLPs, average distance between them 29.5 cM, divided into 9 linkage groups (LGs), total size 1651.47 cM; 'Pera' map: 55 fAFLPs, average distance between them 31.9 cM, divided into 5 LGs, total size 1596.2 cM). The second 'Murcott' map, constructed through linkage analysis of 347 fAFLP markers with 3:1 or 1:1 segregation rates by using JoinMap, resulted in the linkage of 227 markers with an average distance of 4.25 cM among them, divided into 9 LGs of 845 cM. fAFLP loci showing distorted segregation and/or clustered were observed in different LGs of the maps generated by all the software. The use of the 'Murcott' tangor and 'Pera' sweet orange genetic maps in research on identification of citrus QRLs (quantitative resistance loci) to Xylella fastidiosa and QTLs (quantitative trait loci) related to the productivity and quality of the juice, respectively, is discussed.
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Barkley NA, Roose ML, Krueger RR, Federici CT. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1519-31. [PMID: 16699791 DOI: 10.1007/s00122-006-0255-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 02/24/2006] [Indexed: 05/09/2023]
Abstract
Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for specified Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor-joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Poncirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identified five populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.
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Affiliation(s)
- Noelle A Barkley
- Department of Botany and Plant Sciences and Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA 92521, USA.
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Oliveira RPD, Aguilar-Vildoso CI, Cristofani M, Machado MA. Skewed RAPD markers in linkage maps of Citrus. Genet Mol Biol 2004. [DOI: 10.1590/s1415-47572004000300021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Liebhard R, Koller B, Gianfranceschi L, Gessler C. Creating a saturated reference map for the apple (Malus x domestica Borkh.) genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 106:1497-508. [PMID: 12677403 DOI: 10.1007/s00122-003-1209-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2002] [Accepted: 11/01/2002] [Indexed: 05/23/2023]
Abstract
The availability of a high quality linkage map is essential for the detection and the analysis of quantitative traits. Such a map should cover a significant part of the genome, should be densely populated with markers, and in order to gain the maximum advantage should be transferable to populations or cultivars other than the ones on which it has been constructed. An apple genetic linkage map has been constructed on the basis of a segregating population of the cross between the cultivars Fiesta and Discovery. A total of 840 molecular markers, 475 AFLPs, 235 RAPDs, 129 SSRs and 1 SCAR, were used for the two parental maps constructed with JoinMap and spanning 1,140 cM and 1,450 cM, respectively. Large numbers of codominant markers, like SSRs, enable a rapid transfer of the map to other populations or cultivars, allowing the investigation of any chosen trait in another genetic background. This map is currently the most advanced linkage map in apple with regard to genome coverage and marker density. It represents an ideal starting point for future mapping projects in Malus since the stable and transferable SSR frame of the map can be saturated quickly with dominant AFLP markers.
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Affiliation(s)
- R Liebhard
- Swiss Federal Institute of Technology, Institute of Plant Science/Phytopathology, Universitätstrasse 2, 8092 Zurich, Switzerland
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15
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Cervera MT, Storme V, Ivens B, Gusmão J, Liu BH, Hostyn V, Van Slycken J, Van Montagu M, Boerjan W. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 2001; 158:787-809. [PMID: 11404342 PMCID: PMC1461694 DOI: 10.1093/genetics/158.2.787] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.
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Affiliation(s)
- M T Cervera
- Vakgroep Moleculaire Genetica en Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, Ledeganckstraat 35, B-9000 Gent, Belgium
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16
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Guerra M, Dos Santos KG, Barros E Silva AE, Ehrendorfer F. Heterochromatin banding patterns in Rutaceae-Aurantioideae--a case of parallel chromosomal evolution. AMERICAN JOURNAL OF BOTANY 2000. [PMID: 10811798 DOI: 10.2307/2656860] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The heterochromatin banding patterns in the karyotypes of 17 species belonging to 15 genera of Rutaceae subfamily Aurantioideae (= Citroideae) were analyzed with the fluorochromes chromomycin (CMA) and 4'-6-diamidino-2-phenylindole-2HCl (DAPI). All species were diploids, except one tetraploid (Clausena excavata) and two hexaploids [Glycosmis parviflora agg. (aggregate) and G. pentaphylla agg.]. There are only CMA/DAPI bands, including those associated with the nucleolus. Using recent cpDNA (chloroplast DNA) sequence data as a phylogenetic background, it becomes evident that generally more basal genera with rather plesiomorphic traits in their morphology, anatomy, and phytochemistry exhibit very small amounts of heterochromatin (e.g., Glycosmis, Severinia, Swinglea), whereas relatively advanced genera from different clades with more apomorphic characters display numerous large CMA bands (e.g., Merrillia, Feroniella, Fortunella). Heterochromatin increase (from 0.7 to 13.7%) is interpreted as apomorphic. The bands are mostly located in the larger chromosomes and at telomeric regions of larger arms. However, one of the largest chromosome pair has been conserved throughout the subfamily with only very little heterochromatin. The heterochromatin-rich patterns observed in different clades of Aurantioideae appear quite similar, suggesting a kind of parallel chromosomal evolution. In respect to the current classification of the subfamily, it is proposed to divide Murraya s.l. (sensu lato) into Bergera and Murraya s.s. (sensu stricto) and to place the former near Clausena into Clauseneae s.s. and the latter together with Merrillia into Citreae s.l. The subtribes recognized within Clauseneae s.s. and Citreae s.l. appear heterogeneous and should be abandoned. On the other hand, the monophyletic nature of the core group of Citrinae, i.e., the Citrus clade with Eremocitrus, Microcitrus, Clymenia, Poncirus, Fortunella, and Citrus, is well supported.
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Affiliation(s)
- M Guerra
- Universidade Federal de Pernambuco, CCB, Departamento de Botânica, Recife, PE, Brazil; and
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17
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Novelli VM, Machado MA, Lopes CR. Isoenzymatic polymorphism in Citrus spp. and Poncirus trifoliata (L.) Raf. (Rutaceae). Genet Mol Biol 2000. [DOI: 10.1590/s1415-47572000000100030] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Isoenzymatic polymorphism analysis was used to determine genetic variability among species and hybrids of Citrus spp. and one accession of Poncirus trifoliata (L.) Raf. Ten enzymatic systems aspartate aminotransferase (AAT), acid phosphatase (ACP), leucine aminopeptidase (LAP), 6-phosphogluconate dehydrogenase (6-PGD), isocitrate dehydrogenase (IDH), phosphoglucoisomerase (PGI), phosphoglucomutase (PGM), diaphorase (DIA), shikimate dehydrogenase (SKD) and peroxidase (PRX) were analyzed. Twenty loci and 48 alleles were identified. Sweet orange cultivars (C. sinensis (L). Osbeck) showed the highest polymorphism with the largest number of heterozygous loci, although the alleles of those loci were the same in all cultivars, with the exception of Westin and Lima graúda. Mandarins (C. reticulata Blanco) exhibited diverse patterns, whereas Poncirus trifoliata (L.) Raf. showed high variability with all Citrus species and hybrids. Exclusive phenotypes were observed in some enzymatic systems, and similar patterns were found among interspecific hybrids and their putative parents.
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Affiliation(s)
- Valdenice Moreira Novelli
- Universidade Estadual de Feira de Santana, Brasil; Universidade Estadual Paulista Júlio de Mesquita Filho, Brasil
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18
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19
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Fang DQ, Federici CT, Roose ML. A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf. Genetics 1998; 150:883-90. [PMID: 9755216 PMCID: PMC1460362 DOI: 10.1093/genetics/150.2.883] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Resistance to citrus tristeza virus (CTV) was evaluated in 554 progeny of 10 populations derived from Poncirus trifoliata. A dominant gene (Ctv) controlled CTV resistance in P. trifoliata. Twenty-one dominant PCR-based DNA markers were identified as linked to Ctv by bulked segregant analysis. Of the 11 closest markers to Ctv, only 2 segregated in all populations. Ten of these markers were cloned and sequenced, and codominant RFLP markers were developed. Seven RFLP markers were then evaluated in 10 populations. Marker orders were consistent in all linkage maps based on data of single populations or on combined data of populations with similar segregation patterns. In a consensus map, the six closest marker loci spanned 5.3 cM of the Ctv region. Z16 cosegregated with Ctv. C19 and AD08 flanked Ctv at distances of 0.5 and 0.8 cM, respectively. These 3 markers were present as single copies in the Poncirus genome, and could be used directly for bacterial artificial chromosome library screening to initiate a walk toward Ctv. BLAST searches of the GenBank database revealed high sequence similarities between 2 markers and known plant disease resistance genes, indicating that a resistance gene cluster exists in the Ctv region in P. trifoliata.
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Affiliation(s)
- D Q Fang
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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20
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Fang DQ, Federici CT, Roose ML. Development of molecular markers linked to a gene controlling fruit acidity in citrus. Genome 1997; 40:841-9. [DOI: 10.1139/g97-809] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fruit juice pH, titratable acidity, or citric acid content was measured in 6 populations derived from an acidless pummelo (pummelo 2240) (Citrus maxima (Burm.) Merrill). The acidless trait in pummelo 2240 is controlled by a single recessive gene called acitric. Using bulked segregant analysis, three RAPD markers were identified as linked to acitric. RAPD marker OpZ20410, which mapped 1.2 cM from acitric, was cloned and sequenced, and a sequence characterized amplified region (SCAR) marker (SCZ20) was developed. The SCZ20-410 marker allele that is linked to the acitric allele occurs only in pummelo 2240 and other pummelos, and therefore, this SCAR marker should be useful as a dominant or codominant marker for introgressing acitric into mandarins and other citrus species. Using the cloned OpZ20410 band as a hybridization probe revealed a codominant RFLP marker called RFZ20 that mapped 1.2 cM from acitric. Progeny homozygous (acac) for the acitric allele had citric acid content below 10 μM, the minimum level detectable by high pressure liquid chromatography. The citric acid content of fruit juice from progeny predicted to be heterozygous (Acac) for acitric by the above markers was about 30% lower than that of juice from individuals predicted to be homozygous (AcAc) for the normal acid allele. Markers OpZ20410, SCZ20, and RFZ20 were highly polymorphic among 59 citrus accessions, and using one or more of these markers would allow citrus breeders to select seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 or its offspring and other citrus genotypes.Key words: Citrus, fruit acidity, citric acid, RAPD, SCAR, RFLP.
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21
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Gmitter FG, Xiao SY, Huang S, Hu XL, Garnsey SM, Deng Z. A localized linkage map of the citrus tristeza virus resistance gene region. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 92:688-695. [PMID: 24166392 DOI: 10.1007/bf00226090] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/1995] [Accepted: 10/06/1995] [Indexed: 06/02/2023]
Abstract
A localized genetic linkage map was developed of the region surrounding the citrus tristeza virus (CTV) resistance gene (designated Ctv) from Poncirus trifoliate L., a sexually compatible Citrus relative. Bulked segregant analysis (BSA) was used to identify potential resistance-associated RAPD fragment markers in four intergeneric backcross families that were segregating for CTV resistance. Eight RAPD fragments were found that were consistently linked to Ctv in the four families. Map distances and locus order were determined with MAPMAKER 3.0, using the results obtained from 59 individuals in the largest family. Also, a consensus map was constructed with JOINMAP 1.3, using pooled results from the four backcross families. Marker orders were identical, except for 1 marker, on these independently developed maps. Family-specific resistance-associated markers were also identified, as were numerous susceptibility-associated markers. The identification of markers tightly linked to Ctv will enable citrus breeders to identify plants likely to be CTV-resistant by indirect, marker-assisted selection, rather than by labor-intensive direct challenge with the pathogen. These markers also provide a basis for future efforts to isolate Ctv for subsequent genetic manipulation.
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Affiliation(s)
- F G Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, 33850, Lake Alfred, FL, USA
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22
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Liou PC, Gmitter FG, Moore GA. Characterization of the Citrus genome through analysis of restriction fragment length polymorphisms. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 92:425-35. [PMID: 24166267 DOI: 10.1007/bf00223689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/1994] [Accepted: 07/21/1995] [Indexed: 05/15/2023]
Abstract
Studies on the nature of restriction fragment length polymorphisms (RFLPs) were undertaken to characterize the Citrus genome. This type of analysis has not been carried out with any other perennial crop. Citrus reticulata Blanco cv Clementine, C. xparadisi Macf. cv Duncan, and an F1 hybrid (LB 1-21) were used to determine what probe/enzyme combinations revealed polymorphisms in Southern analysis, and a backcross family (LB 1-21x'Clementine') of 65 randomly selected hybrid seedlings was used for some analyses. A majority (73%) of the clones examined from a PstI genomic library appeared to detect single-copy sequences based on RFLP banding patterns, while clones from a cDNA library revealed a lower percentage of single copy sequences. When hybridization stringencies were lowered, 21% of the genomic clones examined revealed greater copy numbers. PstI digestion of 'Duncan' DNA indicated abundant methylation, so the relatively high frequency of multiple-copy sequences observed at moderate stringency cannot be attributed to a lack of methylation of the Citrus DNA. The polymorphisms in banding patterns observed primarily resulted from insertions and/or deletions rather than from base substitutions, and a model is presented to account for the varying patterns obtained from individual probes with different restriction enzymes. Finally, a model for transposon activity in Citrus is proposed, based on observations made during the course of these studies.
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Affiliation(s)
- P C Liou
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, 33850, Lake Alfred, FL, USA
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23
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Lodhi MA, Daly MJ, Ye GN, Weeden NF, Reisch BI. A molecular marker based linkage map of Vitis. Genome 1995; 38:786-94. [PMID: 7672609 DOI: 10.1139/g95-100] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic linkage maps of Vitis (2n = 38) have been constructed from a single interspecific hybrid grape population (60 seedlings) of 'Cayuga White' X 'Aurore'. The maps were primarily based on 422 RAPD markers but also included 16 RFLP and isozyme markers. These maps had an average distance of 6.1 cM between markers and were developed using a double-pseudotestcross strategy. The 'Cayuga White' map had 214 markers covering 1196 cM and that of 'Aurore' spanned over 1477 cM with 225 markers. The 'Cayuga White' map consisted of 20 linkage groups, whereas 22 linkage groups comprised the 'Aurore' map. The number of groups reduced to 19, as in some instances two or more groups from one parent showed homology with a single group from the other parent on the basis of markers heterozygous in both parents. Each linkage group ranged in size from 14 to 135 cM in 'Aurore' and from 14 to 124 cM in 'Cayuga White'. These maps provide enough coverage of the genome to allow quantitative trait locus analysis and map-based gene cloning.
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Affiliation(s)
- M A Lodhi
- Department of Horticultural Sciences, New York State Agricultural Experiment Station, Cornell Unversity, Geneva 14456, USA
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24
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Foolad MR, Arulsekar S, Becerra V, Bliss FA. A genetic map of Prunus based on an interspecific cross between peach and almond. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:262-9. [PMID: 24169773 DOI: 10.1007/bf00220887] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/1994] [Accepted: 02/03/1995] [Indexed: 05/23/2023]
Abstract
A genetic linkage map of Prunus has been constructed using an interspecific F2 population generated from self-pollinating a single F1 plant from a cross between a dwarf peach selection (54P455) and an almond cultivar 'Padre'. Mendelian segregations were observed for 118 markers including 1 morphological (dw), 6 isozymes, 12 plum genomic, 14 almond genomic and 75 peach mesocarp specific cDNA markers. One hundred and seven markers were mapped to 9 different linkage groups covering about 800 cM map distance, and 11 markers remained unlinked. Three loci identified by three cDNA clones, PC8, PC5 and PC68.1, were tightly linked to the dw locus in linkage group 5. Segregation distortion was observed for approximately one-third of the markers, perhaps due to the interspecific nature and the reproductive (i.e. self-incompatibility) differences between peach and almond. This map will be used for adding other markers and genes controlling important traits, identifying the genomic locations and genetic characterizing of the economically important genes in the genus Prunus, as well as for markerassisted selection in breeding populations. Of particular interest are the genes controlling tree growth and form, and fruit ripening and mesocarp development in peach and almond.
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Affiliation(s)
- M R Foolad
- Department of Pomology, University of California, 95616, Davis, CA, USA
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25
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Kijas JM, Fowler JC, Thomas MR. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species. Genome 1995; 38:349-55. [PMID: 7774802 DOI: 10.1139/g95-045] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.
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Affiliation(s)
- J M Kijas
- School of Biological Sciences, Flinders University of South Australia, Adelaide
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26
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Truco MJ, Quiros CF. Structure and organization of the B genome based on a linkage map in Brassica nigra. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 89:590-8. [PMID: 24177935 DOI: 10.1007/bf00222453] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/1993] [Accepted: 03/29/1994] [Indexed: 05/27/2023]
Abstract
We constructed a genetic map on Brassica nigra based on a segregating population of 83 F2 individuals. Three different types of molecular markers were used to build the map including isozymes, restriction fragment length polymorphisms (RFLP), and random amplified polymorphic DNA (RAPD). The final map contained 124 markers distributed in 11 linkage groups. The map covered a total distance of 677 cM with the markers distributed within a mean distance of 5.5cM. Of the sequences found in the B. nigra map, 40% were duplicated and organized into three different types of arrangements. They were either scattered throughout the genome, organized in tandem, or organized in blocks of duplicated loci conserved in more than 1 linkage group.
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Affiliation(s)
- M J Truco
- Department of vegetable Crops, University of California, 95616, Davis, CA, USA
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27
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Fjellstrom RG, Parfitt DE. RFLP inheritance and linkage in walnut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 89:665-670. [PMID: 24178008 DOI: 10.1007/bf00223702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/1993] [Accepted: 05/17/1994] [Indexed: 06/02/2023]
Abstract
Thirty-two low-copy-number genomic DNA clones from a walnut (Juglans sp.) Pst I genomic library were used to establish a molecular-marker linkage map for walnut. The clones were hybridized to restriction-endonuclease-digested DNA from parent walnut trees involved in an interspecific backcross of (J. hindsii x J. regia) x J. regia in order to identify parental polymorphism. Sixty-three backcross progeny were analyzed to determine the inheritance and linkage of 48 RFLP loci. Sixty-six percent of the walnut cloned sequences detected duplicated, but unlinked, loci. Twelve linkage groups were identified by 42 of the RFLP loci. A Poisson probability method for estimating genome size was utilized to calculate the approximate walnut genome length as 1660 cM and to estimate that 138 markers would be needed to cover 95% of the walnut genome within 20 cM of each marker.
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Affiliation(s)
- R G Fjellstrom
- National Forage Seed Production Research Center, USDA/ARS, 3450 Campus Way, 97331, Corvallis, OR, USA
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28
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Cai Q, Guy CL, Moore GA. Extension of the linkage map in Citrus using random amplified polymorphic DNA (RAPD) markers and RFLP mapping of cold-acclimation-responsive loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 89:606-614. [PMID: 24177937 DOI: 10.1007/bf00222455] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/1994] [Accepted: 04/18/1994] [Indexed: 06/02/2023]
Abstract
Genetic mapping with RAPD markers has been initiated in Citrus. Reproducible polymorphism of amplified DNA fragments was obtained with approximately half of the 140 random primers tested, revealing 266 segregating loci. These were tested for linkage using 60 BC1 progeny from an intergeneric cross of Citrus grandis (L.) Osb. x [Citrus grandis (L.) Osb. x Poncirus trifoliata (L.) Raf.]. A core linkage map was constructed that consists of nine linkage groups containing 109 RAPD markers and 51 previously-mapped RFLP and isozyme markers. A further 79 markers that could not be ordered unambiguously because of their allelic constitution were associated with individual linkage groups and are shown in relation to the core map. The core map has a total length of 1192 cM with an average distance of 7.5 cM between loci and is estimated to cover 70-80% of the genome. Loci with distorted segregation patterns clustered on several linkage groups. Individual clusters of loci were skewed in allelic composition toward one or the other parent, usually C. grandis. This relatively-saturated linkage map will eventually be used to identify quantitative trait loci for cold and salt-tolerance in Citrus. As a beginning we have mapped three loci detected by a cold-acclimation-responsive cDNA.
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Affiliation(s)
- Q Cai
- Plant Molecular and Cellular Biology Program, Departments of Environmental and Horticultural Sciences, Institute of Food and Agricultural Sciences, University of Florida, 32611, Gainesville, FL, USA
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29
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Laurent V, Risterucci AM, Lanaud C. Genetic diversity in cocoa revealed by cDNA probes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 88:193-198. [PMID: 24185926 DOI: 10.1007/bf00225897] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/1993] [Accepted: 09/09/1993] [Indexed: 06/02/2023]
Abstract
The variability of the cocoa (Theobroma cacao) nuclear genome was investigated. A total of 203 cocoa clones was surveyed for restriction fragment length polymorphisms (RFLPs) using four restriction endonuclease and 31 seed cDNA probes. A high level of polymorphism has been found. This study points to a structuring of the species that fits with the distinction between the Criollo and Forastero populations. These results combined with previously obtained nuclear rDNA and mtDNA data allow us to propose new hypotheses on the origin and evolution of the different cocoa populations.
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Affiliation(s)
- V Laurent
- AGETROP/CIRAD, BP5035, 34032, Montpellier cedex, France
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30
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Rowland LJ, Levi A. RAPD-based genetic linkage map of blueberry derived from a cross between diploid species (Vaccinium darrowi and V. elliottii). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 87:863-868. [PMID: 24190473 DOI: 10.1007/bf00221139] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/1993] [Accepted: 07/23/1993] [Indexed: 06/02/2023]
Abstract
An initial genetic linkage map for blueberry has been constructed from over 70 random amplified polymorphic DNA (RAPD) markers that segregated 1∶1 in a testcross population of 38 plants. The mapping population was derived from a cross between two diploid blueberry plants: the F1 interspecific hybrid (Vaccinium darrowi Camp x V. elliottii Chapm.) and another V. darrowi plant. The map currently comprises 12 linkage groups (in agreement with the basic blueberry chromosome number) and covers a total genetic distance of over 950cM, with a range of 3-30cM between adjacent markers. The use of such a map for identifying molecular markers linked to genes controlling chilling requirement and cold hardiness is discussed.
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Affiliation(s)
- L J Rowland
- Fruit Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, 20705, Beltsville, MD, USA
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31
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Fauré S, Noyer JL, Horry JP, Bakry F, Lanaud C, Gońzalez de León D. A molecular marker-based linkage map of diploid bananas (Musa acuminata). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1993; 87:517-26. [PMID: 24190325 DOI: 10.1007/bf00215098] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/1993] [Accepted: 04/20/1993] [Indexed: 05/20/2023]
Abstract
A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36% of all loci, mostly favoring the male parent. Chromosome structural rearrangements were believed to be one of the main causes of these distortions. The use of genetic linkage data to further the genetic and evolutionary knowledge of the genus Musa, as well as to help improve the design of breeding strategies, is discussed.
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Affiliation(s)
- S Fauré
- CIRAD-BIOTROP, B.P. 5035, 34032, Montpellier Cedex, France
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Guerra M. Cytogenetics of Rutaceae. V. High chromosomal variability in Citrus species revealed by CMA/DAPI staining. Heredity (Edinb) 1993. [DOI: 10.1038/hdy.1993.131] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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