Unraveling the cryptic genetic variation and population structure of the citrus genotypes with unknown origin (original) (raw)
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Citrus phylogeny and genetic origin of important species as investigated by molecular markers
TAG Theoretical and Applied Genetics, 2000
Citrus phylogeny was investigated using RAPD, SCAR and cpDNA markers. The genotypes analyzed included 36 accessions belonging to Citrus together with 1 accession from each of the related genera Poncirus, Fortunella, Microcitrus and Eremocitrus. Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus and from each other. Within Citrus, the separation into two subgenera, Citrus and Papeda, designated by Swingle, was clearly observed except for C. celebica and C. indica. Almost all the accessions belonging to subgenus Citrus fell into three clusters, each including 1 genotype that was considered to be a true species. Different phylogenetic relationships were revealed with cpDNA data. Citrus genotypes were separated into subgenera Archicitrus and Metacitrus, as proposed by Tanaka, while the division of subgenera Citrus and Papeda disappeared. C. medica and C. indica were quite distant from other citrus as well from related genera. C. ichangensis appeared to be the ancestor of the mandarin cluster, including C. tachibana. Lemon and Palestine sweet lime were clustered into the Pummelo cluster led by C. latipes. C. aurantifolia was located in the Micrantha cluster. Furthermore, genetic origin was studied on 17 cultivated citrus genotypes by the same molecular markers, and a hybrid origin was hypothesized for all the tested genotypes. The assumptions are discussed with respect to previous studies; similar results were obtained for the origin of orange and grapefruit. Hybrids of citron and sour orange were assumed for lemon, Palestine sweet lime, bergamot and Volkamer lemon, while a citron × mandarin hybrid was assumed for Rangpur lime and Rough lemon. For Mexican lime our molecular data indicated C. micrantha to be the female parent and C. medica as the male one.
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 speciWed 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 Pon-cirus 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 identiWed Wve 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.
Application of bioinformatics tools for analysis of genetic diversity in orange (Citrus sinensis L.)
2011
Sweet orange, the most widely grown and consumed citrus type, presents something of a mystery. Four kinds of sweet oranges are recognized: the common, or blond, orange, which is the most important and of which there are many varieties; the blood orange, which has a red pigmentation in the flesh due to the accumulation of anthocyanins; and the navel orange, grown for fresh consumption. In Tunisia, Citrus sinensis culture is spread especially in Cap bon region in the North Est. It is represented by a large number of varieties. AFLP (Amplified Fragment Length Polymorphism) markers were used in order to study genetic diversity. Results have proved a large genetic diversity. AFLP products were analyzed by capillary electrophoresis on an automated ABI Prism 3130 DNA sequencer. Using GeneMapper, AFLP bands were scored, across all genotypes, for presence (1) or absent (0) and transformed into 0/1 binary matrix. Genetic similarities were estimated basing on Nei and Li’s 1972 formula. The sim...
Molecular Characterization of Citrus Cultivars Using DNA Markers
Twenty five SSR primers were used to assess polymorphism in twelve genotypes which belong to four species and one hybrid of citrus. A total of 116 clear and reproducible amplified bands were obtained, out of which 103 were polymorphic. The numbers of amplified DNA bands per primer were ranged from 2 to 9 (Molecular size from 100-1200 bp) with an average of 5.27. Percentage polymorphisms ranged from 75-100 with an average of 89.78% across the genotypes and polymorphism information content (PIC) values from 0.25 to 0.68 having an average of 0.41. The primers clustered the citrus genotypes into two major groups, and further into many sub groups. The results revealed by the two and three dimensional principle component analysis further insured these groupings. The similarity matrices ranged from 0.439 (Cleopatra and Blood Red) to 0.801 (Baramasi and Badri lemon), with an average of 0.582 across all the genotypes. Some markers produced unique alleles in specific genotypes which could be used to discriminate them from the other.
Australian Journal of Crop Science, 2015
Citrus is one of the most important crops of sub-tropical regions worldwide, including acid lime (Citrus aurantifolia). This includes a large group of citrus family. AFLP analysis was done using four primer combinations to monitor genetic relationships between 30 local genotypes and six foreign cultivars. AFLP data analysis revealed the presence of 126 scorable bands which revealed % 69.84 polymorphism. The number of amplified bands for each primer combination was recorded as 26-37 (with an average of 22 bands for each primer combination). The measured polymorphic information content (PIC) had an average of 0.48. The range of similarity was between 0.24 and 0.96. Minimum similarity was found between sweet lime (Citrus limetta) and D8 genotype, while the maximum observed between two genotypes of Minaab region. Samples were not separated using cluster analysis regionally. Instead, samples of Minaab region revealed high level of genetic similarity with one another, in comparison to sam...
Journal of Science and Research: Revista Ciencia e Investigación, 2017
In this study, genetic diversity in 19 citrus cultivars was analyzed using Simple Sequence Repeat (SSR), Inter-simple Sequence Repeat (ISSR) and cleaved amplified polymorphic sequence (CAPS) markers. Nine primers for SSR, nine ISSR primers and two primers for CAPS were used for allele scoring. One chloroplast DNA region (rbcL-ORF106) and one mitochondrial DNA region (18S-5S) were analyzed using cleaved amplified polymorphic sequence (CAPS) marker in 19 citrus accessions grown in Iran. In total, 45 SSR and 131 ISSR polymorphic alleles and tree organelle genome types were detected. Cluster analysis of SSR and ISSR data was performed using UPGMA method and based on Jaccard's coefficient. The result of this investigation showed that the SSR and ISSR primers were highly informative and efficient in detecting genetic variability and relationships of the citrus accessions. CAPS marker analysis results showed that Bakraee and one of off type Mexican lime had banding pattern similar to Clementine Mandarin, while Pummelo regarded as maternal parent of other studied genotypes Citron regarded as father parent showed definite banding pattern among 19 studied genotypes which it confirmed Cytoplasmic inheritance from mother cellular organelles.
PLOS ONE, 2015
Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several PLOS ONE |