Maximum parsimony based resolution of inter-species phylogenetic relationships in Citrus L. (Rutaceae) using ITS of rDNA

Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers

Background

Releasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species.

Results

Here, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange.

Conclusion

Our findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

Background

Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels.

Results

Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap^’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry.

Conclusion

To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.

Citrus species and hybrids depicted by near- and mid-infrared spectroscopy

BACKGROUND

Citrus trees are among the most cultivated plants in the world, with a high economic impact. The wide sexual compatibility among relatives gave rise to a large number of hybrids that are difficult to discriminate. This work sought to explore the ability of infrared spectroscopy to discriminate among Citrus species and/or hybrids and to contribute to the elucidation of its relatedness.

RESULTS

Adult leaves of 18 distinct Citrus plants were included in this work. Near- and mid-infrared (NIR and FTIR) spectra were acquired from leaves after harvesting and a drying period of 1 month. Spectra were modelled by principal component analysis and partial least squares discriminant analysis. Both techniques revealed a high discrimination potential (78.5-95.9%), being the best results achieved with NIR spectroscopy and air-dried leaves (95.9%).

CONCLUSION

Infrared spectroscopy was able to successfully discriminate several Citrus species and/or hybrids. Our results contributed also to enhance insights regarding the studied Citrus species and/or hybrids. Despite the benefit of including additional samples, the results herein obtained clearly pointed infrared spectroscopy as a reliable technique for Citrus species and/or hybrid discrimination. © 2018 Society of Chemical Industry.