Molecular Evidence for Hybrid Origin and Phenotypic Variation of Rosa Section Chinenses

Abstract

Rosa sect. Chinenses (Rosaceae) is an important parent of modern rose that is widely distributed throughout China and plays an important role in breeding and molecular biological research. R. sect. Chinenses has variable morphological traits and mixed germplasm. However, the taxonomic status and genetic background of sect. Chinenses varieties remain unclear. In this study, we collected germplasm resources from sect. Chinenses varieties with different morphological traits. Simple sequence repeat (SSR) markers, chloroplast markers, and single copy nuclear markers were used to explore the genetic background of these germplasm resources. We described the origin of hybridization of rose germplasm resources by combining different molecular markers. The results showed that the flower and hip traits of different species in R. sect. Chinenses were significantly different. The SSR analysis showed that the two wild type varieties have different genetic backgrounds. The double petal varieties of R. sect. Chinenses could be hybrids of two wild type varieties. A phylogenetic analysis showed that the maternal inheritance of sect. Chinenses varieties had two different origins. To some extent, variation in the morphological traits of double petal species of R. sect. Chinenses reflects the influence of cultivation process. This study emphasizes that different genetic markers vary in their characteristics. Therefore, analyzing different genetic markers in could provide an insight into highly heterozygous species.

Comparative Analysis of Complete Chloroplast Genomes of Eight Ficus Species and Insights Into Phylogenetic Relationships of Ficus

“…Among them, the richest repeat type was mono-nucleotides (53-68), followed by di-nucleotides (17)(18)(19)(20), tetra-nucleotides (8-10), tri-nucleotides (4-5), penta-nucleotides (2-4), and hexanucleotides (0-2), respectively. The A/T repeat motif accounted for a large proportion (52-67) among all the repeat types, followed by AT/AT (17)(18)(19), but the other repeat motifs were very rare. Mono-nucleotide repeat motifs (A/T), di-nucleotide repeat motifs (AT/TA), tri-nucleotide repeat motifs (AAG/CTT, AAT/ATT), tetra-nucleotide repeat motifs (AAAG/CTTT, AAAT/ATTT, AATT/AATT, AGAT/ATCT) and pentanucleotides repeat motifs (AAAGG/CCTTT, AATTC/AATTG) were present in each cp genome (Fig.…”

“…We detected 94, 91, 100, 89, 92, 101, 93 and 104 SSR loci in Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa and Ficus virens cp genomes, respectively. Among them, the richest repeat type was mono-nucleotides (53-68), followed by di-nucleotides (17)(18)(19)(20), tetra-nucleotides (8-10), tri-nucleotides (4-5), penta-nucleotides (2-4), and hexanucleotides (0-2), respectively. The A/T repeat motif accounted for a large proportion (52-67) among all the repeat types, followed by AT/AT (17)(18)(19), but the other repeat motifs were very rare.…”

“…The number of repeats each species ranged from 57 (Ficus altissima) to 71 (Ficus auriculata), with palindromic repeats being the most abundant types (39-51), followed by forward repeats (13)(14)(15)(16)(17)(18)(19) and reverse (2-4) repeats, the complement repeats are rare in these 8 cp genomes (Fig. 2c; Table S5).…”

“…Therefore, cp genomes were often used to research the evolution, interspeci c divergence, adaptive population history and phylogeny of related species [12][13][14]. With the coming of the era of whole-genome sequencing, the cp whole genomes are extensively used in phylogenetic differentiation studies, species taxonomic identi cation and genetic breeding [15][16][17][18][19]. Although the cp genomes of some genus Ficus have been reported previously [20][21][22][23][24][25][26][27], the eight Ficus species studied here have not been reported.…”

Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus

“…Therefore, cp genomes have often been used to research the evolution, interspecific divergence, adaptive population history and phylogeny of related species [ 12 , 13 , 14 ]. With the emergence of the whole-genome sequencing era, the whole cp genomes have been extensively used in phylogenetic differentiation studies, species taxonomic identification and genetic breeding [ 15 , 16 , 17 , 18 , 19 ]. Although the cp genomes of some genus of Ficus have been reported previously [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 ], the eight Ficus species studied here have not been reported.…”