A new insight on genetic diversity of sweet oranges: CAPs-SSR and SSR markers

Shahnazari, Narineh; Noormohammadi, Zahra; Sheidai, Masoud; Koohdar, Fahimeh

doi:10.1186/s43141-022-00393-6

Cited by 6 publications

(6 citation statements)

References 24 publications

(26 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Different kinds of molecular markers are now universally used to analyze genetic diversity for many species rapidly and efficiently. Examples include SSR in grape [46,47], chickpea [48], and Prunus armeniaca [49]; RAPD in grape [46], Apiaceae [50] and Piperaceae [51]; And CAPS in Citrus [52], cotton [53] and Camellia sinensis [54]. Although the species of Zanthoxylum are economically important trees in China [55], relatively few studies have focused on their genetic diversity [56].…”

Section: Est-ssr Validationmentioning

confidence: 99%

Six Express Sequence Tag–Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

Deng,

He,

et al. 2023

CIMB

View full text Add to dashboard Cite

Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag–simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.

show abstract

Section: Est-ssr Validationmentioning

confidence: 99%

Six Express Sequence Tag–Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

Deng,

He,

et al. 2023

CIMB

View full text Add to dashboard Cite

show abstract

“…Although the birthplace of citrus is uncertain, Southeast Asia is believed to be its origin. The taxonomy and phylogeny of citrus are challenging due to various factors such as bud mutations rate, the ability of citrus and related genera to interbreed, widespread distribution, and a long history of cultivation (Shahnazari et al, 2022). The principal species of the genus Citrus are C. reticulata (mandarin), C. maxima (Pummelo), and C. medica (Citron) (Wu et al, 2018), while other species such as C. aurantium (sour orange), C. sinensis (sweet orange), C. paradisi (grapefruit), and C. limon (lemon) are derived from successive hybridizations (Mario et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

De novoGenome Assembly, Functional Annotation and SSR Mining ofCitrus reticulata“Kinnow” from Pakistan

Jabeen

Saif

Distefano

et al. 2023

Preprint

View full text Add to dashboard Cite

Citrus reticulata (Blanco) fruit is native to South East Asia and owns many nutritional, medicinal and economic advantages, which is locally known as (Kinnow) and one of the priced mandarin varieties (Dancy, Fuetrells Early and Honey) of Citrus genera renowned for its exclusive taste, vitamin richness, thin peel, long shelf-life and seedless characteristics in Pakistan. However, genetic improvement and breeding strategies for this valued variety are lacking due to the in-housed insufficient genomic and technical resources. Therefore, the current research was initiated to provide the baseline de-novo genome assembly of C. reticulata (seedless kinnow) at a depth of 151x with Illumina paired-end short-read sequencing technology using HiSeq 2500. Whole-genome sequencing resulted in 139,436,350 raw reads (~20.09 GB) of data, however, after removing the low-quality reads (1.08%), duplicated sequences (10.5%) and Illumina adaptors, 137,901,462 clean reads were obtained with (~18.87 GB) of clean data which was further used for downstream variant calling analysis. In total, 348,861 scaffolds were generated with N50 value of 4827 which constitute 263,018,9 contigs ranging from 71-36,213 with a total of 179,984,763 nucleotides. The GC content of the final draft assembly at 71-mer was 34.1%. Moreover, annotation was performed with the (Hayai-Annotation Plants) tool which marked the whole-genome mapping with three main functional databases of interpro, Pfam and gene ontology. Additionally, in-silico identification of 111,032 Simple Sequence Repeats (SSR) was also accomplished with the help of GMATA tool, which may be used for further screening and genetic improvement of the citrus varieties by means of this current assembly as a resource of local reference genome.

show abstract

“…SSR molecular marker technology involves tandem repeat sequence consisting of 1–6 nucleotides as repeat units, which has excellent characteristics such as co-dominant inheritance, high polymorphism, good reproducibility, and stable and accurate results. It has emerged as a key molecular marker technology for plant genetic diversity analysis, population structure research, variety identification, and molecular ID construction [ 4 , 5 , 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

Bai

Zhang

et al. 2023

Plants

View full text Add to dashboard Cite

To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

show abstract

A new insight on genetic diversity of sweet oranges: CAPs-SSR and SSR markers

Cited by 6 publications

References 24 publications

Six Express Sequence Tag–Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

Six Express Sequence Tag–Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species

De novoGenome Assembly, Functional Annotation and SSR Mining ofCitrus reticulata“Kinnow” from Pakistan

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

Contact Info

Product

Resources

About