Genetic diversity, population structure and genetic parameters of fruit traits in Capsicum chinense

Moreira, Aline Fabiana Paladini; Ruas, Paulo Maurício; Ruas, Claudete de Fátima; Baba, Viviane Yumi; Giordani, Willian; Arruda, Isabella Mendonça; Rodrigues, Rosana; Gonçalves, Leandro Simões Azeredo

doi:10.1016/j.scienta.2018.03.012

Cited by 51 publications

(46 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In general, the accessions could not be grouped based on the geographic origin, since the accessions of same geographic areas were classified in different groups. The same observation was presented by Baba et al (2016) [13] and Moreira et al (2018) [14]. The Ward hierarchical clustering analysis of molecular data also allowed the identification of six groups.…”

Section: Discussionsupporting

confidence: 62%

See 1 more Smart Citation

Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm

et al. 2020

Self Cite

View full text Add to dashboard Cite

Loss of biodiversity and ecosystem degradation become major concerns worldwide, making the conservation process an important strategy for maintaining biodiversity. Capsicum chinense Jacq. is the most Brazilian species of the genus, with representatives in different biomes. Anthropic pressure, such as burns, real estate speculation, and changing cultivation habit has led to risks of genetic erosion. Conservation and characterization of conserved accessions are paramount to ensure genetic diversity, useful for the bioeconomy and for genetic improvement. We report the characterization of 55 C. chinense accessions from four different regions of Brazil and one accession from Peru. The accessions were characterized based on 37 morpho-agronomic variables, Inter Simple Sequence Repeats—ISSR and Simple Sequence Repeat—SSR. Qualitative descriptors were analyzed using a descriptive statistical, while the quantitative descriptors were analyzed via F test and significant differences in mean values were separated using Scott-Knott test. The relative contribution of each quantitative trait was determined. A correlation between morphological and molecular distances was calculated. Color of ripe fruit and fruit shape had the largest number of observed classes. Six distinct groups and the joint analysis presented an entanglement rate of 0.58, evidencing the divergence of accessions between the groups of both dendrograms. Bayesian analysis allowed the distinction of two clusters for SSR. A significant variability was observed among accession with potential to integrate several breeding programs.

show abstract

Section: Discussionsupporting

confidence: 62%

“…Preservation of such plant genetic resources is extremely important for plant breeding as well as for society as a whole [15]. In view of the cultural and economic importance of the Capsicum in Brazil, the development of new and improved cultivars carrying characteristics that meet the needs of farmers and the consumers is primordial.…”

Section: Introductionmentioning

confidence: 99%

Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…In China, a majority of the pepper varieties commercially cultivated belong to the species C. annuum, and the market types are classified by fruit shapes, such as the popular blocky, long horn, short horn, and linear-fruits [34,35]. To date, most experiments have evaluated the genetic relationships among several Capsicum species [36,37] or the genetic diversity of C. chinense germplasm from relatively restricted regions [38]. The phylogenetic analysis based on molecular markers and pan-genome confirmed that C. chinense and C. frutescens are more closely related to each other than to C. annuum [37,39].…”

Section: Population Structure Among Inbred C Annuum Linesmentioning

confidence: 99%

Genotyping pepper varieties using Target SNP-seq reveals that population structure clusters according to fruit shape

Du¹,

Yang²,

Chen³

et al. 2019

Preprint

View full text Add to dashboard Cite

Background The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has characterized the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of single-nucleotide polymorphisms (SNPs) was created that consisted of 97 perfect SNPs, which were identified using re-sequencing data from 35 diverse C. annuum lines. Based on this panel, a Target SNP-seq was designed that combined the multiplex amplification of the perfect SNPs with Illumina sequencing to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content (PIC), observed heterozygosity (Ho), expected heterozygosity (He), and minor allele frequency (MAF), which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape; blocky, long horn, short horn, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn, linear, and blocky-fruited populations. A set of 35 core SNPs were then used as KASPar markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis (PCA) and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Notably, two SNP loci, CaSNP118 and CaSNP053, which are located on chromosome 11 and 6 were significantly associated with fruit shape (p < 1.0 × 10 -4) Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of the pepper varieties is significantly influenced by breeding programs focused on fruit shape.

show abstract

“…In this context, the present study aims to know and compare the occurrence and distribution of LTR-RTs on the chromosomes, focusing on Gypsy superfamily that has been predominant in the Capsicum genomes, as well as their association with the diversity of other repetitive sequences. Peppers are among the most important vegetables in the world due to their high versatility and wide range of applications in cooking, industry, and decoration [27]. Therefore, large investments have been made to obtain high throughout sequences of C. annuum, C. chinense and C. baccatum [19,28].…”

mentioning

confidence: 99%

Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

Assis

Baba

Cintra

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposons). Retrotransposons that are transposed using an intermediate RNA and that accumulate in a “copy-and-paste” manner have been screened in three completely sequenced genomes of peppers (Solanaceae family). The goal of this study was to understand the genome relationships among Capsicum annuum , C. chinense and C. baccatum , based on a comparative analysis of the function, diversity and the chromosome distribution of TE lineages in the Capsicum karyotypes. Due to the great commercial importance of pepper in natura , as a spice or as an ornamental plant, these genomes have been widely sequenced, and all of the assemblies are available in the SolGenomics group. These sequences have been used to compare all repetitive fractions from a cytogenomic point of view. Results: The qualification and quantification of LTR-retrotransposons (LTR-RT) families are contrasted with molecular cytogenetics data, and the results show a strong genome similarity between C. annuum and C. chinense as compared to C. baccatum . The Gypsy superfamily is more abundant than Copia , especially for Tekay/Del family members, including a high representation in C. annuum and C. chinense . On the other hand, C. baccatum accumulates more Athila/Tat sequences. The FISH results show retrotransposons differentially scattered along chromosomes, with the exception of CRM family sequences, which mainly have a proximal accumulation associated with heterochromatin bands. Conclusions: The results confirm a close genomic relationship between C. annuum and C. chinense in comparison to C. baccatum . Centromeric GC-rich bands appeared to be associated with the accumulation regions of CRM elements, whereas terminal and subterminal AT- and GC-rich bands do not correspond to the accumulation of the retrotransposons in the three Capsicum species tested here.

show abstract

Genetic diversity, population structure and genetic parameters of fruit traits in Capsicum chinense

Cited by 51 publications

References 47 publications

Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm

Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm

Genotyping pepper varieties using Target SNP-seq reveals that population structure clusters according to fruit shape

Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

Contact Info

Product

Resources

About