Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.

the ankyrin (AnK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. it is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding AnK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper. open Scientific RepoRtS | (2020) 10:4044 | https://doi.drought tolerance 19 , ABA-mediated regulation of reactive oxygen species levels under salt-stress 20 , and several plant diseases 21 , including those generated by fungus such as rice blast 22 . The release of genomic data and the development of bioinformatics analyses have led to comprehensive research on the identification and characterization of the ANK gene family in plants such as Arabidopsis 23 , rice 18 , tomato 24 , maize 25 , Physcomitrella patens 26 and soybean 27 . The number of ANK repeats, genes, and proteins in plants varies considerably across diverse plant species. In Arabidopsis thaliana, 509 ANK repeats encoded by 105 genes were reported, whereas rice contains 175 ANK repeat genes 18,23 .Pepper (Capsicum spp.) is a member of the Solanaceae family and is closely related to potato, tomato, eggplant, tobacco and petunia. Pepper represents an economically important horticultural crop worldwide because of its wide variety of uses, as a food, coloring agent, and spice and in pharmaceuticals, cosmetics and ornamental products as well as for its nutrimental value 28,29 . Despite the importance of pepper, genome-wide studies remain limited. The recent whole-genome sequencing of pepper 28 provided an excellent tool for genome-wide analysis for the identification and characterization of entire gene families present in this crop [30][31][32] . Recently, the ANK repeat domain was identified as one of the major markers linked to capsaicinoid synthesis in Capsicum annuum 33 and Capsicum chinense 34 .The present study aimed to analyze the gene locus and chromosome localization, protein length, ...

Additional index words. genotyping-by-sequencing, ornamental plant, Piedmont azalea, single nucleotide polymorphism Abstract. Rhododendron canescens is a deciduous azalea native to the southeastern United States that is used in landscaping due to its ornamental qualities. A genotyping-bysequencing (GBS) approach was taken to characterize the genetic structure and diversity of a R. canescens germplasm collection. Single nucleotide polymorphisms (SNPs) were identified by two software platforms, STACKS and GBS-SNP-CROP. Three distinct R. canescens populations were detected by STRUCTURE analysis with GBS-SNP-CROP data, whereas two populations were distinguished using STACKS data. Principal component analysis (PCA) with data from both SNP pipelines supported the presence of three populations. Statistical results indicated that there was low genetic differentiation between the populations, but relatively high genetic diversity within populations. The inbreeding coefficient of the R. canescens accessions was low, which would be expected with an outcrossing species. These results suggest that there may be a significant level of gene flow between populations of R. canescens.

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