Pepper (Capsicum spp.) is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world’s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 GenBank pepper accessions (local cultivars and landraces) from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat (SSR) markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages (UPGMA) in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.

Fruit set and development are affected by many phytohormones, including gibberellin.  Little is known regarding molecular mechanism underlying gibberellin mediated fruit set and development especially in Capsicum.  Three gibberellin receptors, CaGID1b.1, CaGID1b.2 and CaGID1c, and a DELLA protein, CaGAI, have been identified in Capsicum annuum L.  During the fruit development, the expression level of CaGID1c was low, and the expression fold change is mild.  However, CaGID1b.1 and CaGID1b.2 were relatively higher and more acute, which indicates that CaGID1b.1 and CaGID1b.2 may play an important role in fruit pericarp, placenta and seed.  Ectopic expressions of CaGID1b.1, CaGID1b.2 and CaGID1c in Arabidopsis double mutant gid1a gid1c increased plant height, among which CaGID1b.2 had the most significant effect; CaGAI reduced plant height in double mutant rga-24/gai-t6, having a similar function to AtGID1 and AtGAI in stem elongation.  Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated that CaGID1b.1 and CaGID1b.2 interact with CaGAI in a GA-dependent manner, while CaGID1c interacts with CaGAI in a GA-independent manner.  Our study reveals the key elements during gibberellin signaling in Capsicum and supports the critical importance of gibberellin for Capsicum fruit set and development.

SSR markers are useful in pepper linkage mapping and gene location. 446 SSR markers have been reported, but they are insufficient. It is costly to develop SSR markers from DNA library, whereas it seems much easy to find in EST sequences in the GenBank of pepper through internet. In this study, attempts have been made to develop SSR markers in the EST sequences by using bioinformatics. EST sequences were trimmed by ‘est-trimmer.pl’ software, while 116915 EST sequences were obtained without poly ‘A’ or poly ‘T’, ranged between 100 and 700 bp. Using ‘e-PCR’ and ‘del.pl’ softwares, SSR sequences were identified. 2 508 microsatellite loci (larger than 20 repeats) were established and 755 SSR primers were designed using SSR finder software and Primer 3 software. There were 498 (0.43%) mono-, 1 026 (0.89%) di-, 518 (0.45%) tri-, 245 (0.21%) tetra-, 114 (0.10%) penta-, and 107 (0.09%) hexa-nucleotide SSRs. The estimated frequency of SSRs was approximately 1/25.12 kb. According to the distribution of SSRs in pepper, the mean length of pepper SSRs was 22.68 bp and the adenine rich repeats such as A/T, AG, AT, AAG, AAAT, and AAAC were predominant in each type of SSRs (mono-, di-, tri-, tetra-, penta-, and hexa-), whereas the C/G, CG, CCG repeats were less abundant. 210 primers were tested in 8 pepper cultivars and the PCR result revealed the existence of polymorphism among 127 (60.48%) SSR primers within 8 pepper cultivars. It is confirmed that pepper EST database could be efficiently exploited for availability of SSR markers.