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Allen Van Deynze - One of the best experts on this subject based on the ideXlab platform.
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characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30k unigene pepper genechip
PLOS ONE, 2013Co-Authors: Theresa Hill, Hamid Ashrafi, Sebastian Reyeschinwo, Kevin Stoffel, Maria Jose Truco, Alexander Kozik, Richard W Michelmore, Allen Van DeynzeAbstract:The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.
Satoshi Tabata - One of the best experts on this subject based on the ideXlab platform.
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development of Capsicum est ssr markers for species identification and in silico mapping onto the tomato genome sequence
Molecular Breeding, 2013Co-Authors: Kenta Shirasawa, Noriko Nagata, Kohei Ishii, Munenori Suzuki, Toshiya Muranaka, Megumi Kobayashi, Sachiko Isobe, Satoshi TabataAbstract:Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding.
Aqeel Ahmad - One of the best experts on this subject based on the ideXlab platform.
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halotolerant plant growth promoting rhizobacteria modulate gene expression and osmolyte production to improve salinity tolerance and growth in Capsicum annum l
Environmental Science and Pollution Research, 2018Co-Authors: Nasim Ahmad Yasin, Waheed Ullah Khan, Waheed Akram, Aqeel Ahmad, Sajid Rashid AhmadAbstract:Some rhizobacteria have demonstrated a noteworthy role in regulation of plant growth and biomass production under biotic and abiotic stresses. The present study was intended to explicate the ameliorative consequences of halotolerant plant growth-promoting rhizobacteria (HPGPR) on growth of Capsicum plants subjected to salt stress. Salt stress was ascertained by supplementing 1 and 2 g NaCl kg−1 soil. The HPGPR positively invigorated growth attributes, chlorophyll, protein contents, and water use efficiency (WUE) of supplemented Capsicum plants under salinity stress conditions. Bacillus fortis strain SSB21 caused highest significant increase in shoot length, root length, and fresh and dry biomass production of Capsicum plants grown under saline conditions. This multi-trait bacterium also increased biosynthesis of proline and up-regulated the expression profiles of stress related genes including CAPIP2, CaKR1, CaOSM1, and CAChi2. On the other hand, B. fortis strain SSB21 inoculated plants exhibited reduced level of ethylene, lipid peroxidation, and reactive oxygen species (ROS). All these together contribute to activate physiological and biochemical processes involved in the mitigation of the salinity induced stress in Capsicum plants.
Kenta Shirasawa - One of the best experts on this subject based on the ideXlab platform.
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Impact of Genomics on Capsicum Breeding
Compendium of Plant Genomes, 2019Co-Authors: Kenta Shirasawa, Noriko Nagata, Toshiya MurakanaAbstract:The genus Capsicum includes several species of cultivated peppers, including Capsicum annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens. Information on plant genomics is essential not only for the efficient and accurate advancement of breeding programs, but also for the correct management of plant genetic resources. Genomes of six Capsicum lines which belong to C. annuum, C. baccatum, and C. chinense have been sequenced using next-generation sequencing (NGS) approaches. Consequently, high-throughput genomewide single-nucleotide polymorphism genotyping techniques based on NGS or DNA microarrays have been developed. Genotyping plant populations enable the evaluation of population structure and detection of genetic loci via quantitative trait locus (QTL) analysis and genomewide association study (GWAS). In this chapter, we introduce the current state of Capsicum genomics and its contribution to Capsicum breeding. Additionally, we report the results of our GWAS based on double-digest restriction-site associated DNA (ddRAD-Seq) analyses performed on 192 Capsicum lines stocked at The Kihara Institute for Biological Research, Yokohama City University, Japan. The genomics information summarized in this chapter will potentially be useful for the development of new and attractive pepper cultivars.
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development of Capsicum est ssr markers for species identification and in silico mapping onto the tomato genome sequence
Molecular Breeding, 2013Co-Authors: Kenta Shirasawa, Noriko Nagata, Kohei Ishii, Munenori Suzuki, Toshiya Muranaka, Megumi Kobayashi, Sachiko Isobe, Satoshi TabataAbstract:Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding.
Gordon Robertson - One of the best experts on this subject based on the ideXlab platform.
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Food Packaging and Shelf Life
Food Packaging and Shelf Life, 2010Co-Authors: Gordon RobertsonAbstract:The effect of modified atmosphere packaging (MAP) along with moisture absorbent was assessed for maintaining quality attributes and extending shelf life of green bell pepper (Capsicum annuum L.) in bulk packages. Under active packaging the quality of Capsicum were based on MAP using permeable polymeric films and sachets of silica gel crystals as moisture absorbents. Pre-designed polypropylene film (38μm) packages were used for storage study under MAP at 8±1°C temperature. The in-pack O2 and CO2 composition and respiration rate in the package headspace was monitored during storage in all the treatments. A modified atmosphere of 4.5% O2, 7.8% CO2 and 4.7% O2, 7.5% CO2 were achieved in the MA packages with and without moisture absorbent, respectively. The active packaging significantly reduced the respiration rate of fruit in the package. These packaged fruits were compared with non-packaged samples, which served as control stored at both ambient conditions (CS) and control at refrigerated temperature (CR). The quality of Capsicums was assessed by physiological weight loss, color (L*, h* and C*) values, firmness, ascorbic acid, decay and marketability. The shelf life of bell pepper was extended to 49 days in active packages, 42 days with MA packages, as compared to 21 days with CR packages and 7 days with CS. Above all, by placing silica crystals sachets in the head space with moisture absorbing ability, could further extend the shelf life of Capsicum 7 days in addition to modified atmosphere packaging alone with 97% fruit marketability.