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Genes
Special Issues
Pepper Genetic Breeding and Germplasm Innovation
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Pepper Genetic Breeding and Germplasm Innovation

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 20 August 2024 | Viewed by 960

Special Issue Editors

Dr. Hailong Yu

E-Mail Website
Guest Editor
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: Capsicum spp.; genetics and genomics; marker-assisted selection, gene/QTL mapping; virus resistance
Dr. Yacong Cao

E-Mail Website
Guest Editor
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: Capsicum spp.; genetics and genomics; marker-assisted selection, gene/QTL mapping; germplasm
Dr. Zhenghai Zhang

E-Mail Website
Guest Editor
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: Capsicum spp.; marker-assisted selection; gene mapping; male sterile and fertility

Special Issue Information

Dear Colleagues,

Pepper (Capsicum spp.) was domesticated in the Americas around 6,000 years ago and has since spread worldwide. In recent years, the traditional breeding methods of pepper have struggled to achieve the complex breeding goals of multi-objective and mostly quantitative traits. With the rapid development of sequencing technology, molecular biology and bioinformatics, and pepper genomics research, molecular breeding technology and a series of molecular markers have been developed. At present, the transcriptome and pan-genome database of Capsicum has been constructed, and the breeding efficiency of pepper has been improved mainly through the construction of molecular genetic maps, molecular markers for quality traits, QTL analysis for quantitative traits, molecular marker-assisted selection and whole genomic selection. In addition, the application of advanced biotechnologies, such as CRISPR/Cas genome-editing tools, enables for an oriented improvement of breeding lines. Together, the sequencing technologies or new breeding techniques (e.g., gene editing) provide exciting opportunities for efficient pepper breeding programs.

This Special Issue, titled “Pepper Genetic Breeding and Germplasm Innovation”, invites all aspects of pepper genetic breeding and germplasm innovation, such as mapping/cloning of important genes, marker-assisted breeding, application of biotechnology tools in pepper, genetic resources of pepper, germplasm innovation of pepper and so on. All types of articles are welcome, including reviews, research and opinion articles.

Dr. Hailong Yu
Dr. Yacong Cao
Dr. Zhenghai Zhang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Capsicum
  • genetics
  • genomics
  • molecular marker-assisted selection
  • multiomics
  • gene/QTL mapping
  • genome-wide association studies
  • germplasm innovation

Published Papers (1 paper)

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Research

14 pages, 3586 KiB  
Article
Optimized Pepper Target SNP-Seq Applied in Population Structure and Genetic Diversity Analysis of 496 Pepper (Capsicum spp.) Lines
by Yihao Wang, Xiaofen Zhang, Jingjing Yang, Bin Chen, Jian Zhang, Wenyue Li, Heshan Du and Sansheng Geng
Genes 2024, 15(2), 214; https://doi.org/10.3390/genes15020214 - 07 Feb 2024
Viewed by 781
Abstract
Peppers are a major vegetable crop worldwide. With the completion of additional genome assemblies, a multitude of single-nucleotide polymorphisms (SNPs) can be utilized for population structure and genetic diversity analysis. In this study, we used target SNP-sequencing as a new high-throughput sequencing technology, [...] Read more.
Peppers are a major vegetable crop worldwide. With the completion of additional genome assemblies, a multitude of single-nucleotide polymorphisms (SNPs) can be utilized for population structure and genetic diversity analysis. In this study, we used target SNP-sequencing as a new high-throughput sequencing technology, screening out 425 perfect SNPs for analyzing the genetic diversity and population structure among 496 pepper lines from five pepper species in China and abroad. The perfect SNP panel exhibited commendable discriminative ability, as indicated by the average values of polymorphism information content, observed heterozygosity, minor allele frequency, and genetic diversity, which were 0.346, 0.011, 0.371, and 0.449, respectively. Based on phylogenetic, population structure, and principal component analyses, 484 C. annuum lines were divided into four subpopulations according to the shape of fruit: blocky fruit, wide-horn fruit, narrow-horn fruit, and linear fruit. These subpopulations displayed clear clustering with minimal or no overlap. Moreover, F statistic (Fst) analysis revealed considerable distinctions among these subpopulations. Additionally, we established a set of 47 core SNPs that could effectively differentiate among all pepper lines. This core SNP set could precisely classify the C. annuum lines into four distinct fruit-shape groups. The blocky and narrow-horn fruit subpopulations displayed the lowest and highest genetic diversity, respectively. This study highlights the importance of fruit shape as a crucial trait in pepper breeding. Moreover, this work indicates the immense potential of optimized target SNP technology in the addition of foreground markers of important traits to improve molecular breeding efficiency, and demonstrates its broad application prospects in the genetic analysis and variety identification of peppers. Full article
(This article belongs to the Special Issue Pepper Genetic Breeding and Germplasm Innovation)
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