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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: closed (20 August 2024) | Viewed by 7623

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

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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

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Published Papers (4 papers)

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Research

14 pages, 2556 KiB  
Article
Conjunctive BSA-Seq and BSR-Seq to Map the Genes of Yellow Leaf Mutations in Hot Peppers (Capsicum annuum L.)
by Guosheng Sun, Changwei Zhang, Xi Shan, Zhenchao Zhang, Wenlong Wang, Wenjun Lu, Zhongliang Dai, Liu E, Yaolong Wang, Zhihu Ma and Xilin Hou
Genes 2024, 15(9), 1115; https://doi.org/10.3390/genes15091115 - 23 Aug 2024
Cited by 2 | Viewed by 996
Abstract
Yellow leaf mutations have been widely used to study the chloroplast structures, the pigment synthesis, the photosynthesis mechanisms and the chlorophyll biosynthesis pathways across various species. For this study, a spontaneous mutant with the yellow leaf color named 96-140YBM was employed to explore [...] Read more.
Yellow leaf mutations have been widely used to study the chloroplast structures, the pigment synthesis, the photosynthesis mechanisms and the chlorophyll biosynthesis pathways across various species. For this study, a spontaneous mutant with the yellow leaf color named 96-140YBM was employed to explore the primary genetic elements that lead to the variations in the leaf color of hot peppers. To identify the pathways and genes associated with yellow leaf phenotypes, we applied sequencing-based Bulked Segregant Analysis (BSA-Seq) combined with BSR-Seq. We identified 4167 differentially expressed genes (DEGs) in the mutant pool compared with the wild-type pool. The results indicated that DEGs were involved in zeatin biosynthesis, plant hormone signal transduction, signal transduction mechanisms, post-translational modification and protein turnover. A total of 437 candidates were identified by the BSA-Seq, while the BSR-Seq pinpointed four candidate regions in chromosomes 8 and 9, containing 222 candidate genes. Additionally, the combination of BSA-Seq and BSR-Seq showed that there were 113 overlapping candidate genes between the two methods, among which 8 common candidates have been previously reported to be related to the development of chloroplasts, the photomorphogenesis and chlorophyll formation of plant chloroplasts and chlorophyll biogenesis. qRT-PCR analysis of the 8 common candidates showed higher expression levels in the mutant pool compared with the wild-type pool. Among the overlapping candidates, the DEG analysis showed that the CaKAS2 and CaMPH2 genes were down-regulated in the mutant pool compared to the wild type, suggesting that these genes may be key contributors to the yellow leaf phenotype of 96-140YBM. This research will deepen our understanding of the genetic basis of leaf color formation and provide valuable information for the breeding of hot peppers with diverse leaf colors. Full article
(This article belongs to the Special Issue Pepper Genetic Breeding and Germplasm Innovation)
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16 pages, 2951 KiB  
Article
Fine Mapping and Candidate Gene Analysis of Two Major Quantitative Trait Loci, qFW2.1 and qFW3.1, Controlling Fruit Weight in Pepper (Capsicum annuum)
by Congcong Guan, Yuan Jin, Zhenghai Zhang, Yacong Cao, Huamao Wu, Daiyuan Zhou, Wenqi Shao, Chuangchuang Yang, Guoliang Ban, Lingling Ma, Xin Wen, Lei Chen, Shanhan Cheng, Qin Deng, Hailong Yu and Lihao Wang
Genes 2024, 15(8), 1097; https://doi.org/10.3390/genes15081097 - 20 Aug 2024
Cited by 1 | Viewed by 1563
Abstract
Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the [...] Read more.
Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, “129−1” (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F2 generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F2 generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC2S2 and BC2S3 populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper. Full article
(This article belongs to the Special Issue Pepper Genetic Breeding and Germplasm Innovation)
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17 pages, 5181 KiB  
Article
Developing an Optimized Protocol for Regeneration and Transformation in Pepper
by Shamsullah Shams, Beenish Naeem, Lingling Ma, Rongxuan Li, Zhenghai Zhang, Yacong Cao, Hailong Yu, Xigang Feng, Yinhui Qiu, Huamao Wu and Lihao Wang
Genes 2024, 15(8), 1018; https://doi.org/10.3390/genes15081018 - 2 Aug 2024
Viewed by 2169
Abstract
Capsicum annuum L. is extensively cultivated in subtropical and temperate regions globally, respectively, when grown in a medium with 8 holding significant economic importance. Despite the availability of genome sequences and editing tools, gene editing in peppers is limited by the lack of [...] Read more.
Capsicum annuum L. is extensively cultivated in subtropical and temperate regions globally, respectively, when grown in a medium with 8 holding significant economic importance. Despite the availability of genome sequences and editing tools, gene editing in peppers is limited by the lack of a stable regeneration and transformation method. This study assessed regeneration and transformation protocols in seven chili pepper varieties, including CM334, Zunla-1, Zhongjiao6 (ZJ6), 0818, 0819, 297, and 348, in order to enhance genetic improvement efforts. Several explants, media compositions, and hormonal combinations were systematically evaluated to optimize the in vitro regeneration process across different chili pepper varieties. The optimal concentrations for shoot formation, shoot elongation, and rooting in regeneration experiments were determined as 5 mg/L of 6-Benzylaminopurine (BAP) with 5 mg/L of silver nitrate (AgNO3), 0.5 mg/L of Gibberellic acid (GA3), and 1 mg/L of Indole-3-butyric acid (IBA), respectively. The highest regeneration rate of 41% was observed from CM334 cotyledon explants. Transformation optimization established 300 mg/L of cefotaxime for bacterial control, with a 72-h co-cultivation period at OD600 = 0.1. This study optimizes the protocols for chili pepper regeneration and transformation, thereby contributing to genetic improvement efforts. Full article
(This article belongs to the Special Issue Pepper Genetic Breeding and Germplasm Innovation)
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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 - 7 Feb 2024
Cited by 3 | Viewed by 2295
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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