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Exploring horticultural traits and disease resistance in Capsicum baccatum through segmental introgression lines

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Abstract

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Segmental introgression and advanced backcross lines were developed and validated as important tools for improving agronomically important traits in pepper, offering improved sensitivity in detecting quantitative trait loci for breeding.

Abstract

Segmental introgression lines (SILs) and advanced backcross lines (ABs) can accelerate genetics and genomics research and breeding in crop plants. This study presents the development of a complete collection of SILs and ABs in pepper using Capsicum annuum cv. ‘CM334’ as the recipient parent and Capsicum baccatum ‘PBC81’, which displays various agronomically important traits including powdery mildew and anthracnose resistance, as donor parent. Using embryo rescue to overcome abortion in interspecific crosses, and marker-assisted selection with genoty**-in-thousands by sequencing (GT-seq) to develop SILs and ABs containing different segments of the C. baccatum genome, we obtained 63 SILs and 44 ABs, covering 94.8% of the C. baccatum genome. We characterized them for traits including powdery mildew resistance, anthracnose resistance, anthocyanin accumulation, trichome density, plant architecture, and fruit morphology. We validated previously known loci for these traits and discovered new sources of variation and quantitative trait loci (QTLs). A total of 15 QTLs were identified, including four for anthracnose resistance with three novel loci, seven for plant architecture, and four for fruit morphology. This is the first complete collection of pepper SILs and ABs validated for agronomic traits and will enhance QTL detection and serve as valuable breeding resources. Further, these SILs and ABs will be useful for comparative genomics and to better understand the genetic mechanisms underlying important agronomic traits in pepper, ultimately leading to improved crop productivity and sustainability.

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Data supporting the results are provided in this article and its supplementary materials. Additionally, the corresponding author can provide other relevant materials upon reasonable request.

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Acknowledgements

This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through Digital Breeding Transformation Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (322062-3) and Institute of Information & communications Technology Planning & Evaluation (IITP) grant funded by the Korea government (MSIT) (No. RS-2023-00227464, Development of new varieties breeding technology with AI for strengthening food sovereignty).

Funding

This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through Digital Breeding Transformation Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (322062-3) and Institute of Information & communications Technology Planning & Evaluation (IITP) grant funded by the Korea government (MSIT) (No. RS-2023-00227464, Development ofnew varieties breeding technology with AI for strengthening food sovereignty).

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Authors and Affiliations

  1. Department of Agriculture, Forestry, and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea

    **kwan Jo, Geon Woo Kim, Seungki Back, Siyoung Jang, Youngin Kim, Hayoung Choi, Seyoung Lee, **-Kyung Kwon & Byoung-Cheorl Kang

  2. Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, Jeonbuk, South Korea

    Koeun Han

  3. HANA SEED, Anseong, Gyeonggi, South Korea

    Yong-Jik Lee

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  1. **kwan Jo
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  2. Geon Woo Kim
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  3. Seungki Back
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Contributions

JJ and B-CK designed the study. JJ and IJ performed the interspecific cross and embryo rescue. SY and KH constructed the GBS library. JJ, SB, and YK performed genoty** and generation advancement. JJ analyzed the sequencing data analysis and QTLs. Y-JL performed disease inoculation. JJ, GWK, and SL participated in phenoty**. JJ and GWK visualized the analyzed data. JJ and HC developed markers. JJ and B-CK drafted the manuscript. JJ, J-KK, DC, and B-CK revised the manuscript. All authors read and approved the final version of the manuscript.

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Correspondence to Byoung-Cheorl Kang.

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122_2023_4422_MOESM1_ESM.pdf

Fig. S1. Measurement of 30 fruit-morphology traits using Tomato Analyzer version 4.0, and five plant-architecture traits. (A) View of Tomato Analyzer. The separated pedicel and fruit body were recognized by yellow edge line. (B) Graphical examples of the measurement method using the program. The unit of the scoring method is described in Table S2. (C) Illustration of plant architecture. (PDF 174 KB)

122_2023_4422_MOESM2_ESM.pdf

Fig. S2. Plant-architecture and fruit-morphology traits showing differences between parental lines. (A–B) Plant-architecture traits (A) Plant height (cm). (B) Branch angle (∠, °). (C–O) Fruit-morphology traits. (C) Fruit weight (g). (D) Perimeter (cm). (E) Area (cm2). (F) Width at mid-height (cm). (G) Maximum width (cm). (H) Height at mid-width (cm). (I) Maximum height (cm). (J) Curved height (cm). (K) Proximal fruit blockiness (ratio). (L) Proximal angle macro (∠, °). (M) Distal angle macro (∠, °). (N) Ovoid (ratio). (O) Width widest pos (ratio). The unit of the scoring method is described in Table S2. (PDF 131 KB)

122_2023_4422_MOESM3_ESM.pdf

Fig. S3. Procedure for embryo rescue following an interspecific cross between C. baccatum ‘PBC81’ and C. annuum ‘CM334’. (A) Fruits of the interspecific crosses. (B) F1 hybrid immature seed. (C) Rescued embryo at the torpedo stage. (D) Five days after the embryo rescue. (E) 10 days after the embryo rescue. (F) 16 days after the embryo rescue. (G, H) Acclimatization of F1 plants. (I) Genotype analysis of F1 hybrids and parents using the modified ZL1-1826 primers. (J) Phenotype of F1 plants. White scale bar indicates 1 m. (PDF 1160 KB)

122_2023_4422_MOESM4_ESM.pdf

Fig. S4. Phenotypic evaluation of anthocyanin accumulation and trichome density of the SILs and ABs. (A) The absence and presence of anthocyanin on the anthers and petals, and yellow corolla spots on the petals, denoted as either 1 or 9. (B) Anthocyanin intensity phenotypes at the nodes. Intensity increases from left to right, and is divided into five categories (1, 3, 5, 7, and 9). (C) Trichome density increases from left to right, and is also divided into five categories (1 to 9). (PDF 370 KB)

122_2023_4422_MOESM5_ESM.pdf

Fig. S5. Phenotypic distribution of anthocyanin accumulation and trichome density of the SILs and ABs. (A) Anther color distribution. (B) Petal tip color distribution. (C) Anthocyanin intensity phenotypes of the nodes. (D) Trichome density distribution. Blue indicates ‘PBC81’; red indicates ‘CM334’. (PDF 26 KB)

122_2023_4422_MOESM6_ESM.pdf

Fig. S6. Phenotypic analysis of disease resistance. (A) Powdery mildew resistance on the leaf. (B) Anthracnose resistance in the green and mature red fruits. (PDF 178 KB)

122_2023_4422_MOESM7_ESM.pdf

Fig. S7. Phenotypic distribution of disease resistance. (A) Powdery mildew resistance. (B) Anthracnose resistance for green fruit. (C) Anthracnose resistance for mature red fruit. Blue indicates ‘PBC81’; red indicates ‘CM334’. (PDF 26 KB)

122_2023_4422_MOESM8_ESM.pdf

Fig. S8. Genotypic analysis of the SILs, ABs, and parental lines using the Ptel1-flanking Tsca dominant marker. (PDF 29 KB)

Fig. S9. QTLs for corolla yellow spot. (PDF 44 KB)

Supplementary file10 (XLSX 438 KB)

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Jo, J., Kim, G.W., Back, S. et al. Exploring horticultural traits and disease resistance in Capsicum baccatum through segmental introgression lines. Theor Appl Genet 136, 233 (2023). https://doi.org/10.1007/s00122-023-04422-x

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