Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis
The recognition of pollen and pistil in the self-incompatibility process is generally determined by the interaction between the pollen <i>S</i> gene and pistil <i>S</i> gene located at the S locus. However, the regulatory mechanism of self-incompatibility in goji remains unkn...
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MDPI AG
2024-02-01
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| author | Cuiping Wang Jiali Wu Yan Gao Guoli Dai Xiaohui Shang Haijun Ma Xin Zhang Wendi Xu Ken Qin |
| author_facet | Cuiping Wang Jiali Wu Yan Gao Guoli Dai Xiaohui Shang Haijun Ma Xin Zhang Wendi Xu Ken Qin |
| author_sort | Cuiping Wang |
| collection | DOAJ |
| description | The recognition of pollen and pistil in the self-incompatibility process is generally determined by the interaction between the pollen <i>S</i> gene and pistil <i>S</i> gene located at the S locus. However, the regulatory mechanism of self-incompatibility in goji remains unknown. In this study, we used the self-compatible strain ‘13–19’ and self-incompatible strain ‘xin9’ from Ningxia as parents to create an F1 hybrid population. Reciprocal cross-pollination was performed within the same plant to evaluate the self-compatibility of the parents and F1 progeny. The parents and progeny were subjected to whole-genome resequencing, and mixed pools of DNA were constructed using 30 self-compatible and 30 self-incompatible individuals. Association analysis using the SNP-index method and Euclidean distance was employed to identify the key candidate region of the S locus. The candidate region was further annotated using the Swiss-Prot database to identify genes within the region. Additionally, transcriptome sequencing data from different organs/tissues, as well as from pistils of self-compatible and self-incompatible strains at control (0 h), short (0.5 h), medium (8 h), and long (48 h) time points after self-pollination and cross-pollination, were analyzed to assess differential gene expression and screen for self-compatibility-related loci. Specific primers were designed for PCR amplification to determine the S-RNase genotypes of the extreme parents. The results revealed that the S locus in goji is located within a 32.2 Mb region on chromosome 2 that contains a total of 108 annotated genes. Differential expression analysis showed that ten genes, including Lba02g01064, were specifically expressed in stamens, with four of them annotated as <i>F-box</i> genes, potentially serving as determinants of self-compatibility in stamens. Lba02g01102 was exclusively expressed in pistils and annotated as an <i>S-RNase</i> gene, likely involved in self-compatibility. The expression of Lba02g01102 in pistils decreased after self-pollination and cross-pollination. Six candidate genes exhibited significant changes after self-pollination and cross-pollination. Both parents and progeny carried two S-RNase alleles, and the <i>S-RNase</i> genotypes showed a significant correlation with self-compatibility, with the self-compatible progeny containing the <i>S8-RNase</i> allele. The identification of the S locus in goji provides molecular markers for future marker-assisted breeding and offers genetic resources for studying the mechanism of self-incompatibility in goji, thus contributing to the improvement of goji varieties. |
| first_indexed | 2024-03-07T22:30:39Z |
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| spelling | doaj.art-7b1a4422aa414a7181ca4e6bb34699ad2024-02-23T15:18:51ZengMDPI AGHorticulturae2311-75242024-02-0110219010.3390/horticulturae10020190Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA AnalysisCuiping Wang0Jiali Wu1Yan Gao2Guoli Dai3Xiaohui Shang4Haijun Ma5Xin Zhang6Wendi Xu7Ken Qin8School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, ChinaSchool of Biological Science and Engineering, North Minzu University, Yinchuan 750021, ChinaInstitute of Goji, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750004, ChinaInstitute of Goji, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750004, ChinaSchool of Biological Science and Engineering, North Minzu University, Yinchuan 750021, ChinaSchool of Biological Science and Engineering, North Minzu University, Yinchuan 750021, ChinaSchool of Biological Science and Engineering, North Minzu University, Yinchuan 750021, ChinaSchool of Biological Science and Engineering, North Minzu University, Yinchuan 750021, ChinaInstitute of Goji, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750004, ChinaThe recognition of pollen and pistil in the self-incompatibility process is generally determined by the interaction between the pollen <i>S</i> gene and pistil <i>S</i> gene located at the S locus. However, the regulatory mechanism of self-incompatibility in goji remains unknown. In this study, we used the self-compatible strain ‘13–19’ and self-incompatible strain ‘xin9’ from Ningxia as parents to create an F1 hybrid population. Reciprocal cross-pollination was performed within the same plant to evaluate the self-compatibility of the parents and F1 progeny. The parents and progeny were subjected to whole-genome resequencing, and mixed pools of DNA were constructed using 30 self-compatible and 30 self-incompatible individuals. Association analysis using the SNP-index method and Euclidean distance was employed to identify the key candidate region of the S locus. The candidate region was further annotated using the Swiss-Prot database to identify genes within the region. Additionally, transcriptome sequencing data from different organs/tissues, as well as from pistils of self-compatible and self-incompatible strains at control (0 h), short (0.5 h), medium (8 h), and long (48 h) time points after self-pollination and cross-pollination, were analyzed to assess differential gene expression and screen for self-compatibility-related loci. Specific primers were designed for PCR amplification to determine the S-RNase genotypes of the extreme parents. The results revealed that the S locus in goji is located within a 32.2 Mb region on chromosome 2 that contains a total of 108 annotated genes. Differential expression analysis showed that ten genes, including Lba02g01064, were specifically expressed in stamens, with four of them annotated as <i>F-box</i> genes, potentially serving as determinants of self-compatibility in stamens. Lba02g01102 was exclusively expressed in pistils and annotated as an <i>S-RNase</i> gene, likely involved in self-compatibility. The expression of Lba02g01102 in pistils decreased after self-pollination and cross-pollination. Six candidate genes exhibited significant changes after self-pollination and cross-pollination. Both parents and progeny carried two S-RNase alleles, and the <i>S-RNase</i> genotypes showed a significant correlation with self-compatibility, with the self-compatible progeny containing the <i>S8-RNase</i> allele. The identification of the S locus in goji provides molecular markers for future marker-assisted breeding and offers genetic resources for studying the mechanism of self-incompatibility in goji, thus contributing to the improvement of goji varieties.https://www.mdpi.com/2311-7524/10/2/190<i>Lycium barbarum</i>self-incompatibilityS locusbulked segregant analysis |
| spellingShingle | Cuiping Wang Jiali Wu Yan Gao Guoli Dai Xiaohui Shang Haijun Ma Xin Zhang Wendi Xu Ken Qin Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis Horticulturae <i>Lycium barbarum</i> self-incompatibility S locus bulked segregant analysis |
| title | Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis |
| title_full | Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis |
| title_fullStr | Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis |
| title_full_unstemmed | Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis |
| title_short | Localization of S-Locus-Related Self-Incompatibility in <i>Lycium barbarum</i> Based on BSA Analysis |
| title_sort | localization of s locus related self incompatibility in i lycium barbarum i based on bsa analysis |
| topic | <i>Lycium barbarum</i> self-incompatibility S locus bulked segregant analysis |
| url | https://www.mdpi.com/2311-7524/10/2/190 |
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