Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant
High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F<sub>2</sub> plants from an interspecific cross (<i>Solanum melongena</i> × <i>S. incanum</i...
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MDPI AG
2022-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/18/10258 |
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| author | Wenxiang Guan Changjiao Ke Weiqi Tang Jialong Jiang Jing Xia Xiaofang Xie Mei Yang Chenfeng Duan Weiren Wu Yan Zheng |
| author_facet | Wenxiang Guan Changjiao Ke Weiqi Tang Jialong Jiang Jing Xia Xiaofang Xie Mei Yang Chenfeng Duan Weiren Wu Yan Zheng |
| author_sort | Wenxiang Guan |
| collection | DOAJ |
| description | High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F<sub>2</sub> plants from an interspecific cross (<i>Solanum melongena</i> × <i>S. incanum</i>) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F<sub>2:3</sub> lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL. |
| first_indexed | 2024-03-09T23:48:18Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:48:18Z |
| publishDate | 2022-09-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-038637e52ca840f1803c6bd798c817942023-11-23T16:38:37ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123181025810.3390/ijms231810258Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in EggplantWenxiang Guan0Changjiao Ke1Weiqi Tang2Jialong Jiang3Jing Xia4Xiaofang Xie5Mei Yang6Chenfeng Duan7Weiren Wu8Yan Zheng9Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaMarine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaHigh-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F<sub>2</sub> plants from an interspecific cross (<i>Solanum melongena</i> × <i>S. incanum</i>) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F<sub>2:3</sub> lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.https://www.mdpi.com/1422-0067/23/18/10258eggplantrecombination bin-based genetic mapanthocyanin pigmentationQTL mapping |
| spellingShingle | Wenxiang Guan Changjiao Ke Weiqi Tang Jialong Jiang Jing Xia Xiaofang Xie Mei Yang Chenfeng Duan Weiren Wu Yan Zheng Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant International Journal of Molecular Sciences eggplant recombination bin-based genetic map anthocyanin pigmentation QTL mapping |
| title | Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant |
| title_full | Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant |
| title_fullStr | Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant |
| title_full_unstemmed | Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant |
| title_short | Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant |
| title_sort | construction of a high density recombination bin based genetic map facilitates high resolution mapping of a major qtl underlying anthocyanin pigmentation in eggplant |
| topic | eggplant recombination bin-based genetic map anthocyanin pigmentation QTL mapping |
| url | https://www.mdpi.com/1422-0067/23/18/10258 |
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