Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis
Abstract Background Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. Res...
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BMC
2024-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10005-x |
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| author | Hongfei Liu Zheng Zheng Ziqi Sun Feiyan Qi Juan Wang Mengmeng Wang Wenzhao Dong Kailu Cui Mingbo Zhao Xiao Wang Meng Zhang Xiaohui Wu Yue Wu Dandan Luo Bingyan Huang Zhongxin Zhang Gangqiang Cao Xinyou Zhang |
| author_facet | Hongfei Liu Zheng Zheng Ziqi Sun Feiyan Qi Juan Wang Mengmeng Wang Wenzhao Dong Kailu Cui Mingbo Zhao Xiao Wang Meng Zhang Xiaohui Wu Yue Wu Dandan Luo Bingyan Huang Zhongxin Zhang Gangqiang Cao Xinyou Zhang |
| author_sort | Hongfei Liu |
| collection | DOAJ |
| description | Abstract Background Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. Results An F2 segregating population derived from a cross between the thick-shelled cultivar Yueyou 18 (YY18) and the thin-shelled cultivar Weihua 8 (WH8) was used to identify the quantitative trait loci (QTLs) for PST. On the basis of a bulked segregant analysis sequencing (BSA-seq), four QTLs were preliminarily mapped to chromosomes 3, 8, 13, and 18. Using the genome resequencing data of YY18 and WH8, 22 kompetitive allele-specific PCR (KASP) markers were designed for the genotyping of the F2 population. Two major QTLs (qPSTA08 and qPSTA18) were identified and finely mapped, with qPSTA08 detected on chromosome 8 (0.69-Mb physical genomic region) and qPSTA18 detected on chromosome 18 (0.15-Mb physical genomic region). Moreover, qPSTA08 and qPSTA18 explained 31.1–32.3% and 16.7–16.8% of the phenotypic variation, respectively. Fifteen genes were detected in the two candidate regions, including three genes with nonsynonymous mutations in the exon region. Two molecular markers (Tif2_A08_31713024 and Tif2_A18_7198124) that were developed for the two major QTL regions effectively distinguished between thick-shelled and thin-shelled materials. Subsequently, the two markers were validated in four F2:3 lines selected. Conclusions The QTLs identified and molecular markers developed in this study may lay the foundation for breeding cultivars with a shell thickness suitable for mechanized peanut shelling. |
| first_indexed | 2024-03-08T12:40:29Z |
| format | Article |
| id | doaj.art-82cf506ef6a7442187699bd75a1807ae |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T12:40:29Z |
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| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-82cf506ef6a7442187699bd75a1807ae2024-01-21T12:11:41ZengBMCBMC Genomics1471-21642024-01-0125111210.1186/s12864-024-10005-xIdentification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysisHongfei Liu0Zheng Zheng1Ziqi Sun2Feiyan Qi3Juan Wang4Mengmeng Wang5Wenzhao Dong6Kailu Cui7Mingbo Zhao8Xiao Wang9Meng Zhang10Xiaohui Wu11Yue Wu12Dandan Luo13Bingyan Huang14Zhongxin Zhang15Gangqiang Cao16Xinyou Zhang17Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureSchool of Life Sciences, Zhengzhou UniversityInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureSchool of Life Sciences, Zhengzhou UniversitySchool of Life Sciences, Zhengzhou UniversityInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureSchool of Agricultural Sciences, Zhengzhou UniversityInstitute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of AgricultureAbstract Background Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. Results An F2 segregating population derived from a cross between the thick-shelled cultivar Yueyou 18 (YY18) and the thin-shelled cultivar Weihua 8 (WH8) was used to identify the quantitative trait loci (QTLs) for PST. On the basis of a bulked segregant analysis sequencing (BSA-seq), four QTLs were preliminarily mapped to chromosomes 3, 8, 13, and 18. Using the genome resequencing data of YY18 and WH8, 22 kompetitive allele-specific PCR (KASP) markers were designed for the genotyping of the F2 population. Two major QTLs (qPSTA08 and qPSTA18) were identified and finely mapped, with qPSTA08 detected on chromosome 8 (0.69-Mb physical genomic region) and qPSTA18 detected on chromosome 18 (0.15-Mb physical genomic region). Moreover, qPSTA08 and qPSTA18 explained 31.1–32.3% and 16.7–16.8% of the phenotypic variation, respectively. Fifteen genes were detected in the two candidate regions, including three genes with nonsynonymous mutations in the exon region. Two molecular markers (Tif2_A08_31713024 and Tif2_A18_7198124) that were developed for the two major QTL regions effectively distinguished between thick-shelled and thin-shelled materials. Subsequently, the two markers were validated in four F2:3 lines selected. Conclusions The QTLs identified and molecular markers developed in this study may lay the foundation for breeding cultivars with a shell thickness suitable for mechanized peanut shelling.https://doi.org/10.1186/s12864-024-10005-xPeanutPod shell thickness (PST)Bulked sergeant analysis sequencing (BSA-seq)Quantitative trait locus (QTL)Kompetitive allele-specific PCR (KASP)Fine mapping |
| spellingShingle | Hongfei Liu Zheng Zheng Ziqi Sun Feiyan Qi Juan Wang Mengmeng Wang Wenzhao Dong Kailu Cui Mingbo Zhao Xiao Wang Meng Zhang Xiaohui Wu Yue Wu Dandan Luo Bingyan Huang Zhongxin Zhang Gangqiang Cao Xinyou Zhang Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis BMC Genomics Peanut Pod shell thickness (PST) Bulked sergeant analysis sequencing (BSA-seq) Quantitative trait locus (QTL) Kompetitive allele-specific PCR (KASP) Fine mapping |
| title | Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis |
| title_full | Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis |
| title_fullStr | Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis |
| title_full_unstemmed | Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis |
| title_short | Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis |
| title_sort | identification of two major qtls for pod shell thickness in peanut arachis hypogaea l using bsa seq analysis |
| topic | Peanut Pod shell thickness (PST) Bulked sergeant analysis sequencing (BSA-seq) Quantitative trait locus (QTL) Kompetitive allele-specific PCR (KASP) Fine mapping |
| url | https://doi.org/10.1186/s12864-024-10005-x |
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