Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.)
Abstract Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09568-y |
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| author | Yuanjin Fang Hua Liu Li Qin Feiyan Qi Ziqi Sun Jihua Wu Wenzhao Dong Bingyan Huang Xinyou Zhang |
| author_facet | Yuanjin Fang Hua Liu Li Qin Feiyan Qi Ziqi Sun Jihua Wu Wenzhao Dong Bingyan Huang Xinyou Zhang |
| author_sort | Yuanjin Fang |
| collection | DOAJ |
| description | Abstract Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components of peanut yield, would facilitate high-yield breeding. A high-density single nucleotide polymorphism (SNP)-based linkage map was constructed using a recombinant inbred lines (RIL) population derived from a cross between the variety Yuanza9102 and a germplasm accession wt09-0023. Kernel weight and size quantitative trait loci (QTLs) were co-localized to a 0.16 Mb interval on Arahy07 using inclusive composite interval mapping (ICIM). Analysis of SNP, and Insertion or Deletion (INDEL) markers in the QTL interval revealed a gene encoding a pentatricopeptide repeat (PPR) superfamily protein as a candidate closely linked with kernel weight and size in cultivated peanut. Examination of the PPR gene family indicated a high degree of collinearity of PPR genes between A. hypogaea and its diploid progenitors, Arachis duranensis and Arachis ipaensis. The candidate PPR gene, Arahy.JX1V6X, displayed a constitutive expression pattern in developing seeds. These findings lay a foundation for further fine mapping of QTLs related to kernel weight and size, as well as validation of candidate genes in cultivated peanut. |
| first_indexed | 2024-03-09T15:27:14Z |
| format | Article |
| id | doaj.art-6f56d16d42204dd0830e949f7cc9247e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:27:14Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6f56d16d42204dd0830e949f7cc9247e2023-11-26T12:25:55ZengBMCBMC Genomics1471-21642023-08-0124111010.1186/s12864-023-09568-yIdentification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.)Yuanjin Fang0Hua Liu1Li Qin2Feiyan Qi3Ziqi Sun4Jihua Wu5Wenzhao Dong6Bingyan Huang7Xinyou Zhang8College of Agriculture, Nanjing Agricultural UniversityHenan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops ImprovementHenan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops ImprovementHenan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops ImprovementHenan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops ImprovementShangqiu Academy of Agriculture and ForestryHenan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops ImprovementHenan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops ImprovementCollege of Agriculture, Nanjing Agricultural UniversityAbstract Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components of peanut yield, would facilitate high-yield breeding. A high-density single nucleotide polymorphism (SNP)-based linkage map was constructed using a recombinant inbred lines (RIL) population derived from a cross between the variety Yuanza9102 and a germplasm accession wt09-0023. Kernel weight and size quantitative trait loci (QTLs) were co-localized to a 0.16 Mb interval on Arahy07 using inclusive composite interval mapping (ICIM). Analysis of SNP, and Insertion or Deletion (INDEL) markers in the QTL interval revealed a gene encoding a pentatricopeptide repeat (PPR) superfamily protein as a candidate closely linked with kernel weight and size in cultivated peanut. Examination of the PPR gene family indicated a high degree of collinearity of PPR genes between A. hypogaea and its diploid progenitors, Arachis duranensis and Arachis ipaensis. The candidate PPR gene, Arahy.JX1V6X, displayed a constitutive expression pattern in developing seeds. These findings lay a foundation for further fine mapping of QTLs related to kernel weight and size, as well as validation of candidate genes in cultivated peanut.https://doi.org/10.1186/s12864-023-09568-yPeanut (Arachis hypogaea L.)Kernel weightKernel sizeQTLs (quantitative trait loci)Pentatricopeptide repeat (PPR) |
| spellingShingle | Yuanjin Fang Hua Liu Li Qin Feiyan Qi Ziqi Sun Jihua Wu Wenzhao Dong Bingyan Huang Xinyou Zhang Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.) BMC Genomics Peanut (Arachis hypogaea L.) Kernel weight Kernel size QTLs (quantitative trait loci) Pentatricopeptide repeat (PPR) |
| title | Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.) |
| title_full | Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.) |
| title_fullStr | Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.) |
| title_full_unstemmed | Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.) |
| title_short | Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.) |
| title_sort | identification of qtl for kernel weight and size and analysis of the pentatricopeptide repeat ppr gene family in cultivated peanut arachis hypogaea l |
| topic | Peanut (Arachis hypogaea L.) Kernel weight Kernel size QTLs (quantitative trait loci) Pentatricopeptide repeat (PPR) |
| url | https://doi.org/10.1186/s12864-023-09568-y |
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