Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L.
Abstract Background Peanut (Arachis hypogaea L., 2n = 2x = 20) is an important industrial and oil crop that is widely grown in more than 100 countries. In recent years, breeders have focused on increasing the seed number per pod to improve their yield in addition to other breeding for other key comp...
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2025-04-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11560-7 |
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| author | Long Li Shunli Cui Xiukun Li Mingyu Hou Yingru Liu Lifeng Liu |
| author_facet | Long Li Shunli Cui Xiukun Li Mingyu Hou Yingru Liu Lifeng Liu |
| author_sort | Long Li |
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| description | Abstract Background Peanut (Arachis hypogaea L., 2n = 2x = 20) is an important industrial and oil crop that is widely grown in more than 100 countries. In recent years, breeders have focused on increasing the seed number per pod to improve their yield in addition to other breeding for other key components of yield, including the pod number, seeds per pod, and 100-seed weight. Results In this study, a secondary population of 1,114 BC1F2 lines was derived from a cross between the parents R45 and JNH3. Two stable major-effect quantitative trait loci of qRMPA09.1 and qRMPA09.2 were detected simultaneously and mapped within chromosomal intervals of approximately 400 Kb and 600 Kb on chromosome A09. Additionally, combined whole-genome and RNA sequencing analyses showed the differential expression of the Arahy.04JNDX gene that belongs to a MYB transcription factor (TF) between the two parents. The AhMYB51 gene was also inferred to influence the number of seeds per pod in peanuts. An examination of the backcross lines L2/L4 showed that AhMYB51 increases the rate of multiple pods per plant (RMSP) primarily by affecting brassinosteroids in the flowers, while its overexpression promotes the length of siliques in Arabidopsis thaliana. Conclusions Our findings provide valuable insights for the cloning of favorable alleles for RMSP in peanuts. The qRMSPA09.1 and qRMSPA09.2 are two novel QTL associated with the RMSP trait, with AhMYB51 predicted as its candidate gene. Moreover, the closely linked polymorphic SNP markers for loci of two significant QTLs may be useful in accelerating marker-assisted breeding in peanuts. |
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| institution | DOAJ |
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| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-c9941a269d7b4479a69aa3091ac8757e2025-08-20T03:18:38ZengBMCBMC Genomics1471-21642025-04-0126111310.1186/s12864-025-11560-7Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L.Long Li0Shunli Cui1Xiukun Li2Mingyu Hou3Yingru Liu4Lifeng Liu5College of Agronomy, State Key Laboratory of North China for Crop Improvement and Regulation/Key laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural UniversityCollege of Agronomy, State Key Laboratory of North China for Crop Improvement and Regulation/Key laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural UniversityCollege of Agronomy, State Key Laboratory of North China for Crop Improvement and Regulation/Key laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural UniversityCollege of Agronomy, State Key Laboratory of North China for Crop Improvement and Regulation/Key laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural UniversityCollege of Agronomy, State Key Laboratory of North China for Crop Improvement and Regulation/Key laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural UniversityCollege of Agronomy, State Key Laboratory of North China for Crop Improvement and Regulation/Key laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural UniversityAbstract Background Peanut (Arachis hypogaea L., 2n = 2x = 20) is an important industrial and oil crop that is widely grown in more than 100 countries. In recent years, breeders have focused on increasing the seed number per pod to improve their yield in addition to other breeding for other key components of yield, including the pod number, seeds per pod, and 100-seed weight. Results In this study, a secondary population of 1,114 BC1F2 lines was derived from a cross between the parents R45 and JNH3. Two stable major-effect quantitative trait loci of qRMPA09.1 and qRMPA09.2 were detected simultaneously and mapped within chromosomal intervals of approximately 400 Kb and 600 Kb on chromosome A09. Additionally, combined whole-genome and RNA sequencing analyses showed the differential expression of the Arahy.04JNDX gene that belongs to a MYB transcription factor (TF) between the two parents. The AhMYB51 gene was also inferred to influence the number of seeds per pod in peanuts. An examination of the backcross lines L2/L4 showed that AhMYB51 increases the rate of multiple pods per plant (RMSP) primarily by affecting brassinosteroids in the flowers, while its overexpression promotes the length of siliques in Arabidopsis thaliana. Conclusions Our findings provide valuable insights for the cloning of favorable alleles for RMSP in peanuts. The qRMSPA09.1 and qRMSPA09.2 are two novel QTL associated with the RMSP trait, with AhMYB51 predicted as its candidate gene. Moreover, the closely linked polymorphic SNP markers for loci of two significant QTLs may be useful in accelerating marker-assisted breeding in peanuts.https://doi.org/10.1186/s12864-025-11560-7AhMYB51MYB transcription factorBulked Segregant analysisPeanut seeds per pod |
| spellingShingle | Long Li Shunli Cui Xiukun Li Mingyu Hou Yingru Liu Lifeng Liu Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. BMC Genomics AhMYB51 MYB transcription factor Bulked Segregant analysis Peanut seeds per pod |
| title | Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. |
| title_full | Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. |
| title_fullStr | Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. |
| title_full_unstemmed | Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. |
| title_short | Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. |
| title_sort | fine mapping and candidate gene analysis of major qtls for number of seeds per pod in arachis hypogaea l |
| topic | AhMYB51 MYB transcription factor Bulked Segregant analysis Peanut seeds per pod |
| url | https://doi.org/10.1186/s12864-025-11560-7 |
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