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Yu X, Li Y, Cui X, Wang X, Li J, Guo R, Yan F, Zhang S, Zhao R, Song D, Si T, Zou X, Wang Y, Zhang X. Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:144. [PMID: 37249697 DOI: 10.1007/s00122-023-04385-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
KEY MESSAGE We developed a new method phenotypic recombination BSA/BSR (PR-BSA/BSR), which could simultaneously identify the candidate genomic regions associated with two traits in a segregating population. Bulked segregant analysis sequencing (BSA-seq) has been widely used for identifying the genomic regions affecting a certain trait. In this study, we developed a modified BSA/bulked segregant RNA-sequencing (BSR-seq) method, which we named phenotypic recombination BSA/BSR (PR-BSA/BSR), to simultaneously identify candidate genomic regions associated with two traits in a segregating population. Lateral branch angle (LBA) and flower-branch pattern (FBP) are two important traits associated with the peanut plant architecture because they affect the planting density and light use efficiency. We generated an F6 population (with two segregating traits) derived from a cross between the inbred lines Pingdu9616 (erect and sequential; ES-type) and Florunner (spreading and alternating; SA-type). The selection of bulks with extreme phenotypes was a key step in this study. Specifically, 30 individuals with recombinant phenotypes [i.e., spreading and sequential (SS-type) and erect and alternating (EA-type)] were selected to generate two bulks. The transcriptomes of individuals were sequenced and then the loci related to LBA and FBP were simultaneously detected via a ΔSNP-index strategy, which involved the direction of positive and negative peaks in the ∆SNP-index plot. The LBA-related locus was mapped to a 6.82 Mb region (101,743,223-108,564,267 bp) on chromosome 15, whereas the FBP-related locus was mapped to a 2.16 Mb region (117,682,534-119,846,824 bp) on chromosome 12. Furthermore, the marker-based classical QTL mapping method was used to analyze the PF-F6 population, which confirmed our PR-BSA/BSR results. Therefore, the PR-BSA/BSR method produces accurate and reliable data.
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Affiliation(s)
- Xiaona Yu
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Yaoyao Li
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xinyuan Cui
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xianheng Wang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Jihua Li
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Rui Guo
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Fanzhuang Yan
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Shaojing Zhang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Ruihua Zhao
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Danlei Song
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Tong Si
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xiaoxia Zou
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Yuefu Wang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xiaojun Zhang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
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Chen M, Li M, Zhao L, Song H. Deciphering evolutionary dynamics of WRKY genes in Arachis species. BMC Genomics 2023; 24:48. [PMID: 36707767 PMCID: PMC9881300 DOI: 10.1186/s12864-023-09149-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea), a progeny of the cross between A. duranensis and A. ipaensis, is an important oil and protein crop from South America. To date, at least six Arachis genomes have been sequenced. WRKY transcription factors (TFs) play crucial roles in plant growth, development, and response to abiotic and biotic stresses. WRKY TFs have been identified in A. duranensis, A. ipaensis, and A. hypogaea cv. Tifrunner; however, variations in their number and evolutionary patterns across various Arachis spp. remain unclear. RESULTS WRKY TFs were identified and compared across different Arachis species, including A. duranensis, A. ipaensis, A. monticola, A. hypogaea cultivars (cv.) Fuhuasheng, A. hypogaea cv. Shitouqi, and A. hypogaea cv. Tifrunner. The results showed that the WRKY TFs underwent dynamic equilibrium between diploid and tetraploid peanut species, characterized by the loss of old WRKY TFs and retention of the new ones. Notably, cultivated peanuts inherited more conserved WRKY orthologs from wild tetraploid peanuts than their wild diploid donors. Analysis of the W-box elements and protein-protein interactions revealed that different domestication processes affected WRKY evolution across cultivated peanut varieties. WRKY TFs of A. hypogaea cv. Fuhuasheng and Shitouqi exhibited a similar domestication process, while those of cv. Tifrunner of the same species underwent a different domestication process based on protein-protein interaction analysis. CONCLUSIONS This study provides new insights into the evolution of WRKY TFs in Arachis spp.
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Affiliation(s)
- Mingwei Chen
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Meiran Li
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Longgang Zhao
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
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Zhong C, Li Z, Cheng Y, Zhang H, Liu Y, Wang X, Jiang C, Zhao X, Zhao S, Wang J, Zhang H, Liu X, Yu H. Comparative Genomic and Expression Analysis Insight into Evolutionary Characteristics of PEBP Genes in Cultivated Peanuts and Their Roles in Floral Induction. Int J Mol Sci 2022; 23:ijms232012429. [PMID: 36293287 PMCID: PMC9604132 DOI: 10.3390/ijms232012429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/20/2022] Open
Abstract
Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in regulating flowering time and various developmental processes. Functions and expression patterns in cultivated peanuts (Arachis hypogaea L.) remain unknown. In this study, 33 PEBP genes in cultivated peanuts were identified and divided into four subgroups: FT, TFL, MFT and FT-like. Gene structure analysis showed that orthologs from A and B genomes in cultivated peanuts had highly similar structures, but some orthologous genes have subgenomic dominance. Gene collinearity and phylogenetic analysis explain that some PEBP genes play key roles in evolution. Cis-element analysis revealed that PEBP genes are mainly regulated by hormones, light signals and stress-related pathways. Multiple PEPB genes had different expression patterns between early and late-flowering genotypes. Further detection of its response to temperature and photoperiod revealed that PEBPs ArahyM2THPA, ArahyEM6VH3, Arahy4GAQ4U, ArahyIZ8FG5, ArahyG6F3P2, ArahyLUT2QN, ArahyDYRS20 and ArahyBBG51B were the key genes controlling the flowering response to different flowering time genotypes, photoperiods and temperature. This study laid the foundation for the functional study of the PEBP gene in cultivated peanuts and the adaptation of peanuts to different environments.
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