Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development
Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection...
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MDPI AG
2024-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/13/23/3281 |
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| author | Fen Zhang Li-Zhen Ling Li-Zhi Gao |
| author_facet | Fen Zhang Li-Zhen Ling Li-Zhi Gao |
| author_sort | Fen Zhang |
| collection | DOAJ |
| description | Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution. |
| format | Article |
| id | doaj-art-e7cc1b4c5ed44b40a4d2edf04d233e96 |
| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-e7cc1b4c5ed44b40a4d2edf04d233e962024-12-13T16:29:46ZengMDPI AGPlants2223-77472024-11-011323328110.3390/plants13233281Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower DevelopmentFen Zhang0Li-Zhen Ling1Li-Zhi Gao2Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, ChinaPlant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, 132, Lanhei Road, Kunming 650204, ChinaEngineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, ChinaAlthough genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations. Conversely, non-neutral evolution of positive and/or artificial selection accelerates the elevated variations at nonconserved binding sites in a population-specific behavior which may have contributed to flower development-related phenotypic variation. Taken together, our results elucidate that miRNA targets involved in flower development are under distinctive selection regimes during rice evolution.https://www.mdpi.com/2223-7747/13/23/3281molecular evolutionsequence polymorphismmicroRNA binding siteflower development<i>Oryza sativa</i> |
| spellingShingle | Fen Zhang Li-Zhen Ling Li-Zhi Gao Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development Plants molecular evolution sequence polymorphism microRNA binding site flower development <i>Oryza sativa</i> |
| title | Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development |
| title_full | Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development |
| title_fullStr | Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development |
| title_full_unstemmed | Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development |
| title_short | Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development |
| title_sort | genome wide dissection of selection on microrna target genes involved in rice flower development |
| topic | molecular evolution sequence polymorphism microRNA binding site flower development <i>Oryza sativa</i> |
| url | https://www.mdpi.com/2223-7747/13/23/3281 |
| work_keys_str_mv | AT fenzhang genomewidedissectionofselectiononmicrornatargetgenesinvolvedinriceflowerdevelopment AT lizhenling genomewidedissectionofselectiononmicrornatargetgenesinvolvedinriceflowerdevelopment AT lizhigao genomewidedissectionofselectiononmicrornatargetgenesinvolvedinriceflowerdevelopment |