1
|
Du J, Li S, Shao J, Song H, Jiang P, Lei C, Bai J, Han L. Genetic diversity analysis and development of molecular markers for the identification of largemouth bass (Micropterus salmoides L.) based on whole-genome re-sequencing. Front Genet 2022; 13:936610. [PMID: 36105092 PMCID: PMC9465168 DOI: 10.3389/fgene.2022.936610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/21/2022] [Indexed: 11/28/2022] Open
Abstract
Largemouth bass (Micropterus salmoides L.) is generally considered to comprise two subspecies, Florida bass (M. floridanus) and Northern Largemouth bass (M. salmoides), which have biological characteristic differences because of their geographical distribution. In this study, whole-genome re-sequencing was performed among 10 Florida and 10 Northern largemouth bass, respectively. In total, 999,793 SNPs and 227,797 InDels were finally identified, and 507,401 SNPs (50.75%) and 116,213 InDels (51.01%) were successfully mapped to annotated 18,629 genes and 14,060 genes, respectively. KEGG classification indicated that most of these genes were focused on the pathways including signal transduction, transport and catabolism, and endocrine system. Genetic diversity analysis indicated that Florida largemouth bass had higher genetic diversity than Northern largemouth bass, indicating that the germplasm quality of Northern largemouth bass had markedly reduced in China. To examine the accuracies of the identified markers, 23 SNPs and eight InDels (the insertions or deletions of more than 45 bp) were randomly selected and detected among Florida largemouth bass, Northern largemouth bass, and their F1 hybrids. The detection efficiencies of all the markers were higher than 95%; nineteen SNPs and three InDels could accurately distinguish the two subspecies and their F1 hybrids with 100% efficiencies. Moreover, the three InDel markers could clearly distinguish the two subspecies and their F1 hybrids with a PCR-based agarose gel electrophoresis. In conclusion, our study established a simple PCR-based method for the germplasm identification of largemouth bass, which will be useful in the germplasm protection, management, and hybridization breeding of largemouth bass.
Collapse
Affiliation(s)
- Jinxing Du
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Shengjie Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- *Correspondence: Shengjie Li,
| | - Jiaqi Shao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongmei Song
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Peng Jiang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Caixia Lei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Bai
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Linqiang Han
- Guangdong Liangshi Aquatic Seed Industry Co Ltd, Foshan, China
| |
Collapse
|
2
|
Silliman K, Zhao H, Justice M, Thongda W, Bowen B, Peatman E. Complex introgression among three diverged largemouth bass lineages. Evol Appl 2021; 14:2815-2830. [PMID: 34950231 PMCID: PMC8674896 DOI: 10.1111/eva.13314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/30/2022] Open
Abstract
Hybrid zones between diverged lineages offer a unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships among these Mobile Delta bass populations, M. salmoides and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.
Collapse
Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Honggang Zhao
- Department of Natural ResourcesCornell UniversityIthacaNew YorkUSA
| | - Megan Justice
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
| | - Bryant Bowen
- Georgia Department of Natural ResourcesSocial CircleGeorgiaUSA
| | - Eric Peatman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| |
Collapse
|
3
|
Gunn JC, Berkman LK, Koppelman J, Taylor AT, Brewer S, Long JM, Eggert LS. Complex patterns of genetic and morphological differentiation in the Smallmouth Bass subspecies (Micropterus dolomieu dolomieu and M. d. velox) of the Central Interior Highlands. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01295-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Ruzich J, Turnquist K, Nye N, Rowe D, Larson WA. Isolation by a hydroelectric dam induces minimal impacts on genetic diversity and population structure in six fish species. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01220-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
8
|
Ballew NG, Mittelbach GG, Scribner KT. Fitness Consequences of Boldness in Juvenile and Adult Largemouth Bass. Am Nat 2017; 189:396-406. [PMID: 28350493 DOI: 10.1086/690909] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To date, most studies investigating the relationship between personality traits and fitness have focused on a single measure of fitness (such as survival) at a specific life stage. However, many personality traits likely have multiple effects on fitness, potentially operating across different functional contexts and stages of development. Here, we address the fitness consequences of boldness, under seminatural conditions, across life stages and functional contexts in largemouth bass (Micropterus salmoides). Specifically, we report the effect of boldness on (1) juvenile survivorship in an outdoor pond containing natural prey and predators and (2) adult reproductive success in three outdoor ponds across three reproductive seasons (years). Juvenile survival was negatively affected by boldness, with bolder juveniles having a lower probability of survival than shyer juveniles. In contrast, bolder adult male bass had greater reproductive success than their shyer male counterparts. Female reproductive success was not affected by boldness. These findings demonstrate that boldness can affect fitness differently across life stages. Further, boldness was highly consistent across years and significantly heritable, which suggests that boldness has a genetic component. Thus, our results support theory suggesting that fitness trade-offs across life stages may contribute to the maintenance of personality variation within populations.
Collapse
|
9
|
Li C, Gowan S, Anil A, Beck BH, Thongda W, Kucuktas H, Kaltenboeck L, Peatman E. Discovery and validation of gene-linked diagnostic SNP markers for assessing hybridization between Largemouth bass (Micropterus salmoides) and Florida bass (M. floridanus). Mol Ecol Resour 2014; 15:395-404. [DOI: 10.1111/1755-0998.12308] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Chao Li
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Spencer Gowan
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Ammu Anil
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Benjamin H. Beck
- United States Department of Agriculture; Agricultural Research Service; Stuttgart National Aquaculture Research Center; Stuttgart AR 72160 USA
| | - Wilawan Thongda
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Huseyin Kucuktas
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Ludmilla Kaltenboeck
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| | - Eric Peatman
- School of Fisheries; Aquaculture and Aquatic Sciences; Auburn University; Auburn AL 36849 USA
| |
Collapse
|