Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations
<i>Hypophthalmichthys molitrix</i> is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on <i>H. molitrix</i> genome level for genetic diversity analysis are limited. In this study, the distri...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-07-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/13/7/1267 |
| _version_ | 1797406242428157952 |
|---|---|
| author | Yajun Wang Hang Sha Xiaohui Li Tong Zhou Xiangzhong Luo Guiwei Zou Yi Chai Hongwei Liang |
| author_facet | Yajun Wang Hang Sha Xiaohui Li Tong Zhou Xiangzhong Luo Guiwei Zou Yi Chai Hongwei Liang |
| author_sort | Yajun Wang |
| collection | DOAJ |
| description | <i>Hypophthalmichthys molitrix</i> is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on <i>H. molitrix</i> genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled <i>H. molitrix</i> genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the <i>H. molitrix</i> genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on <i>H. molitrix.</i> |
| first_indexed | 2024-03-09T03:22:33Z |
| format | Article |
| id | doaj.art-7d477cf685f84737a32204c10cc6e4a9 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T03:22:33Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-7d477cf685f84737a32204c10cc6e4a92023-12-03T15:06:21ZengMDPI AGGenes2073-44252022-07-01137126710.3390/genes13071267Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured PopulationsYajun Wang0Hang Sha1Xiaohui Li2Tong Zhou3Xiangzhong Luo4Guiwei Zou5Yi Chai6Hongwei Liang7Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, College of Animal Science, Yangtze University, Jingzhou 434025, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaEngineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, College of Animal Science, Yangtze University, Jingzhou 434025, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China<i>Hypophthalmichthys molitrix</i> is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on <i>H. molitrix</i> genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled <i>H. molitrix</i> genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the <i>H. molitrix</i> genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on <i>H. molitrix.</i>https://www.mdpi.com/2073-4425/13/7/1267genome-wide identification<i>Hypophthalmichthys molitrix</i>SSRgenetic diversitypopulation structure |
| spellingShingle | Yajun Wang Hang Sha Xiaohui Li Tong Zhou Xiangzhong Luo Guiwei Zou Yi Chai Hongwei Liang Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations Genes genome-wide identification <i>Hypophthalmichthys molitrix</i> SSR genetic diversity population structure |
| title | Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations |
| title_full | Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations |
| title_fullStr | Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations |
| title_full_unstemmed | Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations |
| title_short | Microsatellite Characteristics of Silver Carp (<i>Hypophthalmichthys</i><i>molitrix</i>) Genome and Genetic Diversity Analysis in Four Cultured Populations |
| title_sort | microsatellite characteristics of silver carp i hypophthalmichthys i i molitrix i genome and genetic diversity analysis in four cultured populations |
| topic | genome-wide identification <i>Hypophthalmichthys molitrix</i> SSR genetic diversity population structure |
| url | https://www.mdpi.com/2073-4425/13/7/1267 |
| work_keys_str_mv | AT yajunwang microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT hangsha microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT xiaohuili microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT tongzhou microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT xiangzhongluo microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT guiweizou microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT yichai microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations AT hongweiliang microsatellitecharacteristicsofsilvercarpihypophthalmichthysiimolitrixigenomeandgeneticdiversityanalysisinfourculturedpopulations |