1
|
Yang W, Bai Z, Wang F, Zou M, Wang X, Xie J, Zhang F. Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers. BMC Genomics 2022; 23:597. [PMID: 35974306 PMCID: PMC9382759 DOI: 10.1186/s12864-022-08832-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied. Results We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R2 = 0.3304, p < 0.05), and structure and principal coordinate analyses supported classification of populations into three clusters, which was consistent with the findings of cluster analysis. Conclusions As a rare medicinal plants, the protection of M. savatieri does not look optimistic, and accordingly, protective efforts should be beefed up on the natural wild populations. This study provided novel tools and insights for designing effective collection and conservation strategies for M. savatieri. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08832-x.
Collapse
Affiliation(s)
- Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhiyi Bai
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fuqiang Wang
- Yichun Academy of Sciences, Yichun, 336000, China
| | - Mingzhu Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xinru Wang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| |
Collapse
|
2
|
Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers. Gene 2021; 796-797:145791. [PMID: 34175390 DOI: 10.1016/j.gene.2021.145791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/18/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022]
Abstract
Fragaria nilgerrensis is a diploid wild strawberry widely distributed in Southwest China. Its white color and "peach-like" fragrance of fruits are valuable characters for the genetic improvement of cultivated strawberry plants. Its strong biotic and abiotic resistance and tolerance also enable it to survive in different habitats in the field. In this study, we evaluated the level of genetic variation within and between 16 populations with 169 individuals of F. nilgerrensis using 16 newly developed EST-SSR (expressed sequence tag-simple sequence repeats) markers. The results show that the genetic diversity of this species was high, based on Nei's genetic diversity (0.26) and polymorphic loci (0.41), although it is self-compatible and has clonal propagation. Significant genetic differentiation among populations was also detected by AMOVA analysis (Fst = 0.34), which could be indicative of little gene flow (Nm = 0.43) in F. nilgerrensis. The phylogenetic tree indicates that most of individuals from the same population have clustered together. These populations were not grouped based on the geographical distance, consistent with the Mantel test result (R2 = 0.0063, P > 0.05). All the populations were assigned into two ancestral groups, with some individuals admixed, suggesting ancestral gene flow had occurred between these two groups. Our developed EST-SSR markers as well as the genetic diversity and population structure analysis of F. nilgerrensis are important for genetic improvement in the breeding process. Moreover, the populations that contain high genetic diversity would be a priority for collection and conservation.
Collapse
|
3
|
Zhang J, Yan J, Huang S, Pan G, Chang L, Li J, Zhang C, Tang H, Chen A, Peng D, Biswas A, Zhang C, Zhao L, Li D. Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers. Front Genet 2020; 11:958. [PMID: 33061939 PMCID: PMC7518120 DOI: 10.3389/fgene.2020.00958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei’s genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabis.
Collapse
Affiliation(s)
- Jiangjiang Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jiangtao Yan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siqi Huang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Gen Pan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Li Chang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Jianjun Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Chao Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Huijuan Tang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Anguo Chen
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ashok Biswas
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Cuiping Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Lining Zhao
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Defang Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| |
Collapse
|
4
|
Lyu JI, Ramekar R, Kim DG, Kim JM, Lee MK, Hung NN, Kim JB, Ahn JW, Kang SY, Choi IY, Park KC, Kwon SJ. Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf ( Hibiscus cannabinus L.) Mutant. PLANTS 2020; 9:plants9050631. [PMID: 32423146 PMCID: PMC7285769 DOI: 10.3390/plants9050631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 01/12/2023]
Abstract
Kenaf is a source of fiber and a bioenergy crop that is considered to be a third world crop. Recently, a new kenaf cultivar, "Jangdae," was developed by gamma irradiation. It exhibited distinguishable characteristics such as higher biomass, higher seed yield, and earlier flowering than the wild type. We sequenced and analyzed the transcriptome of apical leaf and stem using Pacific Biosciences single-molecule long-read isoform sequencing platform. De novo assembly yielded 26,822 full-length transcripts with a total length of 59 Mbp. Sequence similarity against protein sequence allowed the functional annotation of 11,370 unigenes. Among them, 10,100 unigenes were assigned gene ontology terms, the majority of which were associated with the metabolic and cellular process. The Kyoto encyclopedia of genes and genomes (KEGG) analysis mapped 8875 of the annotated unigenes to 149 metabolic pathways. We also identified the majority of putative genes involved in cellulose and lignin-biosynthesis. We further evaluated the expression pattern in eight gene families involved in lignin-biosynthesis at different growth stages. In this study, appropriate biotechnological approaches using the information obtained for these putative genes will help to modify the desirable content traits in mutants. The transcriptome data can be used as a reference dataset and provide a resource for molecular genetic studies in kenaf.
Collapse
Affiliation(s)
- Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Rahul Ramekar
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea; (R.R.); (I.-Y.C.)
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Min-Kyu Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Nguyen Ngoc Hung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea; (R.R.); (I.-Y.C.)
| | - Kyoung-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea; (R.R.); (I.-Y.C.)
- Correspondence: (K.-C.P.); (S.-J.K.)
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (J.I.L.); (D.-G.K.); (J.M.K.); (M.-K.L.); (N.N.H.); (J.-B.K.); (J.-W.A.); (S.-Y.K.)
- Correspondence: (K.-C.P.); (S.-J.K.)
| |
Collapse
|
5
|
Li H, Ruan C, Ding J, Li J, Wang L, Tian X. Diversity in sea buckthorn (Hippophae rhamnoides L.) accessions with different origins based on morphological characteristics, oil traits, and microsatellite markers. PLoS One 2020; 15:e0230356. [PMID: 32168329 PMCID: PMC7069629 DOI: 10.1371/journal.pone.0230356] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/27/2020] [Indexed: 01/20/2023] Open
Abstract
Sea buckthorn (Hippophae rhamnoides) is an ecologically and economically important species. Here, we assessed the diversity of 78 accessions cultivated in northern China using 8 agronomic characteristics, oil traits (including oil content and fatty acid composition) in seeds and fruit pulp, and SSR markers at 23 loci. The 78 accessions included 52 from ssp. mongolica, 6 from ssp. sinensis, and 20 hybrids. To assess the phenotypic diversity of these accessions, 8 agronomic fruit traits were recorded and analyzed using principal component analysis (PCA). The first two PCs accounted for approximately 78% of the variation among accessions. The oil contents were higher in pulp (3.46–38.56%) than in seeds (3.88–8.82%), especially in ssp. mongolica accessions. The polyunsaturated fatty acid (PUFA) ratio was slightly lower in the seed oil of hybrids (76.06%) than that of in ssp. mongolica (77.66%) and higher than that of in ssp. sinensis (72.22%). The monounsaturated fatty acid (MUFA) ratio in the pulp oil of ssp. sinensis (57.00%) was highest, and that in ssp. mongolica (51.00%) was equal to the ratio in the hybrids (51.20%). Using canonical correspondence analysis (CCA), we examined the correlation between agronomic traits and oil characteristics in pulp and seeds. Oil traits in pulp from different origins were correlated with morphological groupings (r = 0.8725, p = 0.0000). To assess the genotypic diversity, 23 SSR markers (including 17 loci previously reported) were used among the 78 accessions with 59 polymorphic amplified fragments obtained and an average PIC value of 0.2845. All accessions were classified into two groups based on the UPGMA method. The accessions of ssp. sinensis and ssp. mongolica were genetically distant. The hybrid accessions were close to ssp. mongolica accessions. The 8 agronomic traits, oil characteristics in seed and pulp oils, and 23 SSR markers successfully distinguished the 78 accessions. These results will be valuable for cultivar identification and genetic diversity analysis in cultivated sea buckthorn.
Collapse
Affiliation(s)
- He Li
- School of Life Science, Nanjing University, Nanjing, P.R. China
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian, P.R. China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian, P.R. China
- * E-mail: (CR); (XT)
| | - Jian Ding
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian, P.R. China
| | - Jingbin Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian, P.R. China
| | - Li Wang
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian, P.R. China
| | - Xingjun Tian
- School of Life Science, Nanjing University, Nanjing, P.R. China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, P.R. China
- * E-mail: (CR); (XT)
| |
Collapse
|
6
|
Yang Z, Dai Z, Xie D, Chen J, Tang Q, Cheng C, Xu Y, Wang T, Su J. Development of an InDel polymorphism database for jute via comparative transcriptome analysis. Genome 2018; 61:323-327. [PMID: 29420906 DOI: 10.1139/gen-2017-0191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.
Collapse
Affiliation(s)
- Zemao Yang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Zhigang Dai
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Dongwei Xie
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Jiquan Chen
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Qing Tang
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Chaohua Cheng
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Ying Xu
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| | - Tingzhang Wang
- b Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianguang Su
- a Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha, China
| |
Collapse
|
7
|
Saha D, Rana RS, Chakraborty S, Datta S, Kumar AA, Chakraborty AK, Karmakar PG. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|