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Ren H, Wei Z, Zhou B, Chen X, Gao Q, Zhang Z. Molecular marker development and genetic diversity exploration in Medicago polymorpha. PeerJ 2023; 11:e14698. [PMID: 36684677 PMCID: PMC9851046 DOI: 10.7717/peerj.14698] [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: 04/26/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023] Open
Abstract
Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding.
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Affiliation(s)
- Hailong Ren
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China,Guangzhou Academy of Agricultural Sciences, Guangzhou, Guangdong, China,Hainan Sanya Test Center of Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Bo Zhou
- Hainan Sanya Test Center of Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Xiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiang Gao
- Hainan Sanya Test Center of Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Zhibin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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Verma P, Sharma TR, Srivastava PS, Abdin MZ, Bhatia S. Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers. Mol Biol Rep 2014; 41:5607-25. [PMID: 24893599 DOI: 10.1007/s11033-014-3431-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/21/2014] [Indexed: 12/01/2022]
Abstract
Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement.
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Affiliation(s)
- Priyanka Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India
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