Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species
The genus <i>Vigna</i> is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different <i...
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| Format: | Article |
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MDPI AG
2023-12-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/10/1/34 |
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| author | Pawan Saini Asmita Sirari Belaghihalli N. Gnanesh Kamalpreet Singh Mandahal Navkiran Kaur Ludhar Sharon Nagpal S. A. H. Patel Javed Akhatar Pooja Saini Aditya Pratap Tejinderjit Singh Bains Inderjit Singh Yadav |
| author_facet | Pawan Saini Asmita Sirari Belaghihalli N. Gnanesh Kamalpreet Singh Mandahal Navkiran Kaur Ludhar Sharon Nagpal S. A. H. Patel Javed Akhatar Pooja Saini Aditya Pratap Tejinderjit Singh Bains Inderjit Singh Yadav |
| author_sort | Pawan Saini |
| collection | DOAJ |
| description | The genus <i>Vigna</i> is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different <i>Vigna</i> species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 <i>Vigna</i> species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various <i>Vigna</i> species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different <i>Vigna</i> species accessions. Utilizing allelic data, the 25 <i>Vigna</i> accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of <i>Vigna</i> accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the <i>Vigna</i> genus. |
| first_indexed | 2024-03-08T10:49:35Z |
| format | Article |
| id | doaj.art-ad41330132a348709a66dce4bdc3c612 |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-08T10:49:35Z |
| publishDate | 2023-12-01 |
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| series | Horticulturae |
| spelling | doaj.art-ad41330132a348709a66dce4bdc3c6122024-01-26T16:49:43ZengMDPI AGHorticulturae2311-75242023-12-011013410.3390/horticulturae10010034Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> SpeciesPawan Saini0Asmita Sirari1Belaghihalli N. Gnanesh2Kamalpreet Singh Mandahal3Navkiran Kaur Ludhar4Sharon Nagpal5S. A. H. Patel6Javed Akhatar7Pooja Saini8Aditya Pratap9Tejinderjit Singh Bains10Inderjit Singh Yadav11Department of Plant Breeding and Genetics, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaDepartment of Genetics and Plant Breeding, Sampoorna International Institute of Agri Science & Horticultural Technology, Maddur 571 433, Karnataka, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaDepartment of Plant Pathology, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaDepartment of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144 411, Punjab, IndiaDepartment of Vegetable Science, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaDepartment of Plant Breeding, Genetics and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University (EU), Baru Sahib 173 101, Himachal Pradesh, IndiaICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208 024, Uttar Pradesh, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University (PAU), Ludhiana 141 004, Punjab, IndiaThe genus <i>Vigna</i> is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different <i>Vigna</i> species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 <i>Vigna</i> species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various <i>Vigna</i> species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different <i>Vigna</i> species accessions. Utilizing allelic data, the 25 <i>Vigna</i> accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of <i>Vigna</i> accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the <i>Vigna</i> genus.https://www.mdpi.com/2311-7524/10/1/34mungbean<i>Vigna</i>whole-genome sequenceSSR markersprincipal coordinate analysisgenetic diversity |
| spellingShingle | Pawan Saini Asmita Sirari Belaghihalli N. Gnanesh Kamalpreet Singh Mandahal Navkiran Kaur Ludhar Sharon Nagpal S. A. H. Patel Javed Akhatar Pooja Saini Aditya Pratap Tejinderjit Singh Bains Inderjit Singh Yadav Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species Horticulturae mungbean <i>Vigna</i> whole-genome sequence SSR markers principal coordinate analysis genetic diversity |
| title | Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species |
| title_full | Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species |
| title_fullStr | Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species |
| title_full_unstemmed | Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species |
| title_short | Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (<i>Vigna radiata</i> L. Wilczek): Cross-Species Transferability and Population Genetic Studies in <i>Vigna</i> Species |
| title_sort | assessment of simple sequence repeat ssr markers derived from whole genome sequence wgs of mungbean i vigna radiata i l wilczek cross species transferability and population genetic studies in i vigna i species |
| topic | mungbean <i>Vigna</i> whole-genome sequence SSR markers principal coordinate analysis genetic diversity |
| url | https://www.mdpi.com/2311-7524/10/1/34 |
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