Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>)
Grain Amaranth is the most promising C<sub>4</sub> dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in explo...
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| Format: | Article |
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MDPI AG
2023-02-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/13/2/431 |
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| author | Gautam Vats Dimpi Das Rajat Gupta Akshay Singh Avantika Maurya S. Rajkumar Amit Kumar Singh Rakesh Bharadwaj Sandeep Kumar Surinder Kumar Kaushik Veena Gupta Kuldeep Singh Rakesh Singh |
| author_facet | Gautam Vats Dimpi Das Rajat Gupta Akshay Singh Avantika Maurya S. Rajkumar Amit Kumar Singh Rakesh Bharadwaj Sandeep Kumar Surinder Kumar Kaushik Veena Gupta Kuldeep Singh Rakesh Singh |
| author_sort | Gautam Vats |
| collection | DOAJ |
| description | Grain Amaranth is the most promising C<sub>4</sub> dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 <i>Amaranthus hypochondriacus</i> accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs. |
| first_indexed | 2024-03-11T09:18:20Z |
| format | Article |
| id | doaj.art-da71ff4c2d034fb49402f4dacf8b85f1 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-11T09:18:20Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-da71ff4c2d034fb49402f4dacf8b85f12023-11-16T18:31:04ZengMDPI AGAgriculture2077-04722023-02-0113243110.3390/agriculture13020431Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>)Gautam Vats0Dimpi Das1Rajat Gupta2Akshay Singh3Avantika Maurya4S. Rajkumar5Amit Kumar Singh6Rakesh Bharadwaj7Sandeep Kumar8Surinder Kumar Kaushik9Veena Gupta10Kuldeep Singh11Rakesh Singh12Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaDivision of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaInternational Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, IndiaDivision of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, IndiaGrain Amaranth is the most promising C<sub>4</sub> dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 <i>Amaranthus hypochondriacus</i> accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs.https://www.mdpi.com/2077-0472/13/2/431g-SSRgrain amaranthPIC<i>Amaranthus hypochondriacus</i>genetic diversityPCoA |
| spellingShingle | Gautam Vats Dimpi Das Rajat Gupta Akshay Singh Avantika Maurya S. Rajkumar Amit Kumar Singh Rakesh Bharadwaj Sandeep Kumar Surinder Kumar Kaushik Veena Gupta Kuldeep Singh Rakesh Singh Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>) Agriculture g-SSR grain amaranth PIC <i>Amaranthus hypochondriacus</i> genetic diversity PCoA |
| title | Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>) |
| title_full | Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>) |
| title_fullStr | Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>) |
| title_full_unstemmed | Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>) |
| title_short | Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (<i>Amaranthus hypochondriacus</i>) |
| title_sort | validation of genome wide ssr markers developed for genetic diversity and population structure study in grain amaranth i amaranthus hypochondriacus i |
| topic | g-SSR grain amaranth PIC <i>Amaranthus hypochondriacus</i> genetic diversity PCoA |
| url | https://www.mdpi.com/2077-0472/13/2/431 |
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