Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth ( Amaranthus hypochondriacus )

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 and Rakesh Singh ()
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Gautam Vats: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Dimpi Das: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Rajat Gupta: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Akshay Singh: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Avantika Maurya: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
S. Rajkumar: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Amit Kumar Singh: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Rakesh Bharadwaj: Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Sandeep Kumar: Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Surinder Kumar Kaushik: Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Veena Gupta: Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
Kuldeep Singh: International Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India
Rakesh Singh: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India

Agriculture, 2023, vol. 13, issue 2, 1-14

Abstract: Grain Amaranth is the most promising C 4 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 Amaranthus hypochondriacus 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.

Keywords: g-SSR; grain amaranth; PIC; Amaranthus hypochondriacus; genetic diversity; PCoA; population structure (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2023
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