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

Grain Amaranth is the most promising C4 dicotyledonous pseudocereal and distributed globally. It has an excellent nutritional profile adaptability against a broad range of environmental factors. These traits have renewed interest researchers breeders in exploring this underutilized orphan crop. The present study aimed to validate genome-wide SSR assess genetic diversity among 94 Amaranthus hypochondriacus accessions using 57 genomic (g-SSR) markers developed in-house. A total 36 g-SSRs were recorded as polymorphic amplified 138 alleles, with average 3.83 alleles per locus. Major allele frequency ranged from 0.29 0.98, 0.63 marker. expected heterozygosity 0.03 0.81, 0.46 Polymorphism information content (PIC) 0.79, 0.40, indicating high level polymorphism across amaranth accessions. Population structure analysis resulted into two major clusters irrespective their geographical origin, which suggests there may be sharing common regions High allelic levels indicate significant variability germplasm, can further used future breeding programs.