Genome-wide microsatellites in amaranth: development, characterization, and cross-species transferability.

Area of Science:

• Plant genetics and breeding
• Genomics
• Molecular markers

Background:

• Amaranth (Amaranthus spp.) is a highly nutritious crop with significant diversity but lacks molecular characterization.
• Robust molecular markers are crucial for amaranth crop improvement programs.

Purpose of the Study:

• To develop genome-wide microsatellite markers for Amaranthus hypochondriacus.
• To assess the cross-species transferability and evolutionary relatedness of these markers across ten Amaranthus species.
• To provide tools for amaranth species identification, DNA fingerprinting, and QTL/gene identification.

Main Methods:

• Identification of 13,051 genome-wide microsatellite motifs in the A. hypochondriacus genome.
• Primer design for 1538 suitable motifs and validation of 225 primers.
• Cross-species transferability analysis using 45 microsatellite motifs across ten Amaranthus species.
• Genetic diversity analysis including allele number, gene diversity, heterozygosity, and PIC values.
• Phylogenetic analysis to determine evolutionary relationships.

Main Results:

• 119 out of 225 (52.89%) designed primers were successfully amplified.
• Cross-species transferability ranged from 28.89% (A. dubius) to 86.67% (A. caudatus), indicating significant variability.
• 97 alleles were detected, with average major allele frequency, gene diversity, heterozygosity, and PIC of 0.733, 0.347, 0.06, and 0.291, respectively.
• Genetic dissimilarity coefficients varied widely, and a phylogenetic tree grouped the ten species into three clusters.

Conclusions:

• Genome-wide development and transferability of microsatellite markers provide valuable insights into amaranth species relationships.
• These markers are essential for species identification, DNA fingerprinting, and facilitating genetic studies for amaranth improvement.