PopAmaranth

PopAmaranth provides a population genetics genome browser that displays population-scale genetic variation and selection analyses for grain amaranths (Amaranthus hypochondriacus, A. cruentus, A. caudatus) and their wild relatives (A. hybridus, A. quitensis).

Key Features:

• Genetic variation representation: Displays genetic variation along the Amaranthus hypochondriacus reference sequence derived from whole-genome sequencing of 88 curated accessions.
• Population-scale diversity and selection analysis: Reports population-scale diversity metrics and selection analyses computed from whole-genome sequencing data across curated accessions.
• Domestication history integration: Integrates domestication history to annotate candidate genes and genomic regions associated with domestication.
• Stress-related gene evidence: Provides evidence of changes in genetic diversity in stress-related genes such as MIF1 associated with water stress.
• Convergent evolution detection: Enables identification of convergent evolution signals, exemplified by findings on saponin reduction shared between amaranth and quinoa.
• Species and accession scope: Covers three grain amaranths (Amaranthus hypochondriacus, A. cruentus, A. caudatus) and two wild relatives (A. hybridus, A. quitensis) across 88 curated accessions.

Scientific Applications:

• Target identification for breeding: Identifies genomic target regions and candidate genes for breeding and crop improvement.
• Stress-related gene analysis: Assesses allele frequency and diversity changes in stress-related genes such as MIF1 to elucidate domestication impacts on water stress response.
• Convergent evolution studies: Facilitates comparative analyses to detect convergent reductions in traits like saponin content between amaranth and quinoa.
• Domestication genetics: Supports investigation of the genetic basis and evolutionary history of domestication in grain amaranths.

Methodology:

Uses whole-genome sequencing data from 88 curated accessions to compute population-scale diversity metrics and selection analyses along the Amaranthus hypochondriacus reference sequence.