Genome-wide SNPs and candidate genes underlying the genetic variations for protein and amino acids in pearl millet (Pennisetum glaucum) germplasm

Satbeer Singh, Chandra Bhan Yadav, Nelson Lubanga, Matthew Hegarty, Rattan S. Yadav*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

Main conclusion
A total of 544 significant marker-trait associations and 286 candidate genes associated with total protein and 18 amino acids were identified. Thirty-three candidate genes were found near the strong marker trait associations (– log10P ≥ 5.5).

Abstract
Pearl millet (Pennisetum glaucum) is largely grown as a subsistence crop in South Asia and sub-Saharan Africa. It serves as a major source of daily protein intake in these regions. Despite its importance, no systematic effort has been made to study the genetic variations of protein and amino acid content in pearl millet germplasm. The present study was undertaken to dissect the global genetic variations of total protein and 18 essential and non-essential amino acids in pearl millet, using a set of 435 K Single Nucleotide Polymorphisms (SNPs) and 161 genotypes of the Pearl Millet Inbred Germplasm Association Panel (PMiGAP). A total of 544 significant marker-trait associations (at P < 0.0001; – log10P ≥ 4) were detected and 23 strong marker-trait associations were identified using Bonferroni’s correction method. Forty-eight pleiotropic loci were found in the genome for the studied traits. In total, 286 candidate genes associated with total protein and 18 amino acids were identified. Thirty-three candidate genes were found near strongly associated SNPs. The associated markers and the candidate genes provide an insight into the genetic architecture of the traits studied and are going to be useful in breeding improved pearl millet varieties in the future. Availabilities of improved pearl millet varieties possessing higher protein and amino acid compositions will help combat the rising malnutrition problem via diet.
Original languageEnglish
Article number63
Number of pages11
JournalPlanta
Volume260
Issue number3
Early online date27 Jul 2024
DOIs
Publication statusE-pub ahead of print - 27 Jul 2024

Keywords

  • Essential amino acids
  • GWAS
  • Malnutrition
  • Pearl millet
  • PMiGAP
  • Total protein
  • Gwas
  • Genome-Wide Association Study
  • Genes, Plant
  • Genotype
  • Genome, Plant
  • Total Protein
  • Amino Acids
  • Genetic Variation
  • Pearl Millet
  • Pennisetum
  • Plant Proteins
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci
  • Pmigap

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