Abundant Small Genetic Alterations after Upland Cotton Domestication

Area of Science:

• Plant genetics and genomics
• Crop domestication and evolution
• Molecular biology and bioinformatics

Background:

• Domestication intentionally modifies plant and animal phenotypes through genetic alterations.
• Understanding small genetic changes is crucial for comprehending the domestication process.
• Upland cotton (Gossypium hirsutum) is a vital crop with a complex domestication history.

Purpose of the Study:

• To resequence the genome of wild upland cotton (Gossypium hirsutum var. yucatanense), the putative ancestor of cultivated cotton.
• To compare single nucleotide polymorphism (SNP) and insertion/deletion (InDel) variations between wild and cultivated cotton genomes.
• To identify genetic alterations potentially driven by domestication in cotton.

Main Methods:

• Whole-genome resequencing of wild Gossypium hirsutum var. yucatanense.
• Bioinformatic analysis to identify and compare SNPs and InDels with cultivated Gossypium hirsutum (TM-1).
• Analysis of variations within coding genes, including nonsynonymous SNPs and changes affecting stop codons or reading frames.

Main Results:

• Approximately 6.6 million SNPs and 0.7 million InDels were identified between wild and cultivated cotton genomes.
• Most variations occurred in non-coding regions, but 24,035 genes had nonsynonymous SNPs.
• A significant number of genes (2603) showed altered stop codons or shifted reading frames in domesticated cotton compared to its wild ancestor.

Conclusions:

• Small genetic changes, including SNPs and InDels, significantly reshaped the cotton genome during domestication.
• Mutations altering gene function, possibly restoring it under selective pressure, likely played a key role in cotton domestication.
• The findings provide valuable insights for identifying genes important for future cotton improvement.