Genome and transcriptome analyses reveal parallel altitude adaptation in Chenopodium

Area of Science:

• Genomics
• Evolutionary Biology
• Plant Science

Background:

• Understanding crop adaptation to diverse environments necessitates integrated analysis of genome-wide variation, regulatory networks, and evolutionary dynamics.
• Chenopodium quinoa, a vital pseudocereal, exhibits distinct highland and lowland ecotypes, but the genetic and regulatory underpinnings of its adaptation remain unclear.

Purpose of the Study:

• To investigate the genetic and regulatory mechanisms underlying adaptation in Chenopodium species.
• To explore the roles of coding variation, regulatory divergence, and introgression in parallel adaptation to environmental factors like altitude.

Main Methods:

• Generated a comprehensive genomic and transcriptomic resource from 558 accessions of 20 Chenopodium species.
• Conducted population genomic analyses, comparative analyses for parallel adaptation, and genome-wide expression quantitative trait loci (eQTL) mapping.
• Identified genes and regulatory elements associated with adaptation to altitude and environmental stress.

Main Results:

• Revealed extensive genetic diversity, asymmetric subgenome evolution, and significant interspecific introgression within Chenopodium.
• Identified Chenopodium berlandieri as a source of adaptive variation for cultivated quinoa, particularly in stress and immunity genes.
• Discovered shared targets of selection for altitude adaptation, including nutrient transporter PTR2 and photoperiod regulator CONSTANS, and implicated regulatory structural variation in ELF3 expression for altitude adaptation.

Conclusions:

• Demonstrated that coding variation, regulatory divergence, and introgression collectively drive parallel environmental adaptation in wild and cultivated Chenopodium.
• Provided crucial insights into polyploid crop evolution.
• Offered valuable resources for breeding climate-resilient quinoa varieties.