Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

Crop rotations and intercropping are an ever‐present sustainable practice across a diverse array of agroecosystems. These management practices can suppress weeds, reduce cycles of disease, build soil organic matter, and increase above‐ and belowground biodiversity, all of which improve the yield of a companion or subsequent crop. Here, we propose the terms ‘rotational’ and ‘intercropping value’ as a way to measure the overall effect of these benefits. Additionally, we articulate how to quantify different ecosystem services provided by rotational and intercrops including weed and disease suppression, enhancing microbial communities, and nitrogen fixation using a framework that accounts for how these services support other crops in agroecosystems. By providing a method of identifying and quantifying these rotational and intercropping traits, it may facilitate the breeding of better crops for rotations, for cover cropping, and for intercropping.

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