The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication

Abstract

The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high F ST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline

“…We additionally sequenced 43 mexicana individuals from 3 allopatric reference populations, totalling 348 low-coverage genomes (mean ~1x). To this dataset, we added 55 previously published high-coverage genomes from Palmar Chico [13] as an allopatric maize reference population.…”

“…For an allopatric maize reference population, we used 55 previously published high-coverage maize genomes from Palmar Chico (NCBI: PRJNA616247 [13]). This landrace population grows below the elevational range for mexicana (1,008 m).…”

“…For a parviglumis reference population, we used 50 previously published high-coverage lowland individuals sampled from the ‘Mound’ population at 1,008 m by Palmar Chico [13,101,114] (NCBI: PRJNA616247, see S2 Table). We mapped and filtered reads for these individuals using the pipeline described above and capped base quality scores using BAQ.…”

“…For a parviglumis reference population, we used 50 previously published high-coverage lowland individuals sampled from the ‘Mound’ population at 1,008 m near Palmar Chico [53–55] (NCBI: PRJNA616247, see S2 Table). These maize and parviglumis reference populations were sampled about 1 km apart from each other but maintain high F ST and are isolated by differences in flowering time [54].…”

Gene network simulations provide testable predictions for the molecular domestication syndrome

“…2007) among others. These large QTLs that most likely encode early domestication targets stand as exceptions in the overall architecture of domestication traits dominated by small-effect QTLs as recently reported in maize (Chen et al . 2020).…”