Ana Laura Alonso‐Nieves

Summary: Defining the genetic basis of local adaptation is a key goal of evolutionary biology and crop improvement. Theory predicts that when selective pressures follow differences in the environment, a cline will be established. Clines can be exploited to uncover adaptive variation by association of alleles with the environment. However, monotonic phenotypic change over a cline is not necessarily mirrored in the behavior of genetic variants and population structure can further complicate analysis. To study genetic and phenotypic variation across the environment, we developed a multi‐parent advanced generation inter‐cross (MAGIC) population using eight Mexican native maize ( Zea mays L. ssp. mays ) varieties sourced from distinct agroecological zones. We evaluated the population in a common garden in Mexico and mapped tassel branching and flowering time, two traits that exhibit clinal variation. Variation in tassel branching was dominated by a single QTL with allele effects aligning to a negative elevational cline. By contrast, allele effects associated with 11 identified flowering time QTL were not consistently correlated with any one source environmental factor. Our observations support the prediction that genotype‐environment association will be strongest under simple genetic architecture, although, even then, analysis in native populations may be confounded by population structure.

This study aimed to conduct a diversity analysis of 49 native populations of Coahuila Ratón race of maize ( Zea mays L.) and identify subsets representing this diversity using morphological and genetic traits. Eleven morphological traits and eight additional indices were selected based on the repeatability index (a ratio of genetic variance to environmental plus genetic‐environment interaction variances), which expresses traits with low environmental interaction. Additionally, genetic characterization was performed using single‐nucleotide polymorphisms (SNPs). Genetic diversity was represented through principal component analysis (PCA) and cluster analysis. A positive, non‐significant association of r = 0.262 was found between morphological and genetic traits; in both cases, a pattern of diversity was associated with the populations' adaptation range (low, intermediate, or transition areas). A stratified representative subset was obtained, proportional to the variation of the populations studied, with morphological data accounted for the variation in 24.5% of the populations, while the subsets with genetic data accounted for 20.0% of the populations, representing the maximum allelic variation of the populations based on the heterozygosity coefficient and the average distance of the Ratón race from Coahuila, Mexico.

Defining the genetic basis of local adaptation is fundamental to evolutionary biology and crop improvement. Theory predicts that when selective pressures track differences in the environment, a cline will be established. Such clines might be exploited to uncover adaptive variation by association of alleles with environmental stressors. However, monotonic phenotypic change over a cline is not necessarily mirrored by adaptive genetic variants. Furthermore, population structure can complicate the interpretation of genotype-environment association. To test the assumptions of genotype-environment association in a crop species, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize varieties sourced from distinct agroecological zones. We mapped two clinal traits (tassel branching and flowering time) differing in genetic architecture. Variation in tassel branch number was dominated by a single QTL with allele effects that aligned well with a negative elevational cline. In contrast, we mapped 11 flowering time QTL with allele effects that were not consistently correlated with any one source environmental factor and distinct loci donated by highland and lowland early maturing varieties. Our observations support the theoretical result that genotype-environment association will be strongest under simple genetic architecture, although identification of adaptive alleles may still be confounded by population structure. Plain Language: Nine thousand years of careful selection and cultivation by indigenous farmers has generated a rich diversity of native Mexican maize (corn) varieties, grown from sea level to high mountains, and from jungle to semidesert. By crossing native varieties adapted to different locations, we can uncover important genetic variants conferring tolerance to environmental stressors.

Plant PHO1 proteins play a central role in the translocation and sensing of inorganic phosphate. The maize (Zea maysssp.mays) genome encodes two co‐orthologs of theArabidopsis PHO1gene, designatedZmPho1;2aandZmPho1;2b. Here, we report the characterization of the transposon footprint alleleZmpho1;2a′‐m1.1, which we refer to hereafter aspho1;2a. Thepho1;2aallele is a stable derivative formed by excision of anActivatortransposable element from theZmPho1;2agene. Thepho1;2aallele contains an 8‐bp insertion at the point of transposon excision that disrupts the reading frame and is predicted to generate a premature translational stop. We show that thepho1;2aallele is linked to a dosage‐dependent reduction inPho1;2atranscript accumulation and a mild reduction in seedling growth. Characterization of shoot and root transcriptomes under full nutrient, low nitrogen, low phosphorus, and combined low nitrogen and low phosphorus conditions identified 1100 differentially expressed genes between wild‐type plants and plants carrying thepho1;2amutation. Of these 1100 genes, 966 were upregulated in plants carryingpho1;2a, indicating the wild‐type PHO1;2a to predominantly impact negative gene regulation. Gene set enrichment analysis of thepho1;2a‐misregulated genes revealed associations with phytohormone signaling and the phosphate starvation response. In roots, differential expression was broadly consistent across all nutrient conditions. In leaves, differential expression was largely specific to low phosphorus and combined low nitrogen and low phosphorus conditions. Of 276 genes upregulated in the leaves ofpho1;2amutants in the low phosphorus condition, 153 were themselves induced in wild‐type plants with respect to the full nutrient condition. Our observations suggest thatPho1;2afunctions in the fine‐tuning of the transcriptional response to phosphate starvation through maintenance and/or sensing of plant phosphate status.

PHO1 proteins play a central role in plant inorganic phosphorus translocation and sensing. The maize ( Zea mays ssp. mays ) genome encodes two co-orthologs of the Arabidopsis PHO1 gene, designated ZmPho1;2a and ZmPho1;2b . Here, we report the characterization of the transposon-footprint allele Zmpho1;2a’-m1 . 1 , which we refer to hereafter as pho1;2a . The pho1;2a allele is a stable derivative formed by excision of an Activator element from the ZmPho1;2a gene. The pho1;2a allele contains an 8 bp insertion at the point of excision that disrupts the reading frame and is predicted to generate a premature translational stop. We show that the pho1;2a allele is linked to a dosage-dependent reduction in transcript accumulation and a mild reduction in seedling growth that is enhanced under nutrient deficient conditions. Characterization of the shoot and root transcriptomes of seedlings segregating the pho1;2a mutation under different nutrient conditions revealed pho1;2a to have a dominant effect on patterns of transcript accumulation. Gene set enrichment analysis of the transcripts mis-regulated in pho1;2a mutants suggests that Pho1;2a functions in the fine-tuning of the transcriptional phosphate starvation response. We discuss our results with reference to possible genetic redundancy among maize Pho1 genes and in the context of reports linking functional variation in Pho1;2a to agronomically important traits.