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Concept: Zea

103

Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana, including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10-8 ~3.87 × 10-8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.

Concepts: DNA, Gene, Genetics, Mutation, Maize, Transposon, Genetic algorithm, Zea

29

For more than 40 y, there has been an active discussion over the presence and economic importance of maize (Zea mays) during the Late Archaic period (3000-1800 B.C.) in ancient Peru. The evidence for Late Archaic maize has been limited, leading to the interpretation that it was present but used primarily for ceremonial purposes. Archaeological testing at a number of sites in the Norte Chico region of the north central coast provides a broad range of empirical data on the production, processing, and consumption of maize. New data drawn from coprolites, pollen records, and stone tool residues, combined with 126 radiocarbon dates, demonstrate that maize was widely grown, intensively processed, and constituted a primary component of the diet throughout the period from 3000 to 1800 B.C.

Concepts: Maize, Flower, Mexico, North America, Midwestern United States, Zea, Diet of Japan, Radiocarbon dating

20

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Concepts: Agriculture, Wheat, Poaceae, Root, Maize, Zea, Grass, Poales

5

Adaptation of crops to climate change has motivated an increasing interest in the potential value of novel traits from wild species; maize wild relatives, the teosintes, harbor traits that may be useful to maize breeding. To study the ecogeographic distribution of teosinte we constructed a robust database of 2363 teosinte occurrences from published sources for the period 1842-2016. A geographical information system integrating 216 environmental variables was created for Mexico and Central America and was used to characterize the environment of each teosinte occurrence site. The natural geographic distribution of teosinte extends from the Western Sierra Madre of the State of Chihuahua, Mexico to the Pacific coast of Nicaragua and Costa Rica, including practically the entire western part of Mesoamerica. The Mexican annuals Zea mays ssp. parviglumis and Zea mays ssp. mexicana show a wide distribution in Mexico, while Zea diploperennis, Zea luxurians, Zea perennis, Zea mays ssp. huehuetenangensis, Zea vespertilio and Zea nicaraguensis had more restricted and distinct ranges, representing less than 20% of the total occurrences. Only 11.2% of teosinte populations are found in Protected Natural Areas in Mexico and Central America. Ecogeographical analysis showed that teosinte can cope with extreme levels of precipitation and temperatures during growing season. Modelling teosinte geographic distribution demonstrated congruence between actual and potential distributions; however, some areas with no occurrences appear to be within the range of adaptation of teosintes. Field surveys should be prioritized to such regions to accelerate the discovery of unknown populations. Potential areas for teosintes Zea mays ssp. mexicana races Chalco, Nobogame, and Durango, Zea mays ssp. huehuetenangensis, Zea luxurians, Zea diploperennis and Zea nicaraguensis are geographically separated; however, partial overlapping occurs between Zea mays ssp. parviglumis and Zea perennis, between Zea mays ssp. parviglumis and Zea diploperennis, and between Zea mays ssp. mexicana race Chalco and Zea mays ssp. mexicana race Central Plateau. Assessing priority of collecting for conservation showed that permanent monitoring programs and in-situ conservation projects with participation of local farmer communities are critically needed; Zea mays ssp. mexicana (races Durango and Nobogame), Zea luxurians, Zea diploperennis, Zea perennis and Zea vespertilio should be considered as the highest priority taxa.

Concepts: Maize, Mexico, Zea, Teosinte

5

The effect of domestication and modern breeding on aboveground traits in maize (Zea mays) has been well-characterized, but the impact on root systems and the rhizosphere remain unclear. The transition from wild ecosystems to modern agriculture has focused on selecting traits that yielded the largest aboveground production with increasing levels of crop management and nutrient inputs. Root morphology, anatomy, and ecophysiological processes may have been affected by the substantial environmental and genetic shifts associated with this transition. As a result, root and rhizosphere traits that allow more efficient foraging and uptake in lower synthetic input environments might have been lost. The development of modern maize has led to a shift in microbiome community composition, but questions remain as to the dynamics and drivers of this change during maize evolution and its implications for resource acquisition and agroecosystem functioning under different management practices. Better understanding of how domestication and breeding affected root and rhizosphere microbial traits could inform breeding strategies, facilitate the sourcing of favorable alleles, and open new frontiers to improve resource use efficiency through greater integration of root development and ecophysiology with agroecosystem functioning.

Concepts: Natural selection, Agriculture, Developmental biology, United States, Root, Maize, Domestication, Zea

2

A novel weed has recently emerged, causing serious agronomic damage in one of the most important maize-growing regions of Western Europe, the Northern Provinces of Spain. The weed has morphological similarities to a wild relative of maize and has generally been referred to as teosinte. However, the identity, origin or genetic composition of ‘Spanish teosinte’ was unknown. Here, we present a genome-wide analysis of single-nucleotide polymorphism (SNP) data for Spanish teosinte, sympatric populations of cultivated maize and samples of reference teosinte taxa. Our data are complemented with previously published SNP datasets of cultivated maize and two Mexican teosinte subspecies. Our analyses reveal that Spanish teosinte does not group with any of the currently recognized teosinte taxa. Based on Bayesian clustering analysis and hybridization simulations, we infer that Spanish teosinte is of admixed origin, most likely involving Zea mays ssp. mexicana as one parental taxon, and an unidentified cultivated maize variety as the other. Analyses of plants grown from seeds collected in Spanish maize fields and experimental crosses under controlled conditions reveal that hybridization does occur between Spanish teosinte and cultivated maize in Spain, and that current hybridization is asymmetric, favouring the introgression of Spanish teosinte into cultivated maize, rather than vice versa.

Concepts: United States, Europe, Spain, Maize, Mexico, Andalusia, Zea, Teosinte

2

Seed traits have been targeted by human selection during the domestication of crop species as a way to increase caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays) kernel weight has increased more than ten-fold in the 9000 years since domestication from its wild ancestor, teosinte (Zea mays ssp. parviglumis). In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of ten maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTLs) for kernel area and length with moderate allelic effects that co-localize with kernel weight QTLs. Several genomic regions with strong effects during maize domestication were detected and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTLs with a range of allelic effects enabling future research into the genetic basis of these traits.

Concepts: Genetics, Natural selection, Starch, Quantitative trait locus, Maize, Domestication, Zea, Teosinte

2

Records of the occurrence of wild relatives of maize in South American lowlands are unprecedented, especially in sympatric coexistence with landraces. This fact is relevant, because regions of occurrence of wild relatives of cultivated plants should be a priority for conservation, even if they do not correspond to the center of origin of the species. The aim of this study was to identify and characterize the wild relatives of maize in the Far West of Santa Catarina, southern Brazil. Therefore, phenotypic characterization was performed for five populations, based on 22 morphological traits deemed as fundamental for classifying the species of the genus Zea, and validated through the characterization of chromosomal knobs of two populations. The occurrence and distribution of teosinte populations were described through semi-structured interviews applied to a sample of 305 farmers. A total of 136 teosinte populations were identified; 75% of them occur spontaneously, 17% are cultivated populations, and 8% occur both ways, for the same farm. Populations that were characterized morphologically had trapezoidal fruits mostly, upright tassel branch (4-18), non-prominent main branch and glabrous glumes, with two protruding outer ribs and 8 inner ribs, on average. Cytogenetic analysis identified 10 pairs of homologous chromosomes (2n = 20) with 26 knobs, located in the terminal region of all chromosomes. The similarity of these results with the information reported in the literature indicates that the five populations of wild relatives of maize in this region of Santa Catarina belong to the botanical species Zea luxurians.

Concepts: Gene, Species, Chromosome, Cytogenetics, Maize, Zea, Florianópolis, Teosinte

2

0

Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.

Concepts: DNA, Gene, Genetics, Genotype, Chromosome, Maize, Zea, Teosinte