The evolutionary significance of hybridization and subsequent introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana (hereafter, mexicana) are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. In this study we assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of the maize and mexicana genomes appeared resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these genomic regions and preliminary growth chamber experiments, we found evidence suggestive of the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found for adaptive introgression from maize to mexicana. The methods we have applied here can be replicated widely, and such analyses have the potential to greatly inform our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of spread into sympatry with relatives, should be particularly influential in these studies.

/pdf/the-genomic-signature-of-crop-wild-introgression-in-maize-1jo93jib38.pdf

The Genomic Signature of Crop-Wild Introgression in Maize

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last ∼150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.

https://www.genetics.org/content/genetics/181/4/1399.full.pdf

Historical Divergence and Gene Flow in the Genus Zea

Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. ‘Seeds of Discovery’ (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is expected to aid in effective identification and use of novel alleles and haplotypes for maize improvement. Multi-institutional efforts are required at the global level to systematically explore the maize germplasm to diversify the genetic base of elite breeding materials, create novel varieties and counter the effects of global climate changes.

Diversity in global maize germplasm: Characterization and utilization

The past few years have seen the publication of numerous books and articles on the origins of agriculture, but this work by MacNeish surely ranks as the most idiosyncratic of the bunch. In The Origins of Agriculture and Settled Life, MacNeish carries on in the style of his The Science of Archaeology? These two books are largely autobiographical, the former documenting the evolution of his research, this one attempting to fit global agricultural origins into the developmental rubric he began to develop in Tehuacan. Both recount his lifelong personal quest to reconstruct the texture of the past from the shreds of prehistory, but his indomitable will and seemingly boundless energy and endless excavations have not sufficed to finally lay to rest the question of how and why agriculture started. As he says at the end, \"we have reached no final conclusions.\

The Origins of Agriculture and Settled Life

We examined pollen grains and starch granules from a large number of modern populations of teosinte (wild Zea spp.), maize (Zea mays L.), and closely related grasses in the genus Tripsacum to assess their strengths and weaknesses in studying the origins and early dispersals of maize in its Mesoamerican cradle of origin. We report new diagnostic criteria and question the accuracy of others used previously by investigators to identify ancient maize where its wild ancestor, teosinte, is native. Pollen grains from teosinte overlap in size with those of maize to a much greater degree than previously reported, making the differentiation of wild and domesticated maize in palynological studies difficult. There is presently no valid method for separating maize and teosinte pollen on a morphological basis. Starch grain analysis, a recently developed tool of archaeobotany, appears to be of significant utility in distinguishing the seeds of teosinte from maize. We propose that the differences in starch grain morphology and size between wild and domesticated maize defined in this study may be associated with domestication genes in Zea that have been documented in the starch biosynthesis pathway. As previously reported, phytoliths effectively discriminate the female reproductive structures of Tripsacum, teosinte, and maize. Multiproxy microfossil studies of archaeological and paleoecological contexts appear to be effective tools for investigating the earliest stages of maize domestication and dispersals.

/pdf/identification-of-teosinte-maize-and-tripsacum-in-100q14f6j9.pdf

Identification of teosinte, maize, and Tripsacum in Mesoamerica by using pollen, starch grains, and phytoliths

Gene flow between maize [Zea mays (L.)] and its wild relatives does occur, but at very low frequencies. Experiments were undertaken in Tapachula, Nayarit, Mexico to investigate gene flow between a hybrid maize, landraces of maize and teosinte (Z. mays ssp. mexicana, races Chalco and Central Plateau). Hybridization, flowering synchrony, pollen size and longevity, silk elongation rates, silk and trichome lengths and tassel diameter and morphology were measured. Hybrid and open-pollinated maize ears produced a mean of 8 and 11 seeds per ear, respectively, when hand-pollinated with teosinte pollen, which is approximately 1–2% of the ovules normally produced on a hybrid maize ear. Teosinte ears produced a mean of 0.2–0.3 seeds per ear when pollinated with maize pollen, which is more than one-fold fewer seeds than produced on a maize ear pollinated with teosinte pollen. The pollination rate on a per plant basis was similar in the context of a maize plant with 400–500 seeds and a teosinte plant with 30–40 inflorescences and 9–12 fruitcases per inflorescence. A number of other factors also influenced gene-flow direction: (1) between 90% and 95% of the fruitcases produced on teosinte that was fertilized by maize pollen were sterile; (2) teosinte collections were made in an area where incompatibility systems that limit fertilization are present; (3) silk longevity was much shorter for teosinte than for maize (approx. 4 days vs. approx. 11 days); (4) teosinte produced more pollen on a per plant basis than the landraces and commercial hybrid maize; (5) teosinte frequently produced lateral branches with silks close to a terminal tassel producing pollen. Collectively these factors tend to favor crossing in the direction of teosinte to maize. Our results support the hypothesis that gene flow and the subsequent introgression of maize genes into teosinte populations most probably results from crosses where teosinte first pollinates maize. The resultant hybrids then backcross with teosinte to introgress the maize genes into the teosinte genome. This approach would slow introgression and may help explain why teosinte continues to co-exist as a separate entity even though it normally grows in the vicinity of much larger populations of maize.

Pollination between maize and teosinte: an important determinant of gene flow in Mexico.

Agave potatorum is a wild endemic species of Mexico. Its stems are used for mescal production, which cancels sexual reproduction. Agaves extraction from forests decreases their reproductive success and demographic performance. We evaluated patterns of genetic diversity and structure of wild populations under and without extraction in order to identify effects of its use and actions required for conserving genetic variation. This study was conducted with seven SSR markers in 12 populations representing the entire distribution area of the species. Standard parameters of genetic diversity, differentiation, structure and genetic similarity of populations were calculated and analyzed. The populations studied showed intermediate to high genetic diversity (H
 e
  = 0.36–0.64), compared with other Agave species so far studied. The wild category was the most diverse (H
 T
  = 0.87), but without significant differences with respect to populations under extraction (H
 T
  = 0.72), and two germplasm banks sampled (H
 T
  = 0.69). High structure among populations (Φ
 PR
  = 0.38) and inbreeding levels (F
 IS
  = 0.26, F
 IT
  = 0.55) were identified; a 3 % of genetic diversity being distributed among management status where germplasm banks represent a genetic pool with incipient divergence from the other categories. Bayesian analysis indicated two genetic groups. Our study suggests slight effects of management on genetic diversity of A. potatorum, apparently related to alterations of reproductive biology and pollination patterns.

Effects of traditional management for mescal production on the diversity and genetic structure of Agave potatorum (Asparagaceae) in central Mexico

Bee honey is a highly valued food whose international marketing is controlled by quality standards that are based on its physicochemical properties. One of them is color, which does not reflect a high or low quality, but rather the preferences of certain consumer markets. Color in honey is mostly determined by its floral sources that constantly change throughout the year. This study was intended to record color variations of the honey collected by Apis mellifera . For this purpose, honey was sampled from three selected hives, in an apiary in the town of Huejotitan, state of Jalisco, in western Mexico, on a monthly basis for a year. Color was measured according to the Pfund scale. Humidity was also measured since fermentation due to excessive moisture could spoil the samples. Two additional samples were collected, as well, from the bulk of honey at the time of the harvests, directly from the extractor: one from the spring harvest in May 2012, and the other from the fall harvest in December 2012. A total of 23 samples were obtained from December 2011 to December 2012. Color ranged from 0 mm Pfund (water white) to 85 mm Pfund (light amber) and humidity from 17% to 24%. It was discovered that the samples collected during the peak of the nectar flow, October - November, were contrastingly whiter than the rest. Although requiring more work, since consumers prefer clearer honeys, it is concluded that honey harvested at intervals during the high flow in the hives, with careful consideration of the moisture and making sure to keep honeys from different hives, apiaries and producers separate, a wider variety of honeys would be obtained, with different shades of color and different properties, better targeting the more specialized and demanding markets of today.

Lino de la Cruz-Larios

Papers

Pollination between maize and teosinte: an important determinant of gene flow in Mexico.

Effects of traditional management for mescal production on the diversity and genetic structure of Agave potatorum (Asparagaceae) in central Mexico

Bee Honey Color Variation Throughout the Year in Hejotitán, Jalisco, México.