Genomic, chromosomal and allelic assessment of the amazing diversity of maize
© BioMed Central Ltd 2004
Published: 28 May 2004
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© BioMed Central Ltd 2004
Published: 28 May 2004
A report on the 46th Annual Maize Genetics Conference, Mexico City, Mexico, 11-14 March 2004.
Teosinte thrived in the highlands and valleys of central Mexico 8,000 years ago. Human selection for increased seed number, cob size, poor seed dispersal, and nutritional value domesticated this wild plant into what we recognize today as maize. The 2004 Maize Genetics Conference was the first to be held near the site of the origin of maize and the present-day center of species diversity, and questions about the origin, types and consequences of maize diversity were central to the 42 talks and nearly 200 poster presentations. A starlight tour of the Museo Nacional de Antropología http://www.mna.inah.gob.mx/ allowed delegates to examine the depiction of corn by successive pre-colonial Mexican civilizations for further inspiration.
Ed Buckler (USDA-ARS at Cornell University, Ithaca, USA) has analyzed maize diversity by sequencing 18 genes, in toto or in part, from more than 100 inbred lines. As a benchmark consider that humans have about 0.09% base substitution in pair-wise comparisons and that as a species we are 1.34% different from chimpanzees. Evaluating pairs of modern inbred lines of maize, previous work has shown that there is 1.42% silent diversity in coding regions! In a typical gene there are between 20 and 25 amino-acid polymorphisms among alleles: 30% are radical changes and a further 22% are 'indel' mutations of missing or added amino acids. This tremendous diversity in maize reflects the maintenance of genetic differences from teosinte: domestication did not involve a bottleneck with a handful of representative alleles; rather, present-day corn has alleles that have been filtered by selection over millions of years. Buckler estimated that a single family gathering teosinte seed to supply 10% of their calories would have required 300,000 plants. The several million people of ancient Mexico at the onset of maize domestication probably used seed from teosinte populations of several billions of plants at all stages of domestication. In contrast, only a few tomato or pepper plants suffice in a kitchen, and the domesticated types exhibit correspondingly low genetic diversity.
Using diverse alleles, association genetics can pinpoint which polymorphisms confer specific phenotypes. To avoid false assignments between genotype and phenotype, a robust knowledge of population structure in maize lines allows line history to be separated from independent genetic changes that confer plant properties. Buckler's group and others have further established that linkage disequilibrium (LD), a measure of the recombinational history of chromosomal regions, decays within 1 kilobase (kb) for landraces (traditional varieties grown by subsistence farmers), within 2 kb for modern maize inbred lines used by geneticists, and in roughly 2-20 kb in the elite commercial inbred lines developed in the past decades for the hybrid corn seed industry. For loci with a major impact on productivity and plant architecture, ancient and modern plant breeders have applied stringent selection, and in these cases LD expands to cover a larger region and the drop in allele diversity can be used to link quantitative trait loci (QTLs) to genie regions likely to be important in domestication and yield. For example, four of six genes in the starch biosynthesis pathway show a significant decrease in allele diversity compared to only 5% of randomly selected loci. Recently published work from Buckler and collaborators describes an analysis of ancient maize specimens and showed that particular alleles of Teosinte branched1, which encodes a modulator of stem and floral architecture, and Pbf, encoding a regulator of seed storage protein, were fixed about 4,000 years ago in domesticated maize, whereas favorable alleles of Sugary1, key to producing sweet corn, were not selected in the corn grown in the southwestern USA until approximately 1,000 years ago.
And what has been the fate of teosinte? Jerry Kermicle (University of Wisconsin, Madison, USA) illustrated that it grows robustly in uncultivated areas, and as a weed in Mexican cornfields, often mimicking the morphology of modern maize so closely that farmers cannot recognize it. How does teosinte persist if it is interfertile with domesticated maize? Kermicle explained that haploid maize pollen performs poorly on teosinte silks, where many centimeters separate pollen attachment and the individual ovules on the ear. Teosinte carries dominant alleles of the Gametophyte factor1 (Ga1) locus that confer preferential growth on a Ga1 silk; in contrast, modern corn is ga1 and this pollen is only 1% as successful on teosinte Ga1 silks. This 'trick' is employed commercially to permit selective pollination within small blocks of sweet corn or popcorn despite the billions of wind-borne pollen grains from nearby standard corn. Ga1 alone cannot explain the crossing barrier between teosinte and corn, however, because Mexican landraces of corn carry the Ga1-male acting allele that is compatible with Ga1 teosinte silks. Kermicle reported a second gene, Teosinte crossing barrier1 (Tcb1), that reduces inter-crossing many-fold by restricting pollen with the recessive tcb1 allele from growing on Tcb1 teosinte silks. Interestingly, the dominant Tcb1 allele is found primarily in the weedy teosinte in corn fields, where it effectively blocks pollen flow from maize and may thus contribute to an incipient speciation process.
This talk and many others illustrated that the diversity of maize can be exploited by both molecular and population geneticists to answer fundamental questions about genetic interactions at the allele or karyotypic level within a plant and over short and long evolutionary time scales. The next harvest of maize results will be the 47th Annual Meeting to be held 10-13 March 2005 in Wisconsin, USA http://www.maizegdb.org/.