Genomic screening for artificial selection during domestication and improvement in maize

BACKGROUND: Artificial selection results in phenotypic evolution. Maize (Zea mays L. ssp. mays) was domesticated from its wild progenitor teosinte (Zea mays subspecies parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties. The landraces provided the genetic material for modern plant breeders to select improved varieties and inbred lines by enhancing traits controlling agricultural productivity and performance. Artificial selection during domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. SCOPE: This review is a summary of research on the identification and characterization by population genetics approaches of genes affected by artificial selection in maize. CONCLUSIONS: Analysis of DNA sequence diversity at a large number of genes in a sample of teosintes and maize inbred lines indicated that approx. 2 % of maize genes exhibit evidence of artificial selection. The remaining genes give evidence of a population bottleneck associated with domestication and crop improvement. In a second study to efficiently identify selected genes, the genes with zero sequence diversity in maize inbreds were chosen as potential targets of selection and sequenced in diverse maize landraces and teosintes, resulting in about half of candidate genes exhibiting evidence for artificial selection. Extended gene sequencing demonstrated a low false-positive rate in the approach. The selected genes have functions consistent with agronomic selection for plant growth, nutritional quality and maturity. Large-scale screening for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown. These approaches should also be applicable to other domesticated species if specific demographic conditions during domestication exist.     

A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement

Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3' portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.     

Genetic diversity and evolution of reduced sulfur storage during domestication of maize

The domestication of maize has spanned a period of over 9000 years, during which time its wild relative teosinte underwent natural and artificial selection. We hypothesize that environmental conditions could have played a major role in this process. One factor of environmental variation is soil composition, which includes sulfur availability. Sulfur is reduced during photosynthesis and is used to synthesize cysteine and methionine, which drive the accumulation of δ10 (Zm00001d045937), δ18 (Zm00001d037436), β15 (Zm00001d035760), γ16 (Zm00001d005793), γ27 (Zm00001d020592), and γ50 (Zm00001d020591) zeins, representing the zein2 fraction (z2) of storage proteins in maize seeds. In this study, polymorphisms and haplotypes were detected based on six z2 genes in 60 maize and teosintes lines. Haplotypes were unevenly distributed, and abundant genetic diversity was found in teosintes. Polymorphism was highest in z2δ18, whereas for z2β15 single nucleotide polymorphism (SNP) density and insertion/deletion (indel) abundance were the lowest, indicating differential roles in seed evolution. Indels showed a clustered distribution, and most of these derived from teosintes. The indels not only led to tandem repeat polymorphisms, but also to frameshift mutations, which could also be used as null variants. In addition, neutral evolutionary tests, phylogenetic analyses, and population structures indicated that z2δ10 and z2γ50 had undergone natural selection. Indeed, a natural selection imprint could also be found with z2γ27 and z2γ16, whereas z2δ18 and z2β15 tended to be under neutral evolution. These results suggested that genetic diversity and evolution of a subset of sulfur‐rich zeins could be under environmental adaptation during maize domestication.     

Molecular evidence for post-domestication selection in the <Emphasis Type="Italic">Waxy</Emphasis> gene of Chinese waxy maize

Waxy maize was first reported in China in 1909 and is mainly used in food production in Asia. The evidence for strong domestication selection in the Waxy locus of rice and a selective sweep around its genomic region make us to wonder whether there has been similar selection in Waxy in glutinous maize. To address this issue, DNA sequences of Waxy, three flanking genes and an unlinked gene (Adh1) of 30 accessions sampled from Chinese waxy maize accessions, including representative landraces and inbred lines, were determined in this study. Sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed in the Waxy locus in Chinese waxy maize but not in nonglutinous maize; comparison with the unlinked gene confirmed that this pattern was different to Waxy. Sequence analysis across a 143 kb genomic segment centered on the Waxy locus revealed patterns consistent with a selective sweep in the upstream region of Waxy. The selective sweep detected based on current limited genomic sequences exceeded over 50 kb, indicating strong selection in this or a bigger region. However, No sweep effect was detected in the repetitive downstream region of Waxy. Phylogenetic analysis indicated that Chinese waxy maize was domesticated from the cultivated flint maize (Zea mays ssp. mays) that was introduced from the new world. At least two independent deletions in exon 7 (30 bp) and 10 (15 bp) were identified in the Chinese accessions respectively. These findings demonstrate a similar pattern of domestication selection in the Waxy genomic region in both glutinous maize and rice, suggesting that this pattern in the rise of glutinous phenotype is likely in other cereal crops.     

Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme

Maize domestication from teosinte (Zea mays ssp. parviglumis) was accompanied by an increase of kernel size in landraces. Subsequent breeding has led to a diversification of kernel size and starch content among major groups of inbred lines. We aim at investigating the effect of domestication on duplicated genes encoding a key enzyme of the starch pathway, the ADP-glucose pyrophosphorylase (AGPase). Three pairs of paralogs encode the AGPase small (SSU) and large (LSU) subunits mainly expressed in the endosperm, the embryo and the leaf. We first validated the putative sequence of LSU_leaf through a comparative expression assay of the six genes. Second, we investigated the patterns of molecular evolution on a 2 kb coding region homologous among the six genes in three panels: teosintes, landraces, and inbred lines. We corrected for demographic effects by relying on empirical distributions built from 580 previously sequenced ESTs. We found contrasted patterns of selection among duplicates: three genes exhibit patterns of directional selection during domestication (SSU_end, LSU_emb) or breeding (LSU_leaf), two exhibit patterns consistent with diversifying (SSU_leaf) and balancing selection (SSU_emb) accompanying maize breeding. While patterns of linkage disequilibrium did not reveal sign of coevolution between genes expressed in the same organ, we detected an excess of non-synonymous substitutions in the small subunit functional domains highlighting their role in AGPase evolution. Our results offer a different picture on AGPase evolution than the one depicted at the Angiosperm level and reveal how genetic redundancy can provide flexibility in the response to selection.     

The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping

Previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for association with 31 traits in a population of 817 individuals. Thirty-three significant associations for markers from 15 candidate genes and 10 traits survive correction for multiple testing. Our analyses suggest several new putative causative relationships between specific genes and trait variation in teosinte. For example, two ramosa genes (ra1 and ra2) associate with ear structure, and the MADS-box gene, zagl1, associates with ear shattering. Since zagl1 was previously shown to be a target of selection during maize domestication, we suggest that this gene was under selection for its effect on the loss of ear shattering, a key domestication trait. All observed effects were relatively small in terms of the percentage of phenotypic variation explained (<10%). We also detected several epistatic interactions between markers in the same gene that associate with the same trait. Candidate-gene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte.     

The molecular evolution of terminal ear1, a regulatory gene in the genus Zea.

Nucleotide diversity in the terminal ear1 (te1) gene, a regulatory locus hypothesized to be involved in the morphological evolution of maize (Zea mays ssp. mays), was investigated for evidence of past selection. Nucleotide polymorphism in a 1.4-kb region of te1 was analyzed for a sample of 26 sequences isolated from 12 maize lines, five populations of the maize progenitor, Z. mays ssp. parviglumis, six other Zea populations, and two Tripsacum species. Although nucleotide diversity in te1 in maize is reduced relative to ssp. parviglumis, phylogenetic and statistical analyses of the pattern of polymorphism among these sequences provided no evidence of past selection, indicating that the region of the gene studied was probably not involved in maize evolution. The level of reduction in genetic diversity in te1 in maize relative to its progenitor is comparable to that found in previous reports for isozymes and other neutrally evolving maize genes and is consistent with a genome-wide reduction of genetic diversity resulting from a domestication bottleneck. An estimate of the age (1.2-1.4 million yr) of the maize gene pool based on te1 is roughly consistent with previous estimates based on other neutral genes, but may be biased by the apparently slow synonymous substitution rate at te1.     

A weak effect of background selection on trinucleotide microsatellites in maize

Artificial selection during the domestication of maize is thought to have been predominantly positive and to have had little effect on the surrounding neutral diversity because linkage disequilibrium breaks down rapidly when physical distance increases. However, the degree to which indirect selection has shaped neutral diversity in the maize genome during domestication remains unclear. In this study, we investigate the relationship between local recombination rate and neutral polymorphism in maize and in teosinte using both sequence and microsatellite data. To quantify diversity, we estimate 3 parameters expected to differentially reflect the effects of indirect selection and mutation. We find no general correlation between diversity and recombination, indicating that indirect selection has had no genome-wide impact on maize diversity. However, we detect a weak correlation between heterozygosity and recombination for trinucleotide microsatellites deviating from the stepwise mutation model and located within genes (rho = 0.32, P < 0.03). This result can be explained by a background selection hypothesis. The fact that the same correlation is not confirmed for nucleotide diversity suggests that the strength of purifying selection at or near this class of microsatellites is higher than for nucleotide mutations.     

A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.     

Maize Domestication and Anti-Herbivore Defences: Leaf-Specific Dynamics during Early Ontogeny of Maize and Its Wild Ancestors

As a consequence of artificial selection for specific traits, crop plants underwent considerable genotypic and phenotypic changes during the process of domestication. These changes may have led to reduced resistance in the cultivated plant due to shifts in resource allocation from defensive traits to increased growth rates and yield. Modern maize (Zea mays ssp. mays) was domesticated from its ancestor Balsas teosinte (Z. mays ssp. parviglumis) approximately 9000 years ago. Although maize displays a high genetic overlap with its direct ancestor and other annual teosintes, several studies show that maize and its ancestors differ in their resistance phenotypes with teosintes being less susceptible to herbivore damage. However, the underlying mechanisms are poorly understood. Here we addressed the question to what extent maize domestication has affected two crucial chemical and one physical defence traits and whether differences in their expression may explain the differences in herbivore resistance levels. The ontogenetic trajectories of 1,4-benzoxazin-3-ones, maysin and leaf toughness were monitored for different leaf types across several maize cultivars and teosinte accessions during early vegetative growth stages. We found significant quantitative and qualitative differences in 1,4-benzoxazin-3-one accumulation in an initial pairwise comparison, but we did not find consistent differences between wild and cultivated genotypes during a more thorough examination employing several cultivars/accessions. Yet, 1,4-benzoxazin-3-one levels tended to decline more rapidly with plant age in the modern maize cultivars. Foliar maysin levels and leaf toughness increased with plant age in a leaf-specific manner, but were also unaffected by domestication. Based on our findings we suggest that defence traits other than the ones that were investigated are responsible for the observed differences in herbivore resistance between teosinte and maize. Furthermore, our results indicate that single pairwise comparisons may lead to false conclusions regarding the effects of domestication on defensive and possibly other traits.     

Diversity in global maize germplasm: Characterization and utilization

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.     

Genetic diversity in maize landraces from indigenous settlements of Northeastern Argentina

In South America, native maize germplasm has been extensively studied particularly for the Andean region. However, relatively few genetic diversity studies include materials from the eastern region of the continent. Herein we present a genetic diversity characterization of four Popcorn maize landraces, maintained in indigenous settlements, from Northeastern Argentina (NEA). In addition, one Popcorn landrace from Northwestern Argentina (NWA) was incorporated for comparison. We characterized these landraces using ten microsatellite markers. For the whole data set, a total of 65 alleles were found, with an average of 7.22 alleles per locus. The average gene diversity was 0.370. Global fit to Hardy–Weinberg proportions was observed in all landraces. Global estimates of F _ST revealed a significant differentiation among the populations. Individual Neighbor-joining clustering and Bayesian analyses allowed the recognition of most populations studied. Two main groups were distinguished by the Neighbor-joining clustering of populations. This grouping pattern would be consistent with a hypothesis of successive introductions of Popcorn in South America. The results presented will be useful to design strategies that maximize the utility of maize genetic resources.     

Keepers of maize in Chiapas,Mexico

This study concerns the knowledge and selection of biological diversity of maize (Zea mays) within its center of domestication in Mesoamerica. Maize farmers in central Chiapas of Southern México keep local varieties (landraces) belonging to six races and four race mixtures. Fifteen local varieties are recognized. In spite of widespread adoption of a modern, high yielding variety, maize farmers continue to select local varieties for specific soils and because of agronomic and use criteria. Farmers maintain maize varieties primarily through seed selection. Spatial and temporal separation do not seem sufficient to maintain varieties. The management of improved varieties can lead from a uniform population to a heterogeneous one as hybridization with local maize populations occurs.     

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

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.     

Cloning and characterization of a putative GS3 ortholog involved in maize kernel development

The GS3 gene was the first identified gene controlling the grain size in rice. It has been proven to be involved in the evolution of grain size during domestication. We isolated the maize ortholog, ZmGS3 and investigated its role in the evolution of maize grain size. ZmGS3 has five exons encoding a protein with 198 amino acids, and has domains in common with the rice GS3 protein. Compared with teosinte, maize has reduced nucleotide diversity at ZmGS3, and the reduction is comparable to that found in neutrally evolving maize genes. No positive selection was detected along the length of the gene using either the Hudson–Kreitman–Aguadé or Tajima’s D tests. Phylogenetic analysis reveals a distribution of maize sequences among two different clades, with one clade including related teosinte sequences. The nucleotide polymorphism analysis, selection test and phylogenetic analysis reveal that ZmGS3 has not been subjected to selection, and appears to be a neutrally evolving gene. In maize, ZmGS3 is primarily expressed in immature ears and kernels, implying a role in maize kernel development. Association mapping analysis revealed one polymorphism in the fifth exon that is significantly associated with kernel length in two environments. Also one polymorphism in the promoter region was found to affect hundred kernel weight in both environments. Collectively, these results imply that ZmGS3 is involved in maize kernel development but with different functional polymorphisms and thus, possibly different mechanisms from that of the rice GS3 gene.