Trends Plant Sci. The genetic architecture of teosinte catalyzed and constrained maize domestication. The covariances of additive and dominance effects of each individual were modeled to be proportional to the realized additive and dominance relationship matrices, respectively. We also applied similar crossing scheme to 55 maize landrace parent plants. The authors have declared that no competing interests exist. We computed the selection intensity for each trait and observed weak i across all traits (Fig. 2). It is not surprising to find θM>θT since the domestication process likely depleted variants that contributed beneficially to the structure of the G-matrix. Second, the difference in plant architecture is likely a consequence or correlated response to selection on ear architecture to create a less branched plant with fewer, larger ears. If θdroponei is larger than θT, then the ith trait is said to assist evolution. C/ les bases génétiques de la domestication. S5. Each plant was separated by 30 cm within rows and 76 cm between rows. Based on the model’s variance component estimates, we were able to estimate the proportions of phenotypic variance due to additive genetic variance (heritabilities), dominance genetic variance, and genetic-by-environment variance. Briefly, the imputation is a two-part process with first identifying the parent phase using a heuristic approach, followed by inferring the parent state at each site using a hidden Markov model. Another way to think about the relationship between the G-matrix and the tempo of evolution comes from the multivariate breeder’s equation of R=Gβ. Ce genre comprend le maïs et les téosintes, originaires du Mexique et souvent considérées comme les ancêtres du maïs cultivé. Quel est l’ancêtre sauvage du maïs ? En 1784, l'agronome Antoine Parmentier publie le premier ouvrage sur le maïs. Am J Bot. 1 - Port de la plante : Maïs et téosinte. Individual trait divergence between teosinte and maize landrace appears to have been driven primarily by selection with the exception of a single trait, total grain weight per plant (TGWP). Dans certains cas, les grains avaient perdu, comme ceux du maïs, l’écaille qui les enveloppe … TP téosinte et mais Le maïs est la 3e céréale consommé dans le monde. 1) (17, 18). Our results here suggest that if the ancient farmers were to domesticate teosinte by selecting for only a single trait, EL would be the ideal candidate as EL produced the maximum desired multivariate gains with the least genetic constraint. Fig 2. Based on the model’s variance and covariance component estimates, we were able to estimate additive genetic correlation. 2006; 127: 1309–1321. Differences in plant morphology between teosinte and maize are highlighted in A, while differences in ear morphology are shown in B. Teosinte plant has many branches with multiple ears on each branch and tassel at the tip of the branch; maize plant has few branches with a single ear on each branch and ear at the tip of the branch. Evidence for weak selection on major domestication loci is suggested by the observation that some domestication alleles were not at fixation 5,000 y ago, 4,000 y after the domestication process started at 9000 BP (56). The relationship between effect size and minor allele frequency (MAF). The molecular genetics of crop domestication. S3) and as commonly observed in populations under selection (37). In (A) and (C), QTL in different chromosomes are shown in different colors; R. (A) Density is plotted for the ratio of dominance by additive effects in absolute value. preliminary step in the development of a resource for map-based cloning of domestication and improvement genes in corn. The Environmental Response group is composed of traits that are highly affected by environmental factors. This expectation contradicts the greater VG×E/VP for Reproductive traits in maize, an observation we explore further in Discussion. There are several assumptions in our estimate: (i) constant selection intensity; (ii) constant change in additive genetic variance (VA) and phenotypic variance (VP); and (iii) teosinte VA and VP as initial variances and maize landrace VA and VP as final variances. However, projects seldom go beyond segments <5 cM without subsequent breeding and genotyping lines to identify additional crossovers in a genomic region of interest. We do not capture any email address. (B) Five kinship matrices were calculated by SNPs in quintiles of the F, This work is supported by National Science Foundation Grant IOS 1238014 to J.F.D (. Les images en montrent les caractéristiques par rapport à un pied de maïs normal et par rapport à la téosinte. Furthermore, genetic constraint can be ameliorated over time by the decay of linkage disequilibrium between linked causative factors (68). We obtained 49 selfed and 377 outcross families for teosinte (SI Appendix, Table S10), and 34 selfed and 89 outcross families for maize landrace (SI Appendix, Table S11). Documents. Fig 4. We imputed the GBS data for teosinte and maize landrace using the ParentPhasingPlugin and ImputeProgenyStatesPlugin as implemented in TASSEL5 (79). Teosinte has a plastic growth form, allowing the plant to branch prolifically in good environments to produce hundreds of ears or remain small and weakly branched with just a few ears in poor environments. The comparison of θM and θT indicates while there was substantial constraint early in domestication, it increased over time. We selected parent plants from a modern teosinte and a modern maize landrace population sampled from nearby locations. Of all 16 traits, GE has the smallest θZi and largest |projZRi|, indicating that direct selection for more GE would give an overall response most closely aligned with the evolutionary trajectory as well as maximum gain along the trajectory. Thus, maize evolved to modulate grains per ear or grain weight instead of ear number. To compare the VA between teosinte and the maize landrace, we used the narrow-sense heritabilities (h2=VA/VP), which is a VP-standardized measure of the VA. We observed higher h2 in teosinte (h2=0.39±0.19, ranging from 0.07 to 0.73) than in maize landrace (h2=0.19±0.11, ranging from 0.01 to 0.38) for 15 of 18 traits (Fig. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, Evolution of crop species: Genetics of domestication and diversification, Documenting Domestication: New Genetic and Archaeological Paradigms, Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record, Genetic perspectives on crop domestication, A bountiful harvest: Genomic insights into crop domestication phenotypes, Current perspectives and the future of domestication studies, The natural history of model organisms: Genetic, evolutionary and plant breeding insights from the domestication of maize, A single domestication for maize shown by multilocus microsatellite genotyping, Starch grain and phytolith evidence for early ninth millennium B.P. Univariate QST–FST comparison for all 18 traits. 2A). We mated the teosinte parents with one another to produce a cohort of 4,455 offspring with variable degrees of kinship, and similarly, we mated the maize landrace parents with one another to produce a parallel cohort of 4,398 maize offspring. We thank various members of the J.F.D. (A) The percentage of variance explained by QTL and non-QTL, respectively.…. 4). θZ measures the deviation from Z by selecting on ith trait. Teosinte adapts by varying the number of ears per plant while maintaining constant ear and grain size across environments. Previous studies have also suggested that standing variation can lead to a faster evolution than new mutations (41, 42), thus highlighting the importance of standing variation in domestication. -, Burger JC, Chapman MA, Burke JM. (i) Our single teosinte and maize landrace populations are not apt to be adequate proxies for the ancestral teosinte and resulting maize domesticate. Cell. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. 10.1016/j.cell.2006.12.006 Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We then identified the parents of each progeny from the A-matrix using a custom R script. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. Among the trait groups, Reproductive traits have the highest level of h2, ranging from 0.27 to 0.73 (Fig. Following that, genotypes were called from GBS raw sequencing reads using the TASSEL5-GBS Production Pipeline based on 955,690 SNPs in the ZeaGBSv2.7 Production TagsOnPhysicalMap (TOPM) file (75). Changes in trait means and selection intensities. The QST for each trait is shown as individual line along the horizontal axis and is colored according to trait group. To infer the quantitative genetics of the maize ancestor, teosinte, and how this architecture was altered through domestication, we assayed the correlations among relatives for a set of 18 domestication traits in a large sample of teosinte plants of known pedigree derived from 49 founder teosinte parents chosen to serve a proxy for the ancestral teosinte population from which maize was domesticated. Genotype files are available in Figshare, and phenotype files are available in Datasets S1 and S2. |projZRi| measures the evolutionary gain along Z by selecting on ith trait. eScholarship, California Digital Library, University of California, Darwin C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. Because the genetic line of least resistance (gmax,T) is informative only for the first eigenvector of the G-matrix, we also estimated the angles between observed trait responses to domestication (Z) and each of the first five principal components of G, which accounted for 27.2, 18.8, 15.3, 9.7, and 7.3% of the variation (78.2% in total) (SI Appendix, Fig. First, there is a general reduction in the magnitude of favorable correlations from teosinte to maize landrace (Fig. VCAP by different genomic features. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. Under neutral trait evolution, the coefficient ρST in GB=ρSTGW should be equal to 2FST/(1−FST), where FST is estimated from neutral loci (common SNP markers in this case); however, the coefficient calculated from the traits (ρST,G = 314; 95% CI, 190–908) is significantly higher than the expected coefficient calculated from neutral loci (ρST,N = 0.372; 95% CI, 0.363–0.381). They’re not only recording but also interpreting complex, changing phenomena as they raise awareness with members of the public. While domestication led to repartition of the solar energy captured from many small grains to fewer larger grains, TGWP itself was not modified. Many crops have well-documented archaeological records (3, 4). First, we tested for correlation between teosinte and the maize landrace G-matrices (SI Appendix, Tables S4 and S5) using the Mantel test (29) and found that the G-matrices are not significantly correlated (r = 0.03; P = 0.21). Our estimates for the loss of h2 on individual traits are consistent with the morphological changes during maize domestication and how these morphological changes relate to the maize population’s fitness as a crop. The most significant QTL is labeled as S1_44817082. Our results (Fig. Zea est un genre de plantes monocotylédones de la famille des Poaceae, originaire d'Amérique. The results of this analysis reject the neutral drift model for the differences in trait means between teosinte and maize landrace for all traits except TGWP, for which the population means were nearly equal (Fig. TGWP may be constrained by the ability of the plant to convert solar energy into chemical energy. Under neutral evolution, traits are expected to evolve at the same pace as neutral loci, which is essentially QST = FST (71). Fig 5. INRA. analyzed data; C.J.Y., P.J.B., M.C.R., J.B.H., and J.F.D. Génétique. Au milieu du xviiie siècle, le naturaliste suédois Carl von Linné nomme le maïs Zea mays. Moderate magnitude of i are observed for the Environmental Response group (|i| = 0.0018–0.0026). For example, teosinte plants have many ears along long lateral branches under favorable conditions, but few ears on short branches in poor conditions. Similarly, we also applied Mantel’s test to each trait group to see how each trait group similarity compares to overall similarity. We tested for similarity between teosinte and maize landrace genetic correlation matrices (rg) using Mantel’s test (29). Yang CJ, Samayoa LF, Bradbury PJ, Olukolu BA, Xue W, York AM, Tuholski MR, Wang W, Daskalska LL, Neumeyer MA, Sanchez-Gonzalez JJ, Romay MC, Glaubitz JC, Sun Q, Buckler ES, Holland JB, Doebley JF. (A) Five kinship matrices were calculated by SNPs…, NLM 2 - Un mutant du maïs. Intuitively, fixation of recessive loss-of-function alleles should deplete VD/VP because of reduction of VD due to allele fixation.