We calculated the distance matrices for teosinte and maize landrace as 1−|rg|, where rg is the genetic correlation. As a result, maize landraces serve as a rich source of genetic diversity for breeding modern maize (12). The covariances of genotype-by-environment effects were modeled to be proportional to the additive relationships of individuals tested in a common year and zero for pairs of individuals tested in different years. A comparison of the teosinte and maize landrace G-matrices also informs us that the degree of constraint increased over time. A la suite de croisements entre téosinte et maïs (obtention d’hybrides croisés avec des téosintes, pendant trois générations), les chercheurs ont réussi à obtenir des pieds de téosinte qui présentent des fruits sans cupule. En 1784, l'agronome Antoine Parmentier publie le premier ouvrage sur le maïs. | To explore how evolutionary constraint changed during domestication, we also estimated θM, the angle between the domestication trajectory (Z) and the direction of maximum genetic variation in maize (gmax,M), as a comparison with θT. Ancient farmers were successful in selecting for larger grains and ears (making harvesting seeds much easier), but not overall edible biomass as measured by TGWP, which remained the same between teosinte and maize landrace (Fig. 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. Such constraint would slow progress toward the optimal phenotype and require a circuitous evolutionary path over the generations. As an exception due to poor germination of teosinte seeds, we sampled some of the border plants in the first season and increased the grid to 112 plants by 54 rows in the second season. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. | If θdroponei is smaller than θT=67.3° (angle between Z and gmax,T), then the ith trait is said to constrain evolution. 2011 Jul;188(3):673-81. doi: 10.1534/genetics.111.126508. Xue S, Bradbury PJ, Casstevens T, Holland JB. Increase in constraint from teosinte to maize suggests that domestication reduced advantageous genetic variances and covariances more rapidly than mutation could restore them. Un demi-siècle plus tard, en 1832, le botaniste allemand Heinrich Schrader décrit une poacée (autrefois graminée) d'Amérique centrale, appelée téosinte. S6), and field positions; among the random effects in the model are polygenic additive, dominance, and genetic-by-environment effects. We performed univariate QST–FST tests on the individual traits to ask whether neutral evolution can also be rejected at the individual trait level. Un épisode de Stranger Wallon qui présente certains mécanismes de la domestication et de l'amélioration des plantes cultivées. 10.1016/j.cell.2006.12.006 The most significant QTL is labeled as S3_160586402. gmax is the first eigenvector of the G-matrix, which is taken from eigendecomposition of the G-matrix using eigen function in R (88). Fig 5. 4). This analysis verified three groups of genetically related traits: Vegetative/Flowering Time, Environmental Response, and Reproductive. By dropping one trait at a time and calculating the angle θdroponei between Zi and gmax,T,i, we can estimate the genetic constraint from the remaining 15 traits after dropping trait i. Left end of the bars represents selection intensities estimated from 9,000 generations of selection, and right end represents selection intensities estimated from 4,500 generations of selection. Modern maize typically possesses only a single stalk with few lateral branches that each carries a single large ear. |projZRi| measures the evolutionary gain along Z by selecting on ith trait. The QST for each trait is shown as individual line along the horizontal axis and is colored according to trait group. Given the genetic architecture in teosinte, how strong would selection need to be to complete domestication within the known time frame? The first three subspecies are teosintes; the last is maize, or corn, the only domesticated taxon in the genus Zea. Despite these limitations, we hope our approach will at least promote further thinking and study about domestication and how it was constrained by the genetic architecture of the ancestor and how the genetic architecture of crop species evolved over time. New Phytol. Bayesian comparison analysis showed high similarity in the Vegetative/Flowering Time submatrices (q = 0.31 ± 0.01) but no similarity in the Environmental Response (q = 0.00 ± 0.00) or Reproductive submatrices (q = 0.00 ± 0.00). laboratory, and Panzea, especially Adam Mittermaier, Eric Rentmeester, and Jason Brewer, for their assistance in this project. MAF was calculated from parent data. The most significant QTL is labeled as S7_3086083. Large effect QTL is defined as a QTL with a standardized additive effect greater than 1 phenotypic standard deviation as indicated by blue dotted lines. However, as seen within Reproductive trait group, it is possible to shift the genetic correlations under a sufficiently strong selection force. Moderate conservation between the teosinte and maize landrace genetic correlation matrices can be seen on a broad scale, with stronger conservation within Vegetative/Flowering Time and Environmental Response trait groups to little conservation within Reproductive trait group. La culture du maïs a probablement commencé en Amérique centrale, notamment au Mexique, d'où elle s'est propagée jusqu'au Canada en direction du nord, et jusqu'en Argentine vers le sud. Briefly, among the fixed effects in the model are year, inbreeding coefficient, shading (SI Appendix, Fig. Bibliographie Un ouvrage intitulé « Les Iroquoiens du Saint-Laurent, peuple du maïs », dresse un portrait détaillé de la relation particulière entretenue depuis le fond des âges avec cette plante qui a failli disparaître de notre alimentation avec l’arrivée des français sur le continent américain. In B, multivariate response (Ri) from hypothetical selection on a single ith trait is explored. The genetic architecture of teosinte catalyzed and constrained maize domestication. Le maïs a été domestiqué par l’Homme alors que la téosinte est considérée comme son ancêtre sauvage. Furthermore, genetic constraint can be ameliorated over time by the decay of linkage disequilibrium between linked causative factors (68). NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. Crop domestication has been described as a process of slow evolution, where the selection force is similar or lower than selection force seen in natural selection (53), and maize domestication is no exception to that. The Z vector is also scaled similarly by standardizing the trait mean differences by their genetic SDs. Within each season, we planted the seeds in a randomized design and grid of 100 plants by 30 rows along with borders surrounding the experimental section. S5. Strongest preservation of genetic correlations is observed within the Vegetative/Flowering Time group (r = 0.90; P < 0.05), followed by the Reproductive group (r = 0.79; P < 0.01) and the Environmental Response group (r = 0.77; P < 0.05). S2). Considering that 9,000 y of selection may not have increased yield per plant, it is not too surprising to find that modern maize breeding has only been successful in increasing yield per area but not yield per plant (60). We constructed distance matrices as (1−|rg|) for teosinte and maize landrace and visualized the genetic relationships among traits using principal-coordinate analysis (PCoA) and neighbor-joining (NJ) trees (SI Appendix, Fig. The full model is shown in SI Appendix, Materials and Methods. θZ measures the deviation in direction from Z, while |projZRi| measures the amount of evolutionary gain along Z. Third, because of favorable genetic correlations among most selection targets, ancient farmers had multiple options to select for what a maize ear would become. A case study at the maize domestication QTL teosinte branched1. Available at, Efficient methods to compute genomic predictions, Shrinkage estimation of the realized relationship matrix, TASSEL: Software for association mapping of complex traits in diverse samples, CrossMap: A versatile tool for coordinate conversion between genome assemblies, ASReml User Guide, Release 4.1, Structural Specification, The effect of selection on genetic variability, Predicting cumulated response to directional selection in finite panmictic populations, Effects of population size and linkage on optimal selection intensity, APE: Analyses of phylogenetics and evolution in R language, R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna), Version 3.5.1. Overall, a slow process by weak selection rather than abrupt changes by strong selection as previously suggested seems more likely (17, 59). For this approach, we simulated 18 unique β, where each βi had only a single element with a value of 1 and the remaining elements with a value of zero. 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. The teosinte population is chosen from individuals in the “Mound” population near Palmar Chico, Mexico (latitude, 18.6403°; longitude, −100.3570°; altitude, 1,008 m) that were previously sampled by van Heerwaarden et al. Environmental Response traits are intermediate in this regard (r = 0.80; P = 0.01). Available at, An R package for phylogenetic comparative biology (and other things), Proceedings of the National Academy of Sciences, Earth, Atmospheric, and Planetary Sciences, https://doi.org/10.6084/m9.figshare.7655588, www.pnas.org/lookup/suppl/doi:10.1073/pnas.1820997116/-/DCSupplemental, Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND), Science and Culture: Expedition artists paint a picture of science exploration, Opinion: There’s a better way to address reproducibility and replicability, Journal Club: How an animal’s teeth can reveal where it’s been. Despite having a general depletion in additive genetic variance, the maize landrace still possesses some additive genetic variance that could potentially be useful for future crop improvement. Evolutionary constraint slows trait evolution since selection for improvement of one trait can be offset by decline in another due to a genetic correlation. We fitted a common univariate linear mixed model for each trait using ASReml, version 4 (81), which implements restricted maximum-likelihood (REML) estimation of model parameters. Overall, we see that the teosinte and maize landrace G-matrices have very different structures and predicted evolutionary responses, and these differences cannot be explained by neutral drift alone. 10.3732/ajb.95.2.113 parviglumis) and a single population of maize landrace Tuxpeño (Zea mays ssp. First, selection was clearly focused on ear architecture since most of the traits that define ear architecture suffered a loss of heritable variation and ear morphology changed dramatically. Interestingly, there are four trait–pair correlations that are significant in both teosinte and maize landrace but with opposite signs, indicating a reversal during maize domestication. Similarly, maize landrace has very low h2 for Reproductive traits, suggesting that many beneficial alleles for Reproductive traits were brought to fixation during domestication. 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. To calculate θ, we used the following formula: θ=cos−1(Z^⋅g^max), where θ ranges from 0° to 90°. Despite the loss of genetic diversity by selection and bottleneck, modern maize remains rich in genetic variation, facilitating its pre-Columbian adaptation to diverse habitats from Canada to Chile (15, 16). Also, the genetic correlation between Reproductive and two other groups are stronger in teosinte but depleted in maize landrace. The most significant QTL is labeled as S1_44817082. We observed lower VD/VG in teosinte (VD/VG=0.14±0.11, ranging from 0.04 to 0.36) than maize landrace (VD/VG=0.29±0.26, ranging from 0.00 to 0.86). Our results (Fig. mays) and teosinte (ssp. TGWP may be constrained by the ability of the plant to convert solar energy into chemical energy. PhD dissertation (University of Wisconsin–Madison, Madison, WI), Identification of a functional transposon insertion in the maize domestication gene, Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in, From many, one: Genetic control of prolificacy during maize domestication, Ideal crop plant architecture is mediated by, The detection of disease clustering and a generalized regression approach, Common Principal Components and Related Multivariate Models, Hierarchical comparison of genetic variance-covariance matrices. Documents. La téosinte cultivée dans ces conditions ressemble fortement au maïs, taille des épis exceptée. This is the earliest dated evidence — by 1,200 years — for the presence and use of domesticated maize. L’analyse du maïs et de son ancêtre supposé (le téosinte) montre que les différences génétiques sont relativement restreintes. 2B and SI Appendix, Tables S1 and S2). Each plant was separated by 30 cm within rows and 76 cm between rows. 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). (69). 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). 6B and SI Appendix, Table S9). Phylogenetic analysis and archaeological data revealed that maize originated from a single domestication event in southern Mexico about 9,000 y ago (9, 10). Fortunately, the relative differences among plants for these traits are easily observable by eye and do not require modern tools for selection. Being a wild plant, teosinte may maintain higher h2 than maize as the natural environment is apt to vary more across time and space than the cultivated field (40). To compare individual trait contribution to genetic constraint, we calculated the angle θdroponei between Z and gmax for every ith trait that is dropped from Z and gmax. We found that the overall predicted evolutionary responses are not significantly more correlated than random (r = 0.19; P = 1.00), again suggesting that teosinte and maize landrace G-matrices are quite different. We tested for similarity between teosinte and maize landrace genetic correlation matrices (rg) using Mantel’s test (29). The multivariate QST–FST test indicates that the 18 traits as a whole underwent nonneutral evolution; however, further dissection of individual traits using the univariate QST–FST test reveals that one trait, TGWP, conforms to neutral expectations. While these assumptions can be naive, they represent our best model for estimating i, unlike models proposed in the literature that assume constant environmental variance over generations (83⇓⇓–86). For instance, EL is positively correlated to GE in teosinte, so selection could have been applied to either trait or even both traits concurrently to speed up the process. La domestication de la Téosinte était donc déjà̀ bien avancée il y a plus de 6 000 ans. Ressources. The degree of evolutionary constraint is measured by θT, the angle between Z and gmax,T, where θT ranges from 0° to 90°. (D) The phenotypic effect of QTL S7_3086083. Final GBS dataset has been deposited in the figshare database (76). For example, traits within the Vegetative/Flowering Time group are generally positively correlated, which translates to late flowering plants being taller and having bigger leaves. 6 and SI Appendix, Table S9). (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 (. 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 also applied similar crossing scheme to 55 maize landrace parent plants. Genetic perspectives on crop domestication. 2018 Oct;220(2):395-408. doi: 10.1111/nph.15350. analyzed data; C.J.Y., P.J.B., M.C.R., J.B.H., and J.F.D. On the other hand, eigenstructure comparison of the teosinte and maize landrace genetic correlation matrices yielded slightly different results. Various possibilities due to multivariate selection in maize domestication are explored here. While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory. 3). The researchers, led by Anthony Ranere of Temple University and Dolores Piperno of the … Molecular insights into the evolution of crop plants. Elle présente un tallage abondant et un épi de petite taille qui s’égrène facilement. (A) The distribution of detected QTL for…. S1). This difference suggests that domestication may have favored greater independence of trait groups, for example, disassociating correlations between reproductive traits and flowering time. This result suggests that directional selection on EL alone would yield the most gain and be closest to the evolutionary trajectory with minimal constraint. Maize has a more fixed growth form, producing one or two large ears over a wide range of environments, which represents an adaptation for easy harvest of the grain by its human cultivators. Teosinte plants are taller and broader-leaved than most grasses .Their general growth form is similar to that of maize, although they have much longer lateral branches. Flury hierarchy is implemented in the common principal component (CPC) software (31). Proc Natl Acad Sci U S A. Contributed by John F. Doebley, January 28, 2019 (sent for review December 14, 2018; reviewed by Loren H. Rieseberg and Bruce Walsh). Population genetics comparison of maize and teosinte revealed evidence for recent selection in multiple genomic regions, a moderate bottleneck causing loss in genetic diversity during domestication, and postdomestication gene flow from teosinte into maize that enhanced maize adaptation to diverse environments (11⇓⇓–14). 3 and SI Appendix, Table S3). Among the trait groups, Reproductive showed the most increase in VD/VG from teosinte to maize landrace, while Vegetative/Flowering Time showed the least difference in VD/VG between teosinte and maize landrace. In A, changes in trait mean (μ) are measured as log2(μM/μT) or fold change of maize landrace outcross mean (μM) over teosinte outcross mean (μT). This result is consistent with the expectation that maize domestication focused on restructuring the architecture of the ear more than other aspects of the plant. Fig 7. Nat Rev Genet. 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. A teosinte plant can have several hundred ears, each with only 10 grains, whereas maize typically has only two ears, each with several hundred grains. 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). In contrast, maize plants typically have one or two short branches, each with a single ear at its tip. We observed no apparent depletion of VD/VP in maize landrace relative to teosinte (Fig. 19. The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. S4). C’est à l’origine une plante sauvage : la téosinte, qui a subi des modifications au cours d’un processus de domestication qui a … Our results demonstrate that maize landrace experienced a substantial loss in additive genetic variance, as measured by narrow-sense heritabilities (h2), during domestication compared with teosinte. The maize landrace population was chosen from individuals in a site less than 1 km away from the teosinte population (University of Guadalajara collection JSG-RMM-LCL-529; latitude, 18.6483°; longitude, −100.3542°; altitude, 983 m). 2 - Un mutant du maïs. Changes in trait means and selection intensities. 3 and SI Appendix, Table S3). Among the trait groups, Reproductive traits have the highest level of h2, ranging from 0.27 to 0.73 (Fig. For example, teosinte plants have many ears along long lateral branches under favorable conditions, but few ears on short branches in poor conditions. 2019 Mar 19;116(12):5643-5652. doi: 10.1073/pnas.1820997116. Z is also scaled similarly to the G-matrix, so that values of |projZRi| for different traits can be compared directly.
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