The genomic signature of crop-wild introgression in maize.
The genomic signature of crop-wild introgression in maize.
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DOI：
10.1371/journal.pgen.1003477
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发表时间：
2013-05
期刊：
影响因子：
4.5
通讯作者：
Ross-Ibarra J
中科院分区：
文献类型：
--
作者：
Hufford MB;Lubinksy P;Pyhäjärvi T;Devengenzo MT;Ellstrand NC;Ross-Ibarra J
杂交和随后的渐渗的进化意义早已被认识到，但这些现象的全基因组效应的评估直到最近才成为可能。作物野生研究系统代表了通过杂交研究进化的理想机会。例如，玉米和同种野生大刍草Zea mays ssp.众所周知，墨西哥树（以下简称墨西哥树）在墨西哥高地的田野里进行杂交。尽管基因流动的证据广泛存在，玉米和墨西哥玉米保持着不同的形态，并且在同域生存中已经存在了数千年。无论是基因组的程度，也不了解这些类群之间的基因渗入的进化重要性。在这项研究中，我们评估了全基因组渐渗模式的基础上，39,029单核苷酸多态性基因型在189个个人从9个同域玉米-墨西哥人口和参考异地人口。虽然玉米和墨西哥基因组的部分出现抗基因渗入（特别是附近已知的杂交不亲和性和驯化位点），我们发现了基因渗入的两个方向的基因流的广泛证据。通过这些基因组区域和初步的生长室实验的进一步表征，我们发现的证据表明，自适应墨西哥等位基因纳入玉米在其扩展到墨西哥中部的高地。相比之下，很少有证据表明，从玉米到墨西哥的适应性渐渗。我们在这里应用的方法可以被广泛复制，这样的分析有可能极大地告知我们通过渐渗杂交进化的理解。作物物种，由于其特殊的基因组资源和频繁的历史传播到同域与亲戚，应该在这些研究中特别有影响力。杂交和渐渗已被证明在物种进化中起着关键作用。这些过程可以产生新的适应和分类群的持续多样化所必需的多样性。先前的研究表明，并非基因组的所有区域都同样可渗透渗入。我们已经进行了第一个全基因组的评估模式的相互渗入植物种群。我们发现的证据表明，驯化玉米从一个野生的亲戚，teosinte，在其传播到墨西哥中部的高海拔地区的高原条件的适应。基因流表现出不对称性，有利于大刍草渐渗到玉米中，并且在群体间广泛分布在玉米适应位点。与此相反，基因组区域附近的已知驯化和杂交不亲和位点出现特别耐基因渗入的基因流的两个方向。作物-野生种研究系统由于其丰富的基因组资源和作物扩展过程中基因相互流动的历史，在未来的渐渗研究中应发挥重要作用。
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. Hybridization and introgression have been shown to play a critical role in the evolution of species. These processes can generate the diversity necessary for novel adaptations and continued diversification of taxa. Previous research has suggested that not all regions of a genome are equally permeable to introgression. We have conducted one of the first genome-wide assessments of patterns of reciprocal introgression in plant populations. We found evidence that suggests domesticated maize received adaptation to highland conditions from a wild relative, teosinte, during its spread to the high elevations of central Mexico. Gene flow appeared asymmetric, favoring teosinte introgression into maize, and was widespread across populations at putatively adaptive loci. In contrast, genomic regions near known domestication and cross-incompatibility loci appeared particularly resistant to introgression in both directions of gene flow. Crop-wild study systems should play an important role in future studies of introgression due to their well-developed genomic resources and histories of reciprocal gene flow during crop expansion.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
5.4
作者：
Evans, MMS;Kermicle, JL
通讯作者：
Kermicle, JL
影响因子：
1.9
作者：
DOEBLEY, JF
通讯作者：
DOEBLEY, JF
影响因子：
4.5
作者：
Cornille A;Gladieux P;Smulders MJ;Roldán-Ruiz I;Laurens F;Le Cam B;Nersesyan A;Clavel J;Olonova M;Feugey L;Gabrielyan I;Zhang XG;Tenaillon MI;Giraud T
通讯作者：
Giraud T
影响因子：
64.8
作者：
Doebley, J;Stec, A;Hubbard, L
通讯作者：
Hubbard, L