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      Current Progress in Understanding and Recovering the Wheat Genes Lost in Evolution and Domestication

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          Abstract

          The modern cultivated wheat has passed a long evolution involving origin of wild emmer (WEM), development of cultivated emmer, formation of spelt wheat and finally establishment of modern bread wheat and durum wheat. During this evolutionary process, rapid alterations and sporadic changes in wheat genome took place, due to hybridization, polyploidization, domestication, and mutation. This has resulted in some modifications and a high level of gene loss. As a result, the modern cultivated wheat does not contain all genes of their progenitors. These lost genes are novel for modern wheat improvement. Exploring wild progenitor for genetic variation of important traits is directly beneficial for wheat breeding. WEM wheat ( Triticum dicoccoides) is a great genetic resource with huge diversity for traits. Few genes and quantitative trait loci (QTL) for agronomic, quantitative, biotic and abiotic stress-related traits have already been mapped from WEM. This resource can be utilized for modern wheat improvement by integrating identified genes or QTLs through breeding.

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          Most cited references103

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          Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.

          Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
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            Das Domestikationssyndrom

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              Grinding up wheat: a massive loss of nucleotide diversity since domestication.

              Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample of 101 individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify 2 genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms--by 69% in bread wheat and 84% in durum wheat--with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3--giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness--an important trait for end-use quality in wheat.
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                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                14 August 2020
                August 2020
                : 21
                : 16
                : 5836
                Affiliations
                [1 ]State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; shanjida.rahman@ 123456murdoch.edu.au (S.R.); s.islam@ 123456murdoch.edu.au (S.I.); zitongyu@ 123456outlook.com (Z.Y.); m.she@ 123456murdoch.edu.au (M.S.)
                [2 ]Institute of Evolution, University of Haifa, Haifa 31905, Israel; nevo@ 123456evo.haifa.ac.il
                Author notes
                [* ]Correspondence: w.ma@ 123456murdoch.edu.au
                Author information
                https://orcid.org/0000-0001-5994-0521
                https://orcid.org/0000-0002-1264-866X
                Article
                ijms-21-05836
                10.3390/ijms21165836
                7461589
                32823887
                17bc50be-e07a-40b5-be55-409174f3a0d0
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 14 July 2020
                : 12 August 2020
                Categories
                Review

                Molecular biology
                gene modification,wild emmer wheat,evolution and domestication,novel genes,trait enhancement

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