Wheat genomics and breeding: bridging the gap
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, until very recently efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species due to its large polyploid genome. However, an international public-private effort spanning nine years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat genome assembly in 2017. Shortly thereafter, in 2020, the genome of assemblies of additional fifteen global wheat accessions were released. Wheat has now entered into the pan-genomic era where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays capable of genotyping hundreds of wheat lines using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up a new horizon for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits including grain yield, yield-related traits, end-use quality and resistance to biotic and abiotic stresses. We also enlisted several reported candidate and cloned candidate genes responsible for the aforesaid traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits through the use of (i) clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) mediated gene-editing, (ii) positional cloning methods, and of genomic selection. Finally, we make recommendations on the utilization of genomics for the next-generation wheat breeding and provide a practical example of using the latest, in silico bioinformatics tools that were based on the wheat reference genome sequence.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Format: | Article biblioteca |
Language: | English |
Published: |
CABI
2021
|
Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Genome-Wide Association Study, Abiotic Stress Tolerance, Grain Yield, Genomic Selection, CRISPR/Cas9, Wheat Breeding, TRITICUM AESTIVUM, MARKER-ASSISTED SELECTION, CHROMOSOME MAPPING, ABIOTIC STRESS, GRAIN, QUALITY, QUANTITATIVE TRAIT LOCI, DISEASE RESISTANCE, BIOINFORMATICS, WHEAT, PLANT BREEDING, |
Online Access: | https://hdl.handle.net/10883/21711 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cimmyt-10883-21711 |
---|---|
record_format |
koha |
spelling |
dig-cimmyt-10883-217112024-03-14T15:37:38Z Wheat genomics and breeding: bridging the gap Hussain, B. Akpınar, B.A. Alaux, M. Algharib, A.M. Sehgal, D. Ali, Z. Appels, R. Aradottir, G.I. Batley, J. Bellec, A. Bentley, A.R. Cagirici, H.B. Cattivelli, L. Choulet, F. Cockram, J. Desiderio, F. Devaux, P. Dogramaci, M. Dorado, G. Dreisigacker, S. Edwards, D. El Hassouni, K. Eversole, K. Fahima, T. Figueroa, M. Gálvez, S. Gill, K.S. Govta, L. Gul Kazi, A. Hensel, G. Hernandez, P. Crespo Herrera, L.A. Ibrahim, A.M.H. Kilian, B. Korzun, V. Krugman, T. Yinghui Li Shuyu Liu Mahmoud, A.F. Morgounov, A.I. Muslu, T. Naseer, F. Ordon, F. Paux, E. Perovic, D. Reddy, G.V.P. Reif, J.C. Reynolds, M.P. Roychowdhury, R. Rudd, J.C. Sen, T.Z. Sukumaran, S. Tiwari, V.K. Ullah, N. Unver, T. Yazar, S. Budak, H. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Abiotic Stress Tolerance Grain Yield Genomic Selection CRISPR/Cas9 Wheat Breeding TRITICUM AESTIVUM MARKER-ASSISTED SELECTION CHROMOSOME MAPPING ABIOTIC STRESS GRAIN QUALITY QUANTITATIVE TRAIT LOCI DISEASE RESISTANCE BIOINFORMATICS WHEAT PLANT BREEDING Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, until very recently efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species due to its large polyploid genome. However, an international public-private effort spanning nine years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat genome assembly in 2017. Shortly thereafter, in 2020, the genome of assemblies of additional fifteen global wheat accessions were released. Wheat has now entered into the pan-genomic era where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays capable of genotyping hundreds of wheat lines using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up a new horizon for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits including grain yield, yield-related traits, end-use quality and resistance to biotic and abiotic stresses. We also enlisted several reported candidate and cloned candidate genes responsible for the aforesaid traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits through the use of (i) clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) mediated gene-editing, (ii) positional cloning methods, and of genomic selection. Finally, we make recommendations on the utilization of genomics for the next-generation wheat breeding and provide a practical example of using the latest, in silico bioinformatics tools that were based on the wheat reference genome sequence. Preprint 2021-10-27T00:20:31Z 2021-10-27T00:20:31Z 2021 Article Published Version https://hdl.handle.net/10883/21711 10.31220/agriRxiv.2021.00039 English CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose Open Access Wallingford (United Kingdom) CABI AgriRxiv |
institution |
CIMMYT |
collection |
DSpace |
country |
México |
countrycode |
MX |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cimmyt |
tag |
biblioteca |
region |
America del Norte |
libraryname |
CIMMYT Library |
language |
English |
topic |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Abiotic Stress Tolerance Grain Yield Genomic Selection CRISPR/Cas9 Wheat Breeding TRITICUM AESTIVUM MARKER-ASSISTED SELECTION CHROMOSOME MAPPING ABIOTIC STRESS GRAIN QUALITY QUANTITATIVE TRAIT LOCI DISEASE RESISTANCE BIOINFORMATICS WHEAT PLANT BREEDING AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Abiotic Stress Tolerance Grain Yield Genomic Selection CRISPR/Cas9 Wheat Breeding TRITICUM AESTIVUM MARKER-ASSISTED SELECTION CHROMOSOME MAPPING ABIOTIC STRESS GRAIN QUALITY QUANTITATIVE TRAIT LOCI DISEASE RESISTANCE BIOINFORMATICS WHEAT PLANT BREEDING |
spellingShingle |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Abiotic Stress Tolerance Grain Yield Genomic Selection CRISPR/Cas9 Wheat Breeding TRITICUM AESTIVUM MARKER-ASSISTED SELECTION CHROMOSOME MAPPING ABIOTIC STRESS GRAIN QUALITY QUANTITATIVE TRAIT LOCI DISEASE RESISTANCE BIOINFORMATICS WHEAT PLANT BREEDING AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Abiotic Stress Tolerance Grain Yield Genomic Selection CRISPR/Cas9 Wheat Breeding TRITICUM AESTIVUM MARKER-ASSISTED SELECTION CHROMOSOME MAPPING ABIOTIC STRESS GRAIN QUALITY QUANTITATIVE TRAIT LOCI DISEASE RESISTANCE BIOINFORMATICS WHEAT PLANT BREEDING Hussain, B. Akpınar, B.A. Alaux, M. Algharib, A.M. Sehgal, D. Ali, Z. Appels, R. Aradottir, G.I. Batley, J. Bellec, A. Bentley, A.R. Cagirici, H.B. Cattivelli, L. Choulet, F. Cockram, J. Desiderio, F. Devaux, P. Dogramaci, M. Dorado, G. Dreisigacker, S. Edwards, D. El Hassouni, K. Eversole, K. Fahima, T. Figueroa, M. Gálvez, S. Gill, K.S. Govta, L. Gul Kazi, A. Hensel, G. Hernandez, P. Crespo Herrera, L.A. Ibrahim, A.M.H. Kilian, B. Korzun, V. Krugman, T. Yinghui Li Shuyu Liu Mahmoud, A.F. Morgounov, A.I. Muslu, T. Naseer, F. Ordon, F. Paux, E. Perovic, D. Reddy, G.V.P. Reif, J.C. Reynolds, M.P. Roychowdhury, R. Rudd, J.C. Sen, T.Z. Sukumaran, S. Tiwari, V.K. Ullah, N. Unver, T. Yazar, S. Budak, H. Wheat genomics and breeding: bridging the gap |
description |
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, until very recently efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species due to its large polyploid genome. However, an international public-private effort spanning nine years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat genome assembly in 2017. Shortly thereafter, in 2020, the genome of assemblies of additional fifteen global wheat accessions were released. Wheat has now entered into the pan-genomic era where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays capable of genotyping hundreds of wheat lines using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up a new horizon for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits including grain yield, yield-related traits, end-use quality and resistance to biotic and abiotic stresses. We also enlisted several reported candidate and cloned candidate genes responsible for the aforesaid traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits through the use of (i) clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) mediated gene-editing, (ii) positional cloning methods, and of genomic selection. Finally, we make recommendations on the utilization of genomics for the next-generation wheat breeding and provide a practical example of using the latest, in silico bioinformatics tools that were based on the wheat reference genome sequence. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Abiotic Stress Tolerance Grain Yield Genomic Selection CRISPR/Cas9 Wheat Breeding TRITICUM AESTIVUM MARKER-ASSISTED SELECTION CHROMOSOME MAPPING ABIOTIC STRESS GRAIN QUALITY QUANTITATIVE TRAIT LOCI DISEASE RESISTANCE BIOINFORMATICS WHEAT PLANT BREEDING |
author |
Hussain, B. Akpınar, B.A. Alaux, M. Algharib, A.M. Sehgal, D. Ali, Z. Appels, R. Aradottir, G.I. Batley, J. Bellec, A. Bentley, A.R. Cagirici, H.B. Cattivelli, L. Choulet, F. Cockram, J. Desiderio, F. Devaux, P. Dogramaci, M. Dorado, G. Dreisigacker, S. Edwards, D. El Hassouni, K. Eversole, K. Fahima, T. Figueroa, M. Gálvez, S. Gill, K.S. Govta, L. Gul Kazi, A. Hensel, G. Hernandez, P. Crespo Herrera, L.A. Ibrahim, A.M.H. Kilian, B. Korzun, V. Krugman, T. Yinghui Li Shuyu Liu Mahmoud, A.F. Morgounov, A.I. Muslu, T. Naseer, F. Ordon, F. Paux, E. Perovic, D. Reddy, G.V.P. Reif, J.C. Reynolds, M.P. Roychowdhury, R. Rudd, J.C. Sen, T.Z. Sukumaran, S. Tiwari, V.K. Ullah, N. Unver, T. Yazar, S. Budak, H. |
author_facet |
Hussain, B. Akpınar, B.A. Alaux, M. Algharib, A.M. Sehgal, D. Ali, Z. Appels, R. Aradottir, G.I. Batley, J. Bellec, A. Bentley, A.R. Cagirici, H.B. Cattivelli, L. Choulet, F. Cockram, J. Desiderio, F. Devaux, P. Dogramaci, M. Dorado, G. Dreisigacker, S. Edwards, D. El Hassouni, K. Eversole, K. Fahima, T. Figueroa, M. Gálvez, S. Gill, K.S. Govta, L. Gul Kazi, A. Hensel, G. Hernandez, P. Crespo Herrera, L.A. Ibrahim, A.M.H. Kilian, B. Korzun, V. Krugman, T. Yinghui Li Shuyu Liu Mahmoud, A.F. Morgounov, A.I. Muslu, T. Naseer, F. Ordon, F. Paux, E. Perovic, D. Reddy, G.V.P. Reif, J.C. Reynolds, M.P. Roychowdhury, R. Rudd, J.C. Sen, T.Z. Sukumaran, S. Tiwari, V.K. Ullah, N. Unver, T. Yazar, S. Budak, H. |
author_sort |
Hussain, B. |
title |
Wheat genomics and breeding: bridging the gap |
title_short |
Wheat genomics and breeding: bridging the gap |
title_full |
Wheat genomics and breeding: bridging the gap |
title_fullStr |
Wheat genomics and breeding: bridging the gap |
title_full_unstemmed |
Wheat genomics and breeding: bridging the gap |
title_sort |
wheat genomics and breeding: bridging the gap |
publisher |
CABI |
publishDate |
2021 |
url |
https://hdl.handle.net/10883/21711 |
work_keys_str_mv |
AT hussainb wheatgenomicsandbreedingbridgingthegap AT akpınarba wheatgenomicsandbreedingbridgingthegap AT alauxm wheatgenomicsandbreedingbridgingthegap AT algharibam wheatgenomicsandbreedingbridgingthegap AT sehgald wheatgenomicsandbreedingbridgingthegap AT aliz wheatgenomicsandbreedingbridgingthegap AT appelsr wheatgenomicsandbreedingbridgingthegap AT aradottirgi wheatgenomicsandbreedingbridgingthegap AT batleyj wheatgenomicsandbreedingbridgingthegap AT belleca wheatgenomicsandbreedingbridgingthegap AT bentleyar wheatgenomicsandbreedingbridgingthegap AT cagiricihb wheatgenomicsandbreedingbridgingthegap AT cattivellil wheatgenomicsandbreedingbridgingthegap AT chouletf wheatgenomicsandbreedingbridgingthegap AT cockramj wheatgenomicsandbreedingbridgingthegap AT desideriof wheatgenomicsandbreedingbridgingthegap AT devauxp wheatgenomicsandbreedingbridgingthegap AT dogramacim wheatgenomicsandbreedingbridgingthegap AT doradog wheatgenomicsandbreedingbridgingthegap AT dreisigackers wheatgenomicsandbreedingbridgingthegap AT edwardsd wheatgenomicsandbreedingbridgingthegap AT elhassounik wheatgenomicsandbreedingbridgingthegap AT eversolek wheatgenomicsandbreedingbridgingthegap AT fahimat wheatgenomicsandbreedingbridgingthegap AT figueroam wheatgenomicsandbreedingbridgingthegap AT galvezs wheatgenomicsandbreedingbridgingthegap AT gillks wheatgenomicsandbreedingbridgingthegap AT govtal wheatgenomicsandbreedingbridgingthegap AT gulkazia wheatgenomicsandbreedingbridgingthegap AT henselg wheatgenomicsandbreedingbridgingthegap AT hernandezp wheatgenomicsandbreedingbridgingthegap AT crespoherrerala wheatgenomicsandbreedingbridgingthegap AT ibrahimamh wheatgenomicsandbreedingbridgingthegap AT kilianb wheatgenomicsandbreedingbridgingthegap AT korzunv wheatgenomicsandbreedingbridgingthegap AT krugmant wheatgenomicsandbreedingbridgingthegap AT yinghuili wheatgenomicsandbreedingbridgingthegap AT shuyuliu wheatgenomicsandbreedingbridgingthegap AT mahmoudaf wheatgenomicsandbreedingbridgingthegap AT morgounovai wheatgenomicsandbreedingbridgingthegap AT muslut wheatgenomicsandbreedingbridgingthegap AT naseerf wheatgenomicsandbreedingbridgingthegap AT ordonf wheatgenomicsandbreedingbridgingthegap AT pauxe wheatgenomicsandbreedingbridgingthegap AT perovicd wheatgenomicsandbreedingbridgingthegap AT reddygvp wheatgenomicsandbreedingbridgingthegap AT reifjc wheatgenomicsandbreedingbridgingthegap AT reynoldsmp wheatgenomicsandbreedingbridgingthegap AT roychowdhuryr wheatgenomicsandbreedingbridgingthegap AT ruddjc wheatgenomicsandbreedingbridgingthegap AT sentz wheatgenomicsandbreedingbridgingthegap AT sukumarans wheatgenomicsandbreedingbridgingthegap AT tiwarivk wheatgenomicsandbreedingbridgingthegap AT ullahn wheatgenomicsandbreedingbridgingthegap AT unvert wheatgenomicsandbreedingbridgingthegap AT yazars wheatgenomicsandbreedingbridgingthegap AT budakh wheatgenomicsandbreedingbridgingthegap |
_version_ |
1794797634524807168 |