TY - JOUR
T1 - Capturing Wheat Phenotypes at the Genome Level
AU - Hussain, Babar
AU - Akpınar, Bala A.
AU - Alaux, Michael
AU - Algharib, Ahmed M.
AU - Sehgal, Deepmala
AU - Ali, Zulfiqar
AU - Aradottir, Gudbjorg I.
AU - Batley, Jacqueline
AU - Bellec, Arnaud
AU - Bentley, Alison R.
AU - Cagirici, Halise B.
AU - Cattivelli, Luigi
AU - Choulet, Fred
AU - Cockram, James
AU - Desiderio, Francesca
AU - Devaux, Pierre
AU - Dogramaci, Munevver
AU - Dorado, Gabriel
AU - Dreisigacker, Susanne
AU - Edwards, David
AU - El-Hassouni, Khaoula
AU - Eversole, Kellye
AU - Fahima, Tzion
AU - Figueroa, Melania
AU - Gálvez, Sergio
AU - Gill, Kulvinder S.
AU - Govta, Liubov
AU - Gul, Alvina
AU - Hensel, Goetz
AU - Hernandez, Pilar
AU - Crespo-Herrera, Leonardo Abdiel
AU - Ibrahim, Amir
AU - Kilian, Benjamin
AU - Korzun, Viktor
AU - Krugman, Tamar
AU - Li, Yinghui
AU - Liu, Shuyu
AU - Mahmoud, Amer F.
AU - Morgounov, Alexey
AU - Muslu, Tugdem
AU - Naseer, Faiza
AU - Ordon, Frank
AU - Paux, Etienne
AU - Perovic, Dragan
AU - Reddy, Gadi V.P.
AU - Reif, Jochen Christoph
AU - Reynolds, Matthew
AU - Roychowdhury, Rajib
AU - Rudd, Jackie
AU - Sen, Taner Z.
AU - Sukumaran, Sivakumar
AU - Ozdemir, Bahar Sogutmaz
AU - Tiwari, Vijay Kumar
AU - Ullah, Naimat
AU - Unver, Turgay
AU - Yazar, Selami
AU - Appels, Rudi
AU - Budak, Hikmet
N1 - Publisher Copyright:
Copyright © 2022 Hussain, Akpınar, Alaux, Algharib, Sehgal, Ali, Aradottir, Batley, Bellec, Bentley, Cagirici, Cattivelli, Choulet, Cockram, Desiderio, Devaux, Dogramaci, Dorado, Dreisigacker, Edwards, El-Hassouni, Eversole, Fahima, Figueroa, Gálvez, Gill, Govta, Gul, Hensel, Hernandez, Crespo-Herrera, Ibrahim, Kilian, Korzun, Krugman, Li, Liu, Mahmoud, Morgounov, Muslu, Naseer, Ordon, Paux, Perovic, Reddy, Reif, Reynolds, Roychowdhury, Rudd, Sen, Sukumaran, Ozdemir, Tiwari, Ullah, Unver, Yazar, Appels and Budak.
PY - 2022/7/4
Y1 - 2022/7/4
N2 - 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, 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 9 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 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, 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 characterizing 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 new opportunities 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 focus on reported candidate genes cloned and linked to 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 and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
AB - 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, 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 9 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 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, 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 characterizing 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 new opportunities 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 focus on reported candidate genes cloned and linked to 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 and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
KW - CRISPR/Cas9
KW - QTL cloning
KW - Wheat
KW - abiotic-stress tolerance
KW - disease resistance
KW - genome-wide association
KW - genomic selection
KW - quantitative trait locus mapping
UR - http://www.scopus.com/inward/record.url?scp=85134628015&partnerID=8YFLogxK
U2 - 10.3389/fpls.2022.851079
DO - 10.3389/fpls.2022.851079
M3 - Review article
C2 - 35860541
AN - SCOPUS:85134628015
SN - 1664-462X
VL - 13
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 851079
ER -