Comparative DNA Sequence Analysis of Wheat and Rice Genomes

Sorrells, Mark E.; Rota, Mauricio La; Bermudez-Kandianis, C. E.; Greene, Robert A.; Kantety, Ramesh V.; Munkvold, Jesse; Miftahudin, Miftahudin; Mahmoud, Ahmed A.; Ma, Xuefeng; Gustafson, Perry; Qi, Lili; Echalier, Benjamin; Gill, Bikram S.; Matthews, David E.; Lazo, Gerard R.; Chao, Shiaoman; Anderson, Olin D.; Edwards, H; Linkiewicz, Anna; Dubcovsky, Jorge; Akhunov, Eduard; Dvořák, Jan; Zhang, Deshui; Nguyen, Henry T.; Peng, Junhua; Lapitan, Nora L. V.; González-Hernández, José L.; Anderson, James A.; Hossain, Khwaja; Kalavacharla, Venu; Kianian, Shahryar F.; Choi, Dong-Woog; Close, Timothy J.; Dilbirliği, Muharrem; Gill, Kulvinder S.; Steber, Camille M.; Walker-Simmons, M. K.; McGuire, Patrick E.; Qualset, C. O.

doi:10.1101/gr.1113003

Cited by 368 publications

(8 citation statements)

References 51 publications

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“…Here we report an ordered and annotated assembly (IWGSC RefSeq v1.0) of the 21 chromosomes of the allohexaploid wheat cultivar CS, an achievement that is built on a rich history of chromosome studies in wheat (10)(11)(12), which allowed the integration of genetic and genomic resources. The completeness and accuracy of IWGSC RefSeq v1.0 provide insights into global genome composition and enable the construction of complex gene coexpression networks to identify central regulators in critical pathways, such as flowering-time control.…”

mentioning

confidence: 99%

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Appels

Eversole

Stein

et al. 2018

Science

2,172

1,404

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An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

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mentioning

confidence: 99%

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Appels

Eversole

Stein

et al. 2018

Science

2,172

1,404

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“…In the present study, we also observed that no RuvbL gene was present on homoeologous chromosomes of rice and wheat, suggesting their diverse evolution. For example, TaRuvBL1a genes are present on each of the three chromosomes of homoeologous group 4 (4A, 4B, and 4D); these three genes are orthologues of the rice gene OsRuvBL1a located on rice chromosome 1, which is not homoeologous to chromosome of homoeologous group 4 of wheat (Ahn et al 1993;Sorrells et al 2003). Similarly, RuvBL1b genes are located on 3A, 3B, 3D chromosomes of wheat and an unrelated rice chromosome 7.…”

Section: Taruvbl Genes In Wheat and Related Speciesmentioning

confidence: 99%

Identification and characterization of RuvBL DNA helicase genes for tolerance against abiotic stresses in bread wheat (Triticum aestivum L.) and related species

Chaudhary¹,

Gautam²,

Gahlaut³

et al. 2023

Funct Integr Genomics

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RuvBL helicase genes represent a conserved family of genes, which are known to be involved in providing tolerance against abiotic stresses like heat and drought in plants. We identi ed nine wheat RuvBL genes on nine different chromosomes, belonging to homoeologous groups 2, 3, and 4. Analysis of the structure and function of these genes revealed that the (i) length of genes ranged from 1647 to 2197 bp; (ii) genes exhibit synteny with corresponding genes in related species including Ae. tauschii, Z. mays, O. sativa, H. vulgare and B. distachyon; (iii) gene sequences were associated with cis-elements and transposable elements; (iv) the genes TaRuvBL1a-4A and TaRuvBL1a-4B also carried targets for a widely known miRNA, tae-miR164. Gene ontology revealed that these genes were closely associated with ATPdependent formation of histone acetyltransferase complex. Analysis of the structure and function of RuvBL proteins revealed that (i) proteins were localized mainly in the cytoplasm; (ii) the protein encoded by the representative gene TaRuvBL1a-4A was shown to be involved in protein-protein interactions with ten other proteins; (iii) on the basis of phylogeny, RuvBL proteins were placed in two sub-divisions, namely RuvBL1 and RuvBL2, which were further classi ed into clusters and sub-clusters. In-silico expression analysis suggested that these genes were differentially expressed under heat/drought. The qRT-PCR analysis con rmed that expression of TaRuvBL genes differed among wheat cultivars with varying degrees of thermotolerance. This study advances our understanding of the biological role of wheat RuvBL genes and should help in planning future studies on RuvBL genes in wheat.

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“…To date, studies have identified more candidate genes and generated more breeding applications related to NUE in rice than in wheat [ 22 , 54 ] ( Table 2 ). Translating insights from rice to wheat require herculean efforts, largely because of differences in genomic size and structure [ 22 , 144 , 145 ]. New mutant resources [ 146 ] and transgenic tools [ 147 ], however, increase the feasibility of characterizing candidate genes across a polyploid genome.…”

Section: Puzzles—knowledge Gaps About Modifying Nitrogen Metabolism F...mentioning

confidence: 99%

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

Kasemsap

Bloom

2022

Plants

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Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

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Comparative DNA Sequence Analysis of Wheat and Rice Genomes

Cited by 368 publications

References 51 publications

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Identification and characterization of RuvBL DNA helicase genes for tolerance against abiotic stresses in bread wheat (Triticum aestivum L.) and related species

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

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