Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq

Tian, Tian; Chen, Lijuan; Ai, Yufang; He, Hongwen

doi:10.3390/genes13020224

Cited by 11 publications

(7 citation statements)

References 134 publications

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“…Out of 5842 maize genes, 2565 genes were available in 101 maize MQTL regions previously identified to be associated with drought stress tolerance [40][41][42] . Similarly, out of 5277 rice genes, 2704 genes belonged to 140 rice MQTLs earlier reported to be associated with heat, drought, and salinity stress tolerance [43][44][45][46][47] . The number of conserved genes at corresponding orthologous positions of MQTLs (between 'wheat and maize' and 'wheat and rice') ranged from just a few to hundreds of genes.…”

Section: Candidate Genes Available From Mast-mqtlsmentioning

confidence: 94%

“…www.nature.com/scientificreports/ regions conserved among all the three cereals, genomic positions of gene models underlying wheat MQTLs were compared with the orthologous genes available from rice MQTLs for SS tolerance 42 , DS tolerance 44,45 , HS tolerance 46,47 and maize MQTLs for DS tolerance [40][41][42]120 . MQTLs containing similar gene models located on conserved genomic regions of wheat, barley, rice, and maize were accepted as ortho-MQTLs.…”

Section: Data Availabilitymentioning

confidence: 99%

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Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

Tanin

Saini

Sandhu

et al. 2022

Sci Rep

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In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress (DS), heat stress (HS), salinity stress (SS), water-logging stress (WS), pre-harvest sprouting (PHS), and aluminium stress (AS) which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 189 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.

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Section: Candidate Genes Available From Mast-mqtlsmentioning

confidence: 94%

Section: Data Availabilitymentioning

confidence: 99%

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

Tanin

Saini

Sandhu

et al. 2022

Sci Rep

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show abstract

“…A large number of receptor kinases in crops are related to disease resistance regulation; for example, the LRK10 gene is closely linked to the wheat leaf rust resistance gene Lr10 [44]. Stpk-V, a key member of the powdery mildew resistance gene Pm21, encodes serine/threonine protein kinases, and the wall-associated receptor kinase gene OsWAK1 also plays an important role against rice blast fungus [45,46]. In this study, six A. cristatum receptor kinase genes were identified in the interaction of II-9-3 inoculated with P. triticina.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis Reveals the Gene Expression and Regulatory Characteristics of Broad-Spectrum Immunity to Leaf Rust in a Wheat–Agropyron cristatum 2P Addition Line

Liu

et al. 2022

IJMS

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Wheat leaf rust (caused by Puccinia triticina Erikss.) is among the major diseases of common wheat. The lack of resistance genes to leaf rust has limited the development of wheat cultivars. Wheat–Agropyron cristatum (A. cristatum) 2P addition line II-9-3 has been shown to provide broad-spectrum immunity to leaf rust. To identify the specific A. cristatum resistance genes and related regulatory pathways in II-9-3, we conducted a comparative transcriptome analysis of inoculated and uninoculated leaves of the resistant addition line II-9-3 and the susceptible cultivar Fukuhokomugi (Fukuho). The results showed that there were 66 A. cristatum differentially expressed genes (DEGs) and 1389 wheat DEGs in II-9-3 during P. triticina infection. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and gene set enrichment analysis (GSEA) revealed that the DEGs of II-9-3 were associated with plant–pathogen interaction, MAPK signaling pathway–plant, plant hormone signal transduction, glutathione metabolism, and phenylpropanoid biosynthesis. Furthermore, many defense-related A. cristatum genes, such as two NLR genes, seven receptor kinase-encoding genes, and four transcription factor-encoding genes, were identified. Our results indicated that the key step of resistance to leaf rust involves, firstly, the gene expression of chromosome 2P upstream of the immune pathway and, secondly, the effect of chromosome 2P on the co-expression of wheat genes in II-9-3. The disease resistance regulatory pathways and related genes in the addition line II-9-3 thus could play a critical role in the effective utilization of innovative resources for leaf rust resistance in wheat breeding.

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“…Out of 5,842 maize genes, 2,565 genes were available in 101 maize MQTL regions previously identified to be associated with drought stress tolerance 38,39,40 . Similarly, out of 5,277 rice genes, 2,704 genes belonged to 140 rice MQTLs earlier reported to be associated with heat, drought, and salinity stress tolerance 41,42,43,44,45 . The number of conserved genes at corresponding orthologous positions of MQTLs (between 'wheat and maize' and 'wheat and rice') ranged from just a few to hundreds of genes.…”

Section: Conserved Genomic Regions Control Tolerance To Multiple Abio...mentioning

confidence: 91%

“…This analysis involved the following two steps: (i) gene models from the selected MQTL regions were BLASTed against rice and maize genomes at Ensemble Plants to discover conserved genomic regions, and (ii) the matching rice and maize orthologues were retrieved from the database with their genomic coordinates. In order to identify the ortho-MQTLs from the genomic regions conserved among all the three cereals, genomic positions of gene models underlying wheat MQTLs were compared with the orthologous genes available from rice MQTLs for SS tolerance 41 , DS tolerance 42,43 , HS tolerance 44,45 and maize MQTLs for DS tolerance 38,95,39,40 . MQTLs containing similar gene models located on conserved genomic regions of wheat, barley, rice, and maize were considered ortho-MQTLs.…”

Section: Methodsmentioning

confidence: 99%

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

Tanin

Saini

Sandhu

et al. 2022

Preprint

View full text Add to dashboard Cite

In wheat, a meta-analysis was performed using previously identified QTLs associated with drought stress, heat stress, salinity stress, water-logging stress, pre-harvest sprouting, and aluminium stress which predicted a total of 134 meta-QTLs (MQTLs) that involved at least 28 consistent and stable MQTLs conferring tolerance to five or all six abiotic stresses under study. Seventy-six MQTLs out of the 132 physically anchored MQTLs were also verified with genome-wide association studies. Around 43% of MQTLs had genetic and physical confidence intervals of less than 1 cM and 5 Mb, respectively. Consequently, 539 genes were identified in some selected MQTLs providing tolerance to 5 or all 6 abiotic stresses. Comparative analysis of genes underlying MQTLs with four RNA-seq based transcriptomic datasets unravelled a total of 191 differentially expressed genes which also included at least 11 most promising candidate genes common among different datasets. The promoter analysis showed that the promoters of these genes include many stress responsiveness cis-regulatory elements, such as ARE, MBS, TC-rich repeats, As-1 element, STRE, LTR, WRE3, and WUN-motif among others. Further, some MQTLs also overlapped with as many as 34 known abiotic stress tolerance genes. In addition, numerous ortho-MQTLs among the wheat, maize, and rice genomes were discovered. These findings could help with fine mapping and gene cloning, as well as marker-assisted breeding for multiple abiotic stress tolerances in wheat.

show abstract

Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq

Cited by 11 publications

References 134 publications

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

Comparative Transcriptome Analysis Reveals the Gene Expression and Regulatory Characteristics of Broad-Spectrum Immunity to Leaf Rust in a Wheat–Agropyron cristatum 2P Addition Line

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

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