scholarly journals Meta-QTLs and candidate genes for stripe rust resistance in wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Irfat Jan ◽  
Gautam Saripalli ◽  
Kuldeep Kumar ◽  
Anuj Kumar ◽  
Rakhi Singh ◽  
...  
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Molecular Breeding ◽  
Sugar Transport ◽  
Stripe Rust Resistance ◽  
Consensus Map ◽  
Future Studies ◽  
Lrr Domain

AbstractIn bread wheat, meta-QTL analysis was conducted using 353 QTLs that were available from earlier studies. When projected onto a dense consensus map comprising 76,753 markers, only 184 QTLs with the required information, could be utilized leading to identification of 61 MQTLs spread over 18 of the 21 chromosomes (barring 5D, 6D and 7D). The range for mean R2 (PVE %) was 1.9% to 48.1%, and that of CI was 0.02 to 11.47 cM; these CIs also carried 37 Yr genes. Using these MQTLs, 385 candidate genes (CGs) were also identified. Out of these CGs, 241 encoded known R proteins and 120 showed differential expression due to stripe rust infection at the seedling stage; the remaining 24 CGs were common in the sense that they encoded R proteins as well as showed differential expression. The proteins encoded by CGs carried the following widely known domains: NBS-LRR domain, WRKY domains, ankyrin repeat domains, sugar transport domains, etc. Thirteen breeders’ MQTLs (PVE > 20%) including four pairs of closely linked MQTLs are recommended for use in wheat molecular breeding, for future studies to understand the molecular mechanism of stripe rust resistance and for gene cloning.

scholarly journals Meta-QTL Analysis for Stripe Rust Resistance in Wheat

2021 ◽  
Author(s):  
Irfat Jan ◽  
Gautam Saripalli ◽  
Kuldeep Kumar ◽  
Anuj Kumar ◽  
Rakhi Singh ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Puccinia Striiformis ◽  
Stripe Rust Resistance ◽  
Wheat Cultivars ◽  
Consensus Map ◽  
Sugar Transporters ◽  
Wheat Diseases ◽  
Genes Encoding ◽  
Genomic Regions

Abstract Stripe rust caused by Puccinia striiformis f. sp. tritici Eriks. & E. Henn (Pst) is one of the most prevalent wheat diseases causing upto 70% yield losses worldwide. The present study was conducted in wheat for the first time to identify important meta-QTL (MQTL) regions for their use in developing stripe rust resistant wheat cultivars and to understand the genetic architecture of stripe rust resistance in wheat. For this purpose, a dense consensus map consisting of 76,753 markers was constructed and 353 QTLs from earlier studies were projected on this consensus map. As many as 61 MQTLs were identified using 184 (out of 353) original QTLs. Ten important genomic regions including six breeders’ MQTLs (PVE >20%) and four MQTL hotspots were selected to be used by wheat breeders. As many as 409 important candidate genes (CGs) were also identified, which either encoded known R proteins (265) or showed differential expression (144) due to stripe rust infection. These included genes encoding the following proteins: NBS-LRR, WRKY domains, ankyrin repeat domains, sugar transporters, etc. Overall, the present study provided robust MQTLs and underlying CGs which may be potential targets for molecular breeding for development of stripe rust resistant wheat cultivars or may be the target for future molecular studies to understand the mechanism of stripe rust resistance.

Characterization of Wheat Stripe Rust Resistance Genes in Shaanmai 139

2010 ◽  
Vol 36 (1) ◽  
pp. 109-114 ◽  
Author(s):  
Hong ZHANG ◽  
Zhi-Long REN ◽  
Yin-Gang HU ◽  
Chang-You WANG ◽  
Wan-Quan JI
Keyword(s):  
Stripe Rust ◽  
Resistance Genes ◽  
Rust Resistance ◽  
Stripe Rust Resistance ◽  
Wheat Stripe Rust ◽  
Rust Resistance Genes

Molecular mapping of all stage stripe rust resistance gene YrPak in wheat landrace PI388231

Euphytica ◽  
2021 ◽  
Vol 217 (6) ◽  
Author(s):  
Maryam Tariq ◽  
Javed Iqbal Mirza ◽  
Shaukat Hussain ◽  
Naeela Qureshi ◽  
Kerrie Forrest ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Molecular Mapping ◽  
Rust Resistance Gene ◽  
Stripe Rust Resistance ◽  
Wheat Landrace ◽  
Stripe Rust Resistance Gene

Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages

Euphytica ◽  
2021 ◽  
Vol 217 (1) ◽  
Author(s):  
Sanjaya Gyawali ◽  
Sujan Mamidi ◽  
Shiaoman Chao ◽  
Subhash C. Bhardwaj ◽  
Pradeep S. Shekhawat ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Association Studies ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide Association Studies ◽  
Resistance Qtl ◽  
Genome Wide

scholarly journals The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Tifeng Yang ◽  
Lian Zhou ◽  
Junliang Zhao ◽  
Jingfang Dong ◽  
Qing Liu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Differential Expression ◽  
Candidate Genes ◽  
Complex Traits ◽  
Molecular Breeding ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Sequence Comparisons ◽  
Cold Environments ◽  
Promising Source

Abstract Background Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far. Results In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines. Conclusion Among the 11 QTLs identified in this study, qLTG_sRDP2–10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

scholarly journals Stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal translocation of Triticum monococcum chromosome 5AmL into common wheat

2021 ◽  
Author(s):  
Shisheng Chen ◽  
Joshua Hegarty ◽  
Tao Shen ◽  
Lei Hua ◽  
Hongna Li ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Common Wheat ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Triticum Monococcum ◽  
Rust Resistance Gene ◽  
Stripe Rust Resistance ◽  
Polyploid Wheat ◽  
Stripe Rust Resistance Gene ◽  
A Genome

AbstractKey messageThe stripe rust resistance geneYr34 was transferred to polyploid wheat chromosome 5AL from T. monococcumand has been used for over two centuries.Wheat stripe (or yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is currently among the most damaging fungal diseases of wheat worldwide. In this study, we report that the stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal segment of the cultivated Triticum monococcum subsp. monococcum chromosome 5AmL translocated to chromosome 5AL in polyploid wheat. The diploid wheat species Triticum monococcum (genome AmAm) is closely related to T. urartu (donor of the A genome to polyploid wheat) and has good levels of resistance against the stripe rust pathogen. When present in hexaploid wheat, the T. monococcum Yr34 resistance gene confers a moderate level of resistance against virulent Pst races present in California and the virulent Chinese race CYR34. In a survey of 1,442 common wheat genotypes, we identified 5AmL translocations of fourteen different lengths in 17.5% of the accessions, with higher frequencies in Europe than in other continents. The old European wheat variety “Mediterranean” was identified as a putative source of this translocation, suggesting that Yr34 has been used for over 200 years. Finally, we designed diagnostic CAPS and sequenced-based markers that will be useful to accelerate the deployment of Yr34 in wheat breeding programs to improve resistance to this devastating pathogen.

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