Genomic prediction of Fusarium head blight resistance in early stages using advanced breeding lines in hard winter wheat

Zhang, Jinfeng; Gill, Harsimardeep S.; Brar, Navreet K.; Halder, Jyotirmoy; Ali, Shaukat; Liu, Xiaotian; Bernardo, Amy; Amand, Paul St.; Bai, Guihua; Gill, U. S.; Turnipseed, Brent; Sehgal, Sunish K.

doi:10.1016/j.cj.2022.03.010

Cited by 20 publications

(23 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…They can be used either in MAB programs aimed at developing wheat varieties providing tolerance to multiple abiotic stresses under study or subjected to fine mapping to identify key genes involved in tolerance against multiple abiotic stresses in wheat, as proposed recently for multiple biotic stress resistance in soybean 101 . Markers flanking these MQTLs may be utilized in improving the prediction accuracy of genomic selection for multiple abiotic stress tolerance in wheat 102,103 .…”

Section: Discussionmentioning

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

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

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

View full text Add to dashboard Cite

show abstract

“…Instead, evaluation of individual genotypes with their overall genetic merit toward resistance to the disease through genomic prediction models is a more efficient and feasible approach. In addition, the difficulty of phenotypic screening of the disease in both controlled conditions and field trials (Zhang et al 2022 ) makes genomic selection the best option in FHB resistance breeding. Previous studies have shown the potential of genomic prediction in FHB resistance in wheat (Arruda et al 2015 ; Dong et al 2018 ; Herter et al 2019 ; Rutkoski et al 2012 ; Verges et al 2020 ; Zhang et al 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat

et al. 2023

View full text Add to dashboard Cite

Key message Linkage disequilibrium (LD)-based haplotyping with subsequent SNP tagging improved the genomic prediction accuracy up to 0.07 and 0.092 for Fusarium head blight resistance and spike width, respectively, across six different models. Abstract Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r2 < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.

show abstract

“…The majority of the HWW cultivars from the US Great Plains, including the SDSU winter wheat program, do not carry Fhb1 likely due to yield drag, and ‘TAM 205’ is the only released HWW variety carrying Fhb1 to date ( Zhang et al, 2022 ). Fortunately, several HWW cultivars including Everest, Overland, Lyman, Heyne, Century, and Hondo that exhibit moderate FHB resistance but do not carry Fhb1 have been released in the US HWW region ( Jin et al, 2013 ; Bai et al, 2018 ; Clinesmith et al, 2019 ; Zhang et al, 2022 ), showing the importance of the native FHB resistance in the regional wheat breeding programs. Further, various studies have successfully identified QTLs for native resistance using cultivars such as ‘Art,’ Everest, and Lyman ( Clinesmith et al, 2019 ; Hashimi, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, only a few QTLs with a major effect on FHB resistance, in particular Fhb1 , have been successfully employed in wheat breeding programs ( Bai et al, 2018 ). Contrarily, the majority of the germplasm from the hard winter wheat region of the US relies upon the variation in FHB resistance from native sources including cultivars ‘Everest,’ ‘Overland,’ ‘Lyman,’ and ‘Expedition’ ( Clinesmith et al, 2019 ; Zhang et al, 2022 ). However, the identification of genomic regions underlying native resistance and the development of reliable markers are essential for pyramiding those QTLs to maintain an effective level of FHB resistance in locally adapted wheat backgrounds.…”

Section: Introductionmentioning

confidence: 99%

Multi-Locus Genome-Wide Association Studies to Characterize Fusarium Head Blight (FHB) Resistance in Hard Winter Wheat

et al. 2022

Self Cite

View full text Add to dashboard Cite

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum Schwabe is an important disease of wheat that causes severe yield losses along with serious quality concerns. Incorporating the host resistance from either wild relatives, landraces, or exotic materials remains challenging and has shown limited success. Therefore, a better understanding of the genetic basis of native FHB resistance in hard winter wheat (HWW) and combining it with major quantitative trait loci (QTLs) can facilitate the development of FHB-resistant cultivars. In this study, we evaluated a set of 257 breeding lines from the South Dakota State University (SDSU) breeding program to uncover the genetic basis of native FHB resistance in the US hard winter wheat. We conducted a multi-locus genome-wide association study (ML-GWAS) with 9,321 high-quality single-nucleotide polymorphisms (SNPs). A total of six distinct marker-trait associations (MTAs) were identified for the FHB disease index (DIS) on five different chromosomes including 2A, 2B, 3B, 4B, and 7A. Further, eight MTAs were identified for Fusarium-damaged kernels (FDK) on six chromosomes including 3B, 5A, 6B, 6D, 7A, and 7B. Out of the 14 significant MTAs, 10 were found in the proximity of previously reported regions for FHB resistance in different wheat classes and were validated in HWW, while four MTAs represent likely novel loci for FHB resistance. Accumulation of favorable alleles of reported MTAs resulted in significantly lower mean DIS and FDK score, demonstrating the additive effect of FHB resistance alleles. Candidate gene analysis for two important MTAs identified several genes with putative proteins of interest; however, further investigation of these regions is needed to identify genes conferring FHB resistance. The current study sheds light on the genetic basis of native FHB resistance in the US HWW germplasm and the resistant lines and MTAs identified in this study will be useful resources for FHB resistance breeding via marker-assisted selection.

show abstract

Genomic prediction of Fusarium head blight resistance in early stages using advanced breeding lines in hard winter wheat

Cited by 20 publications

References 55 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

Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat

Multi-Locus Genome-Wide Association Studies to Characterize Fusarium Head Blight (FHB) Resistance in Hard Winter Wheat

Contact Info

Product

Resources

About