Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat

Lozano-Ramírez, Nérida; Dreisigacker, Susanne; Sansaloni, Carolina; He, Xinyao; Sandoval-Islas, José Sergio; Pérez‐Rodríguez, Paulino; Carballo, Aquiles Carballo; Díaz, Cristian Nava; Kishii, Masahiro; Singh, Pawan K.

doi:10.3390/genes13081387

Cited by 10 publications

(17 citation statements)

References 54 publications

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“…Among linkage-based interval mapping studies, eleven studies were conducted for spot blotch ( Kumar et al., 2009 ; Kumar et al., 2010 ; Lillemo et al., 2013 ; Zhu et al., 2014 ; Kumar et al., 2015 ; Singh et al., 2016 ; Singh et al., 2018 ; He et al., 2020 ; Roy et al., 2021 ; Gahtyari et al., 2021 and Kaur et al., 2021 ). Similarly, about a dozen GWA studies (ten studies) were also conducted for spot blotch ( Adhikari et al., 2012 ; Gurung et al., 2014 ; Ahirwar et al., 2018 ; Ayana et al., 2018 ; Jamil et al., 2018 ; Juliana et al., 2019 ; Bainsla et al., 2020 ; Tomar et al., 2021 ; Juliana et al., 2022 ; Lozano-Ramirez et al., 2022 ). The present study is yet another attempt, adding 36 novel MTAs to the ever-growing list of markers associated with resistance against spot blotch.…”

Section: Discussionmentioning

confidence: 99%

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Singh

Gaurav²,

Vasistha³

et al. 2023

Front. Plant Sci.

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Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.

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Section: Discussionmentioning

confidence: 99%

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Singh

Gaurav²,

Vasistha³

et al. 2023

Front. Plant Sci.

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“…Good examples are Chirya genotypes derived from wide hybridization and exhibited good SB resistance, like Chirya 1, Chirya 3 and Chirya 7 ( Sharma et al., 2007 ; Joshi et al., 2007b ). High proportion of SB resistance was reported among the synthetic hexaploids evaluated under controlled conditions ( Lozano-Ramirez et al., 2022 ). However, genotypes with high level of field SB resistance are scarce, a major limitation in the progress of breeding program.…”

Section: Breeding For Disease Resistancementioning

confidence: 99%

Managing spot blotch disease in wheat: Conventional to molecular aspects

Roy

He²,

Gahtyari³

et al. 2023

Front. Plant Sci.

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Spot blotch (SB) caused by Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is one of the devastating diseases of wheat in the warm and humid growing areas around the world. B. sorokiniana can infect leaves, stem, roots, rachis and seeds, and is able to produce toxins like helminthosporol and sorokinianin. No wheat variety is immune to SB; hence, an integrated disease management strategy is indispensable in disease prone areas. A range of fungicides, especially the triazole group, have shown good effects in reducing the disease, and crop-rotation, tillage and early sowing are among the favorable cultural management methods. Resistance is mostly quantitative, being governed by QTLs with minor effects, mapped on all the wheat chromosomes. Only four QTLs with major effects have been designated as Sb1 through Sb4. Despite, marker assisted breeding for SB resistance in wheat is scarce. Better understanding of wheat genome assemblies, functional genomics and cloning of resistance genes will further accelerate breeding for SB resistance in wheat.

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“…In this study, we present results for various genome-based prediction models assessing the epistatic interaction within and between sub-genomes A, B, and D of SHW. We use the data of 443 synthetic SHWs that were genotyped and phenotyped for resistance to three different diseases in a previous study by Lozano-Ramirez [ 25 , 26 ]. In contrast to Dreisigacker [ 19 ], we do not use a hybrid prediction model including general and specific combining abilities of different parental groups— durum and Ae.…”

Section: Introductionmentioning

confidence: 99%

Modeling within and between Sub-Genomes Epistasis of Synthetic Hexaploid Wheat for Genome-Enabled Prediction of Diseases

Cuevas,

González-Diéguez,

Dreisigacker

et al. 2024

Genes

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Common wheat (Triticum aestivum) is a hexaploid crop comprising three diploid sub-genomes labeled A, B, and D. The objective of this study is to investigate whether there is a discernible influence pattern from the D sub-genome with epistasis in genomic models for wheat diseases. Four genomic statistical models were employed; two models considered the linear genomic relationship of the lines. The first model (G) utilized all molecular markers, while the second model (ABD) utilized three matrices representing the A, B, and D sub-genomes. The remaining two models incorporated epistasis, one (GI) using all markers and the other (ABDI) considering markers in sub-genomes A, B, and D, including inter- and intra-sub-genome interactions. The data utilized pertained to three diseases: tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB), for synthetic hexaploid wheat (SHW) lines. The results (variance components) indicate that epistasis makes a substantial contribution to explaining genomic variation, accounting for approximately 50% in SNB and SB and only 29% for TS. In this contribution of epistasis, the influence of intra- and inter-sub-genome interactions of the D sub-genome is crucial, being close to 50% in TS and higher in SNB (60%) and SB (60%). This increase in explaining genomic variation is reflected in an enhancement of predictive ability from the G model (additive) to the ABDI model (additive and epistasis) by 9%, 5%, and 1% for SNB, SB, and TS, respectively. These results, in line with other studies, underscore the significance of the D sub-genome in disease traits and suggest a potential application to be explored in the future regarding the selection of parental crosses based on sub-genomes.

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Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat

Cited by 10 publications

References 54 publications

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Managing spot blotch disease in wheat: Conventional to molecular aspects

Modeling within and between Sub-Genomes Epistasis of Synthetic Hexaploid Wheat for Genome-Enabled Prediction of Diseases

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