Genome-wide association for grain morphology in synthetic hexaploid wheats using digital imaging analysis

Synthetic hexaploid wheat (SHW; Triticum durum L. × Aegilops tauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, Cu, Co, Fe, Li, Mg, Mn, Ni, and Zn) using an inductively coupled mass spectrometer in 123 SHWs for a genome-wide association study (GWAS). A GWAS with 35,648 single nucleotide polymorphism (SNP) markers identified 92 marker-trait associations (MTAs), of which 60 were novel and 40 were within genes, and the genes underlying 20 MTAs had annotations suggesting a potential role in grain mineral concentration. Twenty-four MTAs on the D-genome were novel and showed the potential of Ae. tauschii for improving grain mineral concentrations such as Ca, Co, Cu, Li, Mg, Mn, and Ni. Interestingly, the large number of novel MTAs (36) identified on the AB genome of these SHWs indicated that there is a lot of variation yet to be explored and to be used in the A and B genome along with the D-genome. Regression analysis identified a positive correlation between a cumulative number of favorable alleles at MTA loci in a genotype and grain mineral concentration. Additionally, we identified multi-traits and stable MTAs and recommended 13 top 10% SHWs with a higher concentration of beneficial grain minerals (Cu, Fe, Mg, Mn, Ni, and Zn), a large number of favorable alleles compared to low ranking genotypes and checks that could be utilized in the breeding program for the genetic biofortification. This study will further enhance our understanding of the genetic architecture of grain minerals in wheat and related cereals.

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Genome-Wide Association Study for Multiple Biotic Stress Resistance in Synthetic Hexaploid Wheat

International Journal of Molecular Sciences ◽

10.3390/ijms20153667 ◽

2019 ◽

Vol 20 (15) ◽

pp. 3667 ◽

Cited By ~ 5

Author(s):

Madhav Bhatta ◽

Alexey Morgounov ◽

Vikas Belamkar ◽

Stephen N. Wegulo ◽

Abdelfattah A. Dababat ◽

...

Keyword(s):

Genetic Variation ◽

Stress Resistance ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Wheat Cultivars ◽

Biotic Stresses ◽

Genome Wide ◽

Wide Range ◽

Synthetic Hexaploid ◽

Genomic Regions

Genetic resistance against biotic stress is a major goal in many wheat breeding programs. However, modern wheat cultivars have a limited genetic variation for disease and pest resistance and there is always a possibility of the evolution of new diseases and pests to overcome previously identified resistance genes. A total of 125 synthetic hexaploid wheats (SHWs; 2n = 6x = 42, AABBDD, Triticum aestivum L.) were characterized for resistance to fungal pathogens that cause wheat rusts (leaf; Puccinia triticina, stem; P. graminis f.sp. tritici, and stripe; P. striiformis f.sp. tritici) and crown rot (Fusarium spp.); cereal cyst nematode (Heterodera spp.); and Hessian fly (Mayetiola destructor). A wide range of genetic variation was observed among SHWs for multiple (two to five) biotic stresses and 17 SHWs that were resistant to more than two stresses. The genomic regions and potential candidate genes conferring resistance to these biotic stresses were identified from a genome-wide association study (GWAS). This GWAS study identified 124 significant marker-trait associations (MTAs) for multiple biotic stresses and 33 of these were found within genes. Furthermore, 16 of the 33 MTAs present within genes had annotations suggesting their potential role in disease resistance. These results will be valuable for pyramiding novel genes/genomic regions conferring resistance to multiple biotic stresses from SHWs into elite bread wheat cultivars and providing further insights on a wide range of stress resistance in wheat.

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Genome-wide association study reveals favorable alleles associated with common bunt resistance in synthetic hexaploid wheat

Euphytica ◽

10.1007/s10681-018-2282-4 ◽

2018 ◽

Vol 214 (11) ◽

Cited By ~ 12

Author(s):

Madhav Bhatta ◽

Alexey Morgounov ◽

Vikas Belamkar ◽

Aysel Yorgancılar ◽

P. Stephen Baenziger

Keyword(s):

Association Study ◽

Hexaploid Wheat ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Synthetic Hexaploid Wheat ◽

Common Bunt ◽

Favorable Alleles ◽

Genome Wide ◽

Synthetic Hexaploid ◽

Bunt Resistance

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Combining Digital Imaging and Genome Wide Association Mapping to Dissect Uncharacterized Traits in Plant/Pathogen Interactions

10.1101/296939 ◽

2018 ◽

Cited By ~ 1

Author(s):

Rachel F. Fordyce ◽

Nicole E. Soltis ◽

Celine Caseys ◽

Raoni Gwinner ◽

Jason A. Corwin ◽

...

Keyword(s):

Disease Resistance ◽

Botrytis Cinerea ◽

Plant Pathogen ◽

Digital Imaging ◽

Plant Disease Resistance ◽

Plant Disease ◽

Lesion Size ◽

Genome Wide Association ◽

Genome Wide ◽

Plant Pathogen Interactions

AbstractPlant resistance to generalist pathogens with broad host ranges, such as Botrytis cinerea, is typically quantitative and highly polygenic. Recent studies have begun to elucidate the molecular genetic basis underpinning plant-pathogen interactions using commonly measured traits including lesion size and/or pathogen biomass. Yet with the advent of digital imaging and phenomics, there are a large number of additional resistance traits available to study quantitative resistance. In this study, we used high-throughput digital imaging analysis to investigate previously uncharacterized visual traits of plant-pathogen interactions related disease resistance using the Arabidopsis thaliana/Botrytis cinerea pathosystem. Using a large collection of 75 visual traits collected from every lesion, we focused on lesion color, lesion shape, and lesion size, to test how these aspects of the interaction are genetically related. Using genome wide association (GWA) mapping in A. thaliana, we show that lesion color and shape are genetically separable traits associated with plant-disease resistance. Using defined mutants in 23 candidate genes from the GWA mapping, we could identify and show that novel loci associated with each different plant-pathogen interaction trait, which expands our understanding of the functional mechanisms driving plant disease resistance.SummaryDigital imaging allows the identification of genes controlling novel lesion traits.

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Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

International Journal of Molecular Sciences ◽

10.3390/ijms19103011 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3011 ◽

Cited By ~ 33

Author(s):

Madhav Bhatta ◽

Alexey Morgounov ◽

Vikas Belamkar ◽

P. Baenziger

Keyword(s):

Drought Stress ◽

Grain Yield ◽

Association Study ◽

Hexaploid Wheat ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Synthetic Hexaploid Wheat ◽

Phenotypic Variance ◽

Genome Wide ◽

Synthetic Hexaploid

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker–trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions.

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