Browsing by Author "Griffiths AG"

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    A novel mutation in IAA16 is associated with dicamba resistance in Chenopodium album
    (John Wiley and Sons Ltd on behalf of Society of Chemical Industry, 2024-07) Ghanizadeh H; He L; Griffiths AG; Harrington KC; Carbone V; Wu H; Tian K; Bo H; Xinhui D
    BACKGROUND: Resistance to dicamba in Chenopodium album was first documented over a decade ago, however, the molecular basis of dicamba resistance in this species has not been elucidated. In this research, the resistance mechanism in a dicamba-resistant C. album phenotype was investigated using a transcriptomics (RNA-sequence) approach. RESULTS: The dose-response assay showed that the resistant (R) phenotype was nearly 25-fold more resistant to dicamba than a susceptible (S) phenotype of C. album. Also, dicamba treatment significantly induced transcription of the known auxin-responsive genes, Gretchen Hagen 3 (GH3), small auxin-up RNAs (SAURs), and 1-aminocyclopropane-1-carboxylate synthase (ACS) genes in the susceptible phenotype. Comparing the transcripts of auxin TIR/AFB receptors and auxin/indole-3-acetic acid (AUX/IAA) proteins identified from C. album transcriptomic analysis revealed that the R phenotype contained a novel mutation at the first codon of the GWPPV degron motif of IAA16, resulting in an amino acid substitution of glycine (G) with aspartic acid (D). Sequencing the IAA16 gene in other R and S individuals further confirmed that all the R individuals contained the mutation. CONCLUSION: In this research, we describe the dicamba resistance mechanism in the only case of dicamba-resistant C. album reported to date. Prior work has shown that the dicamba resistance allele confers significant growth defects to the R phenotype investigated here, suggesting that dicamba-resistant C. album carrying this novel mutation in the IAA16 gene may not persist at high frequencies upon removal of dicamba application.
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    Estimation of quantitative genetic parameters for dry matter yield and vegetative persistence-related traits in a white clover training population
    (Wiley Periodicals LLC on behalf of Crop Science Society of America, 2022-11-21) Ehoche OG; Arojju SK; Cousins G; O'Connor JR; Maw B; Tate JA; Lockhart PJ; Jahufer MZZ; Griffiths AG; Resende Jr M
    White clover (Trifolium repens L.), an economically important forage legume in temperate pastures, provides quality herbage and plant-available nitrogen. Enhancing breeding efforts to improve dry matter (DM) yield and vegetative persistence will increase on-farm value of this forage. To increase genetic gain for such traits, breeding tools like genomic selection have proven to be highly valuable in other crops. However, its success relies on a sufficiently large training population and key fundamentals of selective breeding, that is, presence of additive variation. We investigated quantitative genetic parameters for spring DM yield and vegetative persistence in a white clover training population comprising 200 half-sibling (HS) families. This population was established in a replicated cattle-grazed, mixed-sward field trial at two contrasting locations and assessed for spring DM yield and stolon-related vegetative persistence traits over a 3-yr period. The additive variation and genotype × environment interactions, comprising the effects from year, season, and location were significant (P <.05) for most traits. Narrow-sense heritability for all traits ranged from low (.13; post-summer stolon branches) to high (.73; leaf size) and there was a positive phenotypic correlation (.28) between spring DM yield and stolon number. These results indicate that both spring DM yield and persistence can be concurrently improved through selective breeding in the current population. We also demonstrated that applying a high selection pressure produces the highest predicted genetic gain. There is, however, a trade-off between genetic gain and diversity in the population for the long-term success of a breeding program.
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    Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover.
    (Springer Nature, 2025-01-23) Ehoche OG; Arojju SK; Jahufer MZZ; Jauregui R; Larking AC; Cousins G; Tate JA; Lockhart PJ; Griffiths AG
    Genomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone. Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from -0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100-120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28-124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.
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    Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.
    (Frontiers Media S.A., 2022-01-09) Pearson SM; Griffiths AG; Maclean P; Larking AC; Hong SW; Jauregui R; Miller P; McKenzie CM; Lockhart PJ; Tate JA; Ford JL; Faville MJ; Xie W; Rodriguez VM
    Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.