Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

Browse

Filters

2023 - 20255

Settings

Start date: 2023Subject: search.filters.subject.Plant Breeding

Search Results

Now showing 1 - 5 of 5
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    Variations in the 24 h temporal patterns and time budgets of grazing, rumination, and idling behaviors in grazing dairy cows in a New Zealand system.
    (Oxford University Press, 2023-01-28) Iqbal MW; Draganova I; Henry Morel PC; Todd Morris S
    This study investigated the variations in the temporal distributions and the lengths of times utilized for grazing, ruminating, and idling behaviors by grazing dairy cows over 24 h. Spring-calved lactating dairy cows (N = 54) from three breeds, Holstein-Friesian (HFR), Jersey (JE), and KiwiCross (KC) in different lactations (1st, 2nd, 3rd) and with different breeding worth index values (103 < BW > 151) were selected. The cows were managed through a rotational grazing scheme and milked once a day at 0500 hours. The cows grazed mainly pasture and consumed additional feeds (maize silage and turnips) in the summer and autumn seasons. AfiCollar was used to record grazing and rumination behaviors (min/h) in the individual cows throughout the lactation period (~270 d). The time neither utilized for grazing nor rumination was counted as idling behavior (min/h). A repeat measure design with PROC MIXED was performed in SAS considering the effects of breed, lactation, individual cow, the hour of the day, season, day within the season, and supplementary feed within the season to evaluate the difference in grazing, rumination, and idling behaviors. Hour of the day, season, day within season, and supplementary feed had significant effects on grazing, rumination, and idling behaviors. Regardless of the season and supplementary feed, cows spent most of the daytime grazing and most of the nighttime ruminating. Grazing activity remained consistently high throughout the day with two peaks around dawn and dusk and a short peak around midnight. Rumination activity remained high from the late evening until early morning. Grazing and ruminating patterns were similar between different breeds and lactations, however, JE cows grazed slightly longer than HFR and KC, and first-lactation cows grazed slightly longer than those in higher lactations. The onset and cessation of grazing activity by the cows were adjusted according to varying day lengths by season. Cows finished grazing earlier when they consumed additional supplements or silage along with pasture. Cows from different breed groups and lactations spent most of their 24 h grazing followed by ruminating and idling. Season and supplementary feed potentially affected the variations in behavior time budgets. These findings should support improving measures for grazing management to address pasture allocation and additional feed demands, and animal welfare in varying environmental and/or managemental conditions.
  • Thumbnail Image
    Item
    Protothecosis in four dogs in New Zealand.
    (Taylor and Francis Group, 2023-09-04) Price PSA; Klobukowska HJ; Castillo-Alcala F; Foxwell JA; Orbell GMB; Brown S; Irving AC
    CASE HISTORIES: Medical records of four dogs diagnosed with protothecosis in New Zealand were reviewed. The dogs were aged between 4 and 9 years and three of the four dogs were female. Breeds were one Labrador, one Miniature Schnauzer and two crossbreeds. The reasons for initial veterinary evaluation were a cough and opaque appearance of the right eye (Case 1), diarrhoea (Cases 2 and 3), and cutaneous disease (Case 4). CLINICAL FINDINGS: The ocular signs were characterised by panuveitis, retinal detachment and secondary glaucoma. Gastrointestinal signs included chronic haemorrhagic diarrhoea due to colitis. Three cases had disseminated infection and developed both bilateral, blinding, ocular disease and chronic gastrointestinal disease. Cutaneous signs consisted of draining fistulae over the olecranon, multifocal cutaneous nodules, and ulceration and tracts of the foot pads. Disseminated protothecosis was confirmed by histopathology of biopsied ocular tissues in Cases 1 and 2 and by gastrointestinal biopsies in Case 3. Prototheca spp. were also identified in cytological specimens from Cases 1 and 4 and recovered by culture in Cases 2 and 4. Cutaneous protothecosis was diagnosed in Case 4 initially by cytology and histopathology of skin lesions, and Prototheca zopfii was confirmed by PCR of cultured organisms. TREATMENT AND OUTCOME: Prior to diagnosis of protothecosis, a variety of treatments were prescribed to treat the gastrointestinal and ocular signs. After diagnosis, only Cases 2 and 4 received medication aimed at treating the protothecal infection, which was itraconazole in both cases. Following the progression of clinical signs and concerns about quality of life, all four dogs were euthanised. DIAGNOSIS: Disseminated protothecosis in three dogs, cutaneous protothecosis in one dog. CLINICAL RELEVANCE: Canine protothecosis is rarely reported, despite the ubiquity of the causal algae, and the disease usually carries an extremely grave prognosis when infection is generalised. In New Zealand, protothecosis should be considered as a differential diagnosis in dogs with panuveitis, chorioretinitis or retinal detachment, colitis, or nodular, ulcerative or fistulating cutaneous lesions.
  • Thumbnail Image
    Item
    Genomic architecture of resistance to latania scale (H. lataniae) in kiwifruit (A. chinensis var. chinensis)
    (BioMed Central Ltd, 2023-10-31) Flay C; Tahir J; Hilario E; Fraser L; Stannard K; Symonds V; Datson P
    BACKGROUND: Latania scale (Hemiberlesia lataniae Signoret) is an armoured scale insect known to cause damage to kiwifruit plants and fruit, which ultimately reduces crop values and creates post-harvest export and quarantine issues. Resistance to H. lataniae does exist in some commercial cultivars of kiwifruit. However, some of the commercial cultivars bred in New Zealand have not inherited alleles for resistance to H. lataniae carried by their parents. To elucidate the architecture of resistance in the parents and develop molecular markers to assist breeding, these experiments analysed the inheritance of resistance to H. lataniae from families related to commercial cultivars. RESULTS: The first experiment identified a 15.97 Mb genomic region of interest for resistance to H. lataniae in rtGBS data of 3.23 to 19.20 Mb on chromosome 10. A larger population was then QTL mapped, which confirmed the region of interest as the sole locus contributing to H. lataniae resistance. inDel markers mapping the region of low recombination under the QTL peak further narrowed the region associated with H. lataniae resistance to a 5.73 Mb region. CONCLUSIONS: The kiwifruit populations and genomic methods used in this study identify the same non-recombinant region of chromosome 10 which confers resistance of A. chinensis var. chinensis to H. lataniae. The markers developed to target the H. lataniae resistance loci will reduce the amount of costly and time-consuming phenotyping required for breeding H. lataniae scale resistance into new kiwifruit cultivars.
  • Thumbnail Image
    Item
    Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes
    (BioMed Central Ltd, 2023-05-05) Angelin-Bonnet O; Thomson S; Vignes M; Biggs PJ; Monaghan K; Bloomer R; Wright K; Baldwin S
    BACKGROUND: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. RESULTS: When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. CONCLUSION: This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.