Massey Research Online - Browsing by Author "Tate JA"

Browsing by Author "Tate JA"

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A roadmap of phylogenomic methods for studying polyploid plant genera
(John Wiley and Sons, Inc., on behalf of Botanical Society of America, 2024-04-22) Ning W; Meudt HM; Tate JA
Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.
Cytonuclear Coordination Is Not Immediate upon Allopolyploid Formation in Tragopogon miscellus (Asteraceae) Allopolyploids.
(2015) Sehrish T; Symonds VV; Soltis DE; Soltis PS; Tate JA
Allopolyploids, formed by hybridization and chromosome doubling, face the immediate challenge of having duplicated nuclear genomes that interact with the haploid and maternally inherited cytoplasmic (plastid and mitochondrial) genomes. Most of our knowledge of the genomic consequences of allopolyploidy has focused on the fate of the duplicated nuclear genes without regard to their potential interactions with cytoplasmic genomes. As a step toward understanding the fates of nuclear-encoded subunits that are plastid-targeted, here we examine the retention and expression of the gene encoding the small subunit of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco; rbcS) in multiple populations of allotetraploid Tragopogon miscellus (Asteraceae). These polyploids formed recently (~80 years ago) and repeatedly from T. dubius and T. pratensis in the northwestern United States. Examination of 79 T. miscellus individuals from 10 natural populations, as well as 25 synthetic allotetraploids, including reciprocally formed plants, revealed a low percentage of naturally occurring individuals that show a bias in either gene (homeolog) loss (12%) or expression (16%), usually toward maintaining the maternal nuclear copy of rbcS. For individuals showing loss, seven retained the maternally derived rbcS homeolog only, while three had the paternally derived copy. All of the synthetic polyploid individuals examined (S0 and S1 generations) retained and expressed both parental homeologs. These results demonstrate that cytonuclear coordination does not happen immediately upon polyploid formation in Tragopogon miscellus.
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.
On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)
(BioMed Central, 2009) Tate JA; Joshi P; Soltis KA; Soltis P; Soltis D
Background: Polyploidy (whole-genome duplication) is an important speciation mechanism,particularly in plants. Gene loss, silencing, and the formation of novel gene complexes are some ofthe consequences that the new polyploid genome may experience. Despite the recurrent natureof polyploidy, little is known about the genomic outcome of independent polyploidization events.Here, we analyze the fate of genes duplicated by polyploidy (homoeologs) in multiple individualsfrom ten natural populations of Tragopogon miscellus (Asteraceae), all of which formedindependently from T. dubius and T. pratensis less than 80 years ago.Results: Of the 13 loci analyzed in 84 T. miscellus individuals, 11 showed loss of at least one parentalhomoeolog in the young allopolyploids. Two loci were retained in duplicate for all polyploidindividuals included in this study. Nearly half (48%) of the individuals examined lost a homoeologof at least one locus, with several individuals showing loss at more than one locus. Patterns of losswere stochastic among individuals from the independently formed populations, except that the T.dubius copy was lost twice as often as T. pratensis.Conclusion: This study represents the most extensive survey of the fate of genes duplicated byallopolyploidy in individuals from natural populations. Our results indicate that the road to genomedownsizing and ultimate genetic diploidization may occur quickly through homoeolog loss, but withsome genes consistently maintained as duplicates. Other genes consistently show evidence ofhomoeolog loss, suggesting repetitive aspects to polyploid genome evolution.
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.
Ploidy variation in Rhododendron subsection Maddenia and its implications for conservation.
(Oxford University Press on behalf of the Annals of Botany Company, 2023-06-01) Hu L; Tate JA; Gardiner SE; MacKay M; Loureiro J
Polyploidy, which is common in plants, can confound taxon recognition and hence conservation assessments. In the taxonomically complex genus Rhododendron, 25 % of the over 1,300 taxa are considered under threat and 27 % Near Threatened or Data Deficient, with their taxonomy needing to be resolved urgently. Although ploidy levels of Rhododendron taxa range from diploid (2x) to dodecaploid (12x) according to previous reports, the extent of polyploidy across the genus has not been examined. We first summarized the taxonomic distribution of polyploids in the genus based on the literature. Then as a case study, we estimated ploidy levels of 47 taxa in subsection Maddenia (subgenus Rhododendron, section Rhododendron) using flow cytometry, together with verification of meiotic chromosome counts for representative taxa. The summary of reported ploidy in Rhododendron indicates that polyploidy is most common in subgenera Pentanthera and Rhododendron. In subsection Maddenia, all examined taxa are diploids except for the R. maddenii complex that shows a high ploidy variation (2-8x, 12x). We investigated ploidy level of 12 taxa in subsection Maddenia for the first time, and estimated genome sizes of two Rhododendron species. Knowledge of ploidy levels will inform phylogenetic analysis of unresolved species complexes. Overall, our study of subsection Maddenia provides a model for examining multiple issues including taxonomic complexity, ploidy variation and geographic distribution in relation to biodiversity conservation.
Polyploidy on islands - concerted evolution and gene loss amid chromosomal stasis
(Oxford University Press on behalf of the Annals of Botany Company, 2023-01-01) Joshi P; Ansari H; Dickson R; Ellison NW; Skema C; Tate JA
BACKGROUND AND AIMS: Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. METHODS: We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1, was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. KEY RESULTS: The chromosome number for all species investigated was 2n = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius, had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1, indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. CONCLUSIONS: Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing.
Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data
(CSIRO Publishing, 2022-05-05) Prebble JM; Symonds VV; Tate JA; Meudt HM; Wilson P
A taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis L.; Boraginaceae) is presented here. Climate-edaphic niches are modelled and compared for five species in the pygmy group, namely, M. antarctica Hook.f., M. brevis de Lange & Barkla, M. drucei (L.B.Moore) de Lange & Barkla, M. pygmaea Colenso and M. glauca (G.Simpson & J.S.Thomson) de Lange & Barkla, and one unnamed putative taxon, M. "Volcanic Plateau". In this case, niche-modelling data mostly do not aid species delimitation, but morphological and genetic data provide evidence for recognising the following three species within the group: M. brevis and M. glauca (both endemic to New Zealand), and an enlarged M. antarctica (native to New Zealand, Campbell Island and Chile). Myosotis antarctica is here circumscribed to include M. antarctica sens. strict., M. drucei and M. pygmaea. The following two allopatric subspecies of M. antarctica are recognised on the basis of minor morphological differences: subsp. antarctica (formerly M. antarctica from Campbell Island and Chile, M. drucei and M. "Volcanic Plateau") and subsp. traillii Kirk (formerly known by New Zealand botanists as M. pygmaea Colenso, an illegitimate name). For all three species, which are considered Threatened or At Risk, most of their genetic variation is partitioned between rather than within populations, meaning that conserving as many populations as possible should be the priority to minimise risk of extinction.
The compounding effects of high pollen limitation, selfing rates and inbreeding depression leave a New Zealand tree with few viable offspring.
(2015-10) Van Etten ML; Tate JA; Anderson SH; Kelly D; Ladley JJ; Merrett MF; Peterson PG; Robertson AW
BACKGROUND AND AIMS: Interactions between species are especially sensitive to environmental changes. The interaction between plants and pollinators is of particular interest given the potential current global decline in pollinators. Reduced pollinator services can be compensated for in some plant species by self-pollination. However, if inbreeding depression is high, selfed progeny could die prior to reaching adulthood, leading to cryptic recruitment failure. METHODS: To examine this scenario, pollinator abundance, pollen limitation, selfing rates and inbreeding depression were examined in 12 populations of varying disturbance levels in Sophora microphylla (Fabaceae), an endemic New Zealand tree species. KEY RESULTS: High pollen limitation was found in all populations (average of 58 % reduction in seed production, nine populations), together with high selfing rates (61 % of offspring selfed, six populations) and high inbreeding depression (selfed offspring 86 % less fit, six populations). Pollen limitation was associated with lower visitation rates by the two endemic bird pollinators. CONCLUSIONS: The results suggest that for these populations, over half of the seeds produced are genetically doomed. This reduction in the fitness of progeny due to reduced pollinator service is probably important to population dynamics of other New Zealand species. More broadly, the results suggest that measures of seed production or seedling densities may be a gross overestimate of the effective offspring production. This could lead to cryptic recruitment failure, i.e. a decline in successful reproduction despite high progeny production. Given the global extent of pollinator declines, cryptic recruitment failure may be widespread.
Understanding Rhododendron intraspecific compatibility in botanic garden collections for species conservation
(CSIRO Publishing, 2024-09-19) Hu L; Gardiner SE; Tate JA; MacKay MB; Nolan R
Context Controlled pollination is an important technique for maintaining intraspecific diversity in integrated plant conservation practices, particularly in genera such as Rhododendron, where open pollination usually produces hybrids with unknown paternal lineages. Aims This study investigated the capacity for viable seed set from self- and intraspecific cross-pollination for Rhododendron taxa in different categories of the International Union for Conservation of Nature (IUCN) Red List, to guide conservation management of threatened species in botanic garden collections. Methods The following five taxa of subsection Maddenia were studied: R. dalhousiae var. dalhousiae (Least Concern), R. dalhousiae var. rhabdotum (Vulnerable), R. lindleyi (Least Concern), R. nuttallii (Near Threatened), and R. excellens (Vulnerable). Controlled pollination was performed on selected garden accessions, and seed germination was tested at an alternating temperature regime of 15/25°C, 8 h photoperiod, and ~6 μmol m−2 s−1 photosynthetic photon flux density (PPFD). Key results Intraspecific compatibilities varied among different taxa and between self- and outcross treatments. X-ray images for Rhododendron seeds showed low capacity to predict seed germination. Neither X-ray scan nor fungicide (Ridomil) treatment showed any adverse impact on seed germination, which has positive implications for seed-banking and subsequent raising of Rhododendron seedlings. Conclusions Controlled intraspecific pollination can be used to maintain diversity of ex situ accessions for selected Rhododendron species. However, the zero or low compatibility demonstrated in some species, such as R. excellens, suggests that these species may require a different approach. Implications Intraspecific pollination should be evaluated for each Rhododendron species before a propagation program is initiated in ex situ conservation.

Browsing by Author "Tate JA"

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