Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K "SNP-Chip" was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.Daniela Iamartino, Ezequiel L. Nicolazzi, Curtis P. Van Tassell, James M. Reecy, Eric R. Fritz-Waters, James E. Koltes, Stefano Biffani, Tad S. Sonstegard, Steven G. Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramelli, Angelo Coletta, José F. Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A.A. de Oliveira, Marcela G. Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L. William

Effects of rare kidney diseases on kidney failure: a longitudinal analysis of the UK National Registry of Rare Kidney Diseases (RaDaR) cohort

Background Individuals with rare kidney diseases account for 5–10% of people with chronic kidney disease, but constitute more than 25% of patients receiving kidney replacement therapy. The National Registry of Rare Kidney Diseases (RaDaR) gathers longitudinal data from patients with these conditions, which we used to study disease progression and outcomes of death and kidney failure. Methods People aged 0–96 years living with 28 types of rare kidney diseases were recruited from 108 UK renal care facilities. The primary outcomes were cumulative incidence of mortality and kidney failure in individuals with rare kidney diseases, which were calculated and compared with that of unselected patients with chronic kidney disease. Cumulative incidence and Kaplan–Meier survival estimates were calculated for the following outcomes: median age at kidney failure; median age at death; time from start of dialysis to death; and time from diagnosis to estimated glomerular filtration rate (eGFR) thresholds, allowing calculation of time from last eGFR of 75 mL/min per 1·73 m2 or more to first eGFR of less than 30 mL/min per 1·73 m2 (the therapeutic trial window). Findings Between Jan 18, 2010, and July 25, 2022, 27 285 participants were recruited to RaDaR. Median follow-up time from diagnosis was 9·6 years (IQR 5·9–16·7). RaDaR participants had significantly higher 5-year cumulative incidence of kidney failure than 2·81 million UK patients with all-cause chronic kidney disease (28% vs 1%; p<0·0001), but better survival rates (standardised mortality ratio 0·42 [95% CI 0·32–0·52]; p<0·0001). Median age at kidney failure, median age at death, time from start of dialysis to death, time from diagnosis to eGFR thresholds, and therapeutic trial window all varied substantially between rare diseases. Interpretation Patients with rare kidney diseases differ from the general population of individuals with chronic kidney disease: they have higher 5-year rates of kidney failure but higher survival than other patients with chronic kidney disease stages 3–5, and so are over-represented in the cohort of patients requiring kidney replacement therapy. Addressing unmet therapeutic need for patients with rare kidney diseases could have a large beneficial effect on long-term kidney replacement therapy demand. Funding RaDaR is funded by the Medical Research Council, Kidney Research UK, Kidney Care UK, and the Polycystic Kidney Disease Charity

The diversification of plant cytosolic small heat shock proteins preceded the divergence of mosses.

A cDNA library was constructed with mRNA isolated from heat-stressed cell cultures of Funaria hygrometrica (Bryophyta, Musci, Funariaceae). cDNA clones encoding six cytosolic small heat shock proteins (sHSPs) were identified using differential screening. Phylogenetic analysis of these sHSP sequences with other known sHSPs identified them as members of the previously described higher plant cytosolic class I and II families. Four of the F. hygrometrica sHSPs are members of the cytosolic class I family, and the other two are members of the cytosolic class II family. The presence of members of the cytosolic I and II sHSP families in a bryophyte indicates that these gene families are ancient, and evolved at least 450 MYA. This result also indicates that the plant sHSP gene families duplicated much earlier than did the well-studied phytochrome gene family. Members of the cytosolic I and II sHSP families are developmentally regulated in seeds and flowers in higher plants. Our findings show that the two cytosolic sHSP families evolved before the appearance of these specialized structures. Previous analysis of angiosperm sHSPs had identified class- or family-specific amino acid consensus regions and determined that rate heterogeneity exists among the different sHSP families. The analysis of the F. hygrometrica sHSP sequences reveals patterns and rates of evolution distinct from those seen among angiosperm sHSPs. Some, but not all, of the amino acid consensus regions identified in seed plants are conserved in the F. hygrometrica sHSPs. Taken together, the results of this study illuminate the evolution of the sHSP gene families and illustrate the importance of including representatives of basal land plant lineages in plant molecular evolutionary studies

Triticum aestivum cDNAs homologous to nuclear-encoded mitochondrion-localized small heat shock proteins.

Two cDNAs, TaHSP23.5 and TaHSP23.6, encoding proteins with homology to mitochondrion-localized (MT) small heat shock proteins (sHSPs) were isolated from a heat shock cDNA library from Triticum aestivum (wheat). TaHSP23.5 specified a 214 amino acid protein and TaHSP23.6 specified a 216 amino acid protein. Amino acid sequence identity was only 45.7% between the two proteins. However, both proteins showed greater identity to MT sHSPs of other plant species than to any other sHSPs from wheat. Amino acid sequence alignments with other MT sHSPs identified the putative amino terminus of the mature proteins and consensus regions specific to this class of sHSPs. Transcripts of both genes were absent from control tissues, but strongly induced by heat stress. Phylogenetic analysis indicates that these two wheat genes arose by duplication after the divergence of monocots and dicots

Evolution, structure and function of the small heat shock proteins in plants.

The α-crystallin-related, small heat shock proteins (smHSPs) are ubiquitous in nature, but are unusually abundant and diverse in higher plants as opposed to other eukaryotes. The smHSPs range in size from {small tilde}17 to 30 kDa and share a conserved C-terminal domain common to all eukaryotic smHSPs and to the α-crys-tallin proteins of the vertebrate eye lens. In higher plants six nuclear gene families encoding smHSPs have been defined. Each gene family encodes proteins found in a distinct cellular compartment, including the cytosol, chloroplast, ER, and mitochondrion. Evolutionary analysis suggests that the smHSP gene families arose by gene duplication and divergence prior to the radiation of angiosperms. In general, the smHSPs are not found in normal vegetative tissues, but accumulate to high levels in response to heat stress. Specific smHSPs are also expressed during various phases of plant development as part of the endogenous developmental programme. Thus, although the smHSPs are apparently not essential for basal cell functions as are the high molecular weight HSPs such as HSP90, HSP70 and HSP60, their functions are likely to be critical for survival and recovery from heat stress as well as for specific developmental processes. Biochemical analysis indicates that smHSPs are found in high molecular weight complexes between 200–400 kDa that are most likely composed solely of multiple smHSP subunits. Purified recombin-ant plant smHSPs facilitate reactivation of chemically denatured enzymes in a nucleotide-independent fashion and also prevent heat-induced aggregation or reverse inactivation of protein substrates. Based on these data, it is suggested that smHSPs act in vivo as a type of molecular chaperone to bind partially denatured proteins preventing irreversible protein inactivation and aggregation, and that smHSP chaperone activity contributes to the development of thermotolerance. Evolution, structure and function of the small heat shock proteins in plants. J Exp Bot (PDF Download Available). Available from: http://www.researchgate.net/publication/31147982_Evolution_structure_and_function_of_the_small_heat_shock_proteins_in_plants._J_Exp_Bot [accessed Nov 10, 2015]

Prescribed fire increases plant–pollinator network robustness to losses of rare native forbs

Restoration efforts often focus on changing the composition and structure of invaded plant communities, with two implicit assumptions: (1) functional interactions with species of other trophic levels, such as pollinators, will reassemble automatically when native plant diversity is restored and (2) restored communities will be more resilient to future stressors. However, the impact of restoration activities on pollinator richness, plant–pollinator interaction network structure, and network robustness is incompletely understood. Leveraging a restoration chronosequence in Pacific Northwest prairies, we examined the effects of restoration-focused prescribed fire and native forb replanting on floral resources, pollinator visitation, and plant–pollinator network structure. We then simulated the effects of plant species loss/removal scenarios on secondary extinction cascades in the networks. Specifically, we explored three management-relevant plant loss scenarios (removal of an abundant exotic forb, removal of an abundant forb designated a noxious weed, and loss of the rarest native forb) and compared them to control scenarios. Pyrodiversity and proportion of area recently burned increased the abundance and diversity of floral resources, with concomitant increases in pollinator visitation and diversity. Pyrodiversity also decreased network connectance and nestedness, increased modularity, and buffered networks against secondary extinction cascades. Rare forbs contributed disproportionately to network robustness in less restored prairies, while removal of typical “problem” plants like exotic and noxious species had relatively small impacts on network robustness, particularly in prairies with a long history of restoration activities. Restoration actions aimed mainly at improving the diversity and abundance of pollinator-provisioning plants may also produce plant–pollinator networks with increased resilience to plant species losses. © 2023 The Authors. Ecological Applications published by Wiley Periodicals LLC on behalf of The Ecological Society of America.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

The Arabidopsis ClpB/Hsp100 family of proteins: Chaperones for stress and chloroplast development.

The Casein lytic proteinase/heat shock protein 100 (Clp/Hsp100) proteins are chaperones that act to remodel/disassemble protein complexes and/or aggregates using the energy of ATP. In plants, one of the best-studied proteins from this family is cytosolic ClpB1 (At1g74310), better known in Arabidopsis as AtHsp101, which is a heat shock protein required for acclimation to high temperatures. Three other ClpB homologues have been identified in the Arabidopsis genome (ClpB2, ClpB3 and ClpB4; At4g14670, At5g15450 and At2g25140). To define further the roles of these chaperones in plants we investigated their intracellular localization, evolutionary relationships, patterns of expression and the phenotypes of corresponding T-DNA insertion mutants. We first found that ClpB2 was misannotated; there is no functional ClpB/Hsp100 gene at this locus. By fusing the putative transit peptides of ClpB3 and ClpB4 with GFP, we showed that these proteins are targeted to the chloroplast and mitochondrion, respectively, and we therefore designated them as ClpB-p and ClpB-m. Phylogenetic analysis supports two major lineages of ClpB proteins in plants, an ‘eukaryotic’, cytosol/nuclear-localized group containing AtHsp101, and an organelle-localized lineage, containing both ClpB-p and ClpB-m. Although AtHsp101, ClpB-p and ClpB-m transcripts all accumulate dramatically at high temperatures, the T-DNA insertion mutants of ClpB-p and ClpB-m show no evidence of seedling heat stress phenotypes similar to those observed in AtHsp101 mutants. Strikingly, ClpB-p knockouts were seedling lethals, failing to accumulate chlorophyll or properly develop chloroplasts. Thus, in plants, the function of ClpB/Hsp100 proteins is not restricted to heat stress, but a specific member of the family provides housekeeping functions that are essential to chloroplast development