Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait associated region within a 173 kb linkage block was identified and variants in the region were characterised, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the third exon of gene 20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximise protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterisation and modification.

Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses

ABSTRACT African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus. IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.

Unusual cryptosporidiosis cases in Swedish patients: extended molecular characterization ofCryptosporidium viatorumandCryptosporidiumchipmunk genotype I

SUMMARYMost human cases of cryptosporidiosis are caused byCryptosporidium parvumorCryptosporidium hominis, but the use of molecular diagnostic methods has revealed that several other less common species or genotypes can also be involved. Here, we describe two unusual causes of cryptosporidiosis, one being the recently described speciesCryptosporidium viatorumand the otherCryptosporidiumchipmunk genotype I. Two Swedish patients who were infected withC. viatorumhad travelled to Kenya and Guatemala, respectively, and two others had been infected withCryptosporidiumchipmunk genotype I in Sweden. None of these four patients were immunocompromised, and all four showed classical symptoms of cryptosporidiosis. We performed extensive molecular characterization, including analysis of four loci. The twoC. viatorumisolates were found to differ slightly at the 70-kDa heat shock protein locus, which may indicate a local geographical variation in this species that has previously been described exclusively on the Indian subcontinent.

Characteristics of modern triticale quality: commercially significant flour traits and cookie quality

Triticale (Triticosecale × Wittmack) is a high yielding cereal crop with the potential to increase grain production for human food in the coming decades. The quality of triticale flour is usually intermediate between its progenitor species; however, there are considerable differences in quality and response to agronomic conditions among cultivars. The aim of this research was to quantify existing genetic variation to provide preliminary data for classification of triticale cultivars for a milling market. Eleven triticale cultivars from three growing environments were compared with five wheat cultivars bred for various end users. Average protein content, milling yield, thousand-kernel weight, test weight, hardness, colour and ash content supported previous reports. One cultivar was identified with grain hardness and milling yield equivalent to durum wheat, suggesting a null allele at the rye softness protein locus. Ash content was higher than wheat, particularly in the flour despite lower extraction rates, suggesting triticale naturally stores more minerals in its endosperm and the benchmark for milling-grade triticale should be higher than the standard for wheat. Cookie dough weight of triticale was significantly lower per unit volume, indicating current baking processes must be altered to deal with the generally poor water retention of triticale. Significant differences were observed among cultivars for cookie quality and some produced cookies equivalent to soft wheat. There is a clear need to classify cultivars into suitability for various end users to facilitate production and marketing of quality triticale.