ultivated peanut or groundnut (A. hypogaea L.) is among the most important oil and food legumes, grown on 25 million ha between latitudes 40° N and 40° S with annual production of ~46 million tons (http://www.fao.org/faostat/en/#home). It presumably was domesticated in South America ~6,000 years ago and then was widely distributed in post-Columbian times 1. Combining richness in seed oil (~46-58%) and protein (~22-32%), peanut is important in fighting malnutrition and ensuring food security.

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified over 100 selective sweeps specific to domestic rabbits, but only a relatively small number of fixed (or nearly fixed) SNPs for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved non-coding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that due to a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few ‘domestication loci’.

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SUMMARY Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high‐quality, chromosome‐scale genome assembly of P. trifoliata. The 264.9‐Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein‐coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species‐specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C‐repeat/DREB binding factor (CBF)‐dependent and CBF‐independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non‐dwarfing type. The high‐quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.

Degranulation of mast cells in response to Ag or the calcium mobilizing agent, thapsigargin, is dependent on emptying of intracellular stores of Ca2+ and the ensuing influx of external Ca2+, also referred to as store-operated calcium entry. However, it is unlikely that the calcium release-activated calcium channel is the sole mechanism for the entry of Ca2+ because Sr2+ and other divalent cations also permeate and support degranulation in stimulated mast cells. In this study we show that influx of Ca2+ and Sr2+ as well as degranulation are dependent on the presence of the canonical transient receptor potential (TRPC) channel protein TRPC5, in addition to STIM1 and Orai1, as demonstrated by knock down of each of these proteins by inhibitory RNAs in a rat mast cell (RBL-2H3) line. Overexpression of STIM1 and Orai1, which are known to be essential components of calcium release-activated calcium channel, allows entry of Ca2+ but not Sr2+, whereas overexpression of STIM1 and TRPC5 allows entry of both Ca2+ and Sr2+. These and other observations suggest that the Sr2+-permeable TRPC5 associates with STIM1 and Orai1 in a stoichiometric manner to enhance entry of Ca2+ to generate a signal for degranulation.

Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.

The molecular mechanisms of symbiosis in cultivated peanut with a ‘crack entry’ infection process are largely understudied. In this study, we investigated the root transcriptional profiles of two pairs of non-nodulating (nod−) and nodulating (nod+) sister inbred peanut lines, E4/E5 and E7/E6, and their nod+ parents, F487A and PI262090 during rhizobial infection and nodule initiation by using RNA-seq technology. A total of 143, 101, 123, 215, 182, and 289 differentially expressed genes (DEGs) were identified in nod− E4, E7 and nod+ E5, E6, F487A, and PI262090 after inoculation with Bradyrhizobium sp. Different deficiencies at upstream of symbiotic signaling pathway were revealed in the two nod− genotypes. DEGs specific in nod+ genotypes included orthologs to some known symbiotic signaling pathway genes, such as NFR5, NSP2, NIN, ERN1, and many other novel and/or functionally unknown genes. Gene ontology (GO) enrichment analysis of nod+ specific DEGs revealed 54 significantly enriched GO terms, including oxidation-reduction process, metabolic process, and catalytic activity. Genes related with plant defense systems, hormone biosynthesis and response were particularly enriched. To our knowledge, this is the first report revealing symbiosis-related genes in a genome-wide manner in peanut representative of the ‘crack entry’ species.

Activation of phospholipase D (PLD) and protein kinase C (PKC) as well as calcium mobilization are essential signals for degranulation of mast cells. However, the exact role of PLD in degranulation remains undefined. In this study we have tested the hypothesis that the PLD product, phosphatidic acid, and diacylglycerides generated therefrom might promote activation of PKC. Studies were conducted in two rodent mast cell lines that were stimulated with Ag via FcεRI and a pharmacologic agent, thapsigargin. Diversion of production of phosphatidic acid to phosphatidylbutanol (the transphosphatidylation reaction) by addition of l-butanol suppressed both the translocation of diacylglyceride-dependent isoforms of PKC to the membrane and degranulation. Tertiary-butanol, which is not a substrate for the transphosphatidylation, had a minimal effect on PKC translocation and degranulation, and 1-butanol itself had no effect on PKC translocation when PKC was stimulated directly with phorbol ester, 12-O-tetradecanoylphorbol-13-acetate. Also, in cells transfected with small inhibitory RNAs directed against PLD1 and PLD2, activation of PLD, generation of diacylglycerides, translocation of PKC, and degranulation were all suppressed. Phorbol ester, which did not stimulate degranulation by itself, restored degranulation when used in combination with thapsigargin whether PLD function was disrupted with 1-butanol or the small inhibitory RNAs. However, degranulation was not restored when cells were costimulated with Ag and phorbol ester. These results suggested that the production of phosphatidic acid by PLD facilitates activation of PKC and, in turn, degranulation, although additional PLD-dependent processes appear to be critical for Ag-mediated degranulation.