PbCOL8 is a clock-regulated flowering time repressor in pear

The floral transition is controlled by diverse endogenous and exogenous cues. In many species, COL (CONSTANS-like) genes integrate light and circadian clock signals to regulate flowering time. However, little is known about COLs in perennial woody plants. Here, we identified 15 PbCOLs in pear (Pyrus bretschneideri). PbCOLs were classified into three groups by phylogenetic tree analysis using protein sequences. Multiple sequence alignment analysis revealed conserved B-box and CCT (CO, CO-like, and TOC1) domains in all PbCOL members. This result suggested that PbCOLs might possess conserved functions as other species. Six PbCOLs were found to be regulated by both circadian clock and photoperiod. Here, we showed that PbCOL8, a member of group 2, suppressed the flowering signal integrators FT and SOC1 and could repress flowering time. These findings will contribute to elucidation of the mechanism of floral initiation in pear.     

The nuclear transcription factor PKNOX2 is a candidate gene for substance dependence in European-origin women

Substance dependence or addiction is a complex environmental and genetic disorder that results in serious health and socio-economic consequences. Multiple substance dependence categories together, rather than any one individual addiction outcome, may explain the genetic variability of such disorder. In our study, we defined a composite substance dependence phenotype derived from six individual diagnoses: addiction to nicotine, alcohol, marijuana, cocaine, opiates or other drugs as a whole. Using data from several genomewide case-control studies, we identified a strong (Odds ratio  = 1.77) and significant (p-value = 7E-8) association signal with a novel gene, PBX/knotted 1 homeobox 2 (PKNOX2), on chromosome 11 with the composite phenotype in European-origin women. The association signal is not as significant when individual outcomes for addiction are considered, or in males or African-origin population. Our findings underscore the importance of considering multiple addiction types and the importance of considering population and gender stratification when analyzing data with heterogeneous population.     

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions

FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) are two genes that, unless plants are vernalized, greatly delay flowering time in Arabidopsis thaliana. Natural loss-of-function mutations in FRI cause the early flowering growth habits of many A. thaliana accessions. To quantify the variation among wild accessions due to FRI, and to identify additional genetic loci in wild accessions that influence flowering time, we surveyed the flowering times of 145 accessions in long-day photoperiods, with and without a 30-day vernalization treatment, and genotyped them for two common natural lesions in FRI. FRI is disrupted in at least 84 of the accessions, accounting for only approximately 40% of the flowering-time variation in long days. During efforts to dissect the causes for variation that are independent of known dysfunctional FRI alleles, we found new loss-of-function alleles in FLC, as well as late-flowering alleles that do not map to FRI or FLC. An FLC nonsense mutation was found in the early flowering Van-0 accession, which has otherwise functional FRI. In contrast, Lz-0 flowers late because of high levels of FLC expression, even though it has a deletion in FRI. Finally, eXtreme array mapping identified genomic regions linked to the vernalization-independent, late-flowering habit of Bur-0, which has an alternatively spliced FLC allele that behaves as a null allele.     

Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.)

Cucumber mosaic virus (CMV) is one of the most destructive viruses in the Solanaceae family. Simple inheritance of CMV resistance in peppers has not previously been documented; all previous studies have reported that resistance to this virus is mediated by several partially dominant and recessive genes. In this study, we showed that the Capsicum annuum cultivar ‘Bukang’ contains a single dominant resistance gene against CMV_Korean and CMV_FNY strains. We named this resistance gene Cmr1 (Cucumber mosaic resistance 1). Analysis of the cellular localization of CMV using a CMV green fluorescent protein construct showed that in ‘Bukang,’ systemic movement of the virus from the epidermal cell layer to mesophyll cells is inhibited. Genetic mapping and FISH analysis revealed that the Cmr1 gene is located at the centromeric region of LG2, a position syntenic to the ToMV resistance locus (Tm-1) in tomatoes. Three SNP markers were developed by comparative genetic mapping: one intron-based marker using a pepper homolog of Tm-1, and two SNP markers using tomato and pepper BAC sequences mapped near Cmr1. We expect that the SNP markers developed in this study will be useful for developing CMV-resistant cultivars and for fine mapping the Cmr1 gene.     

Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time

Previous QTL mapping identified a Brassica nigra homolog to Arabidopsis thaliana CO as a candidate gene affecting flowering time in B. nigra. Transformation of an A. thaliana co mutant with two different alleles of the B. nigra CO (Bni COa) homolog, one from an early-flowering B. nigra plant and one from a late one, did not show any differential effect of the two alleles on flowering time. The DNA sequence of the coding region of the two alleles was also identical, showing that nucleotide variation influencing flowering time must reside outside the coding region of Bni COa. In contrast, the nucleotide sequence of the B. nigra COL1 (Bni COL1) gene located 3.5 kb upstream of Bni COa was highly diverged between the alleles from early and late plants. One indel polymorphism in the Bni COL1 coding region, present in several natural populations of B. nigra, displayed a significant association with flowering time within a majority of these populations. These data indicate that a quantitative trait nucleotide (QTN) affecting flowering time is located within or close to the Bni COL1 gene. The intergenic sequence between Bni COL1 and Bni COa displayed a prominent peak of divergence 1 kb downstream of the Bni COL1 coding region. This region could contain regulatory elements for the downstream Bni COa gene. Our data suggest that a naturally occurring QTN for flowering time affects the function or expression of either Bni COL1 or Bni COa.     

Climate drives among‐year variation in natural selection on flowering time

To predict long‐term responses to climate change, we need to understand how changes in temperature and precipitation elicit both immediate phenotypic responses and changes in natural selection. We used 22 years of data for the perennial herb Lathyrus vernus to examine how climate influences flowering phenology and phenotypic selection on phenology. Plants flowered earlier in springs with higher temperatures and higher precipitation. Early flowering was associated with a higher fitness in nearly all years, but selection for early flowering was significantly stronger in springs with higher temperatures and lower precipitation. Climate influenced selection through trait distributions, mean fitness and trait?fitness relationships, the latter accounting for most of the among‐year variation in selection. Our results show that climate both induces phenotypic responses and alters natural selection, and that the change in the optimal phenotype might be either weaker, as for spring temperature, or stronger, as for precipitation, than the optimal response.