Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome

Shwachman-Diamond syndrome (SDS; OMIM: #260400) is caused by variants in SBDS (Shwachman-Bodian-Diamond syndrome gene), which encodes a protein that plays an important role in ribosome assembly. Recent reports suggest that recessive variants in EFL1 are also responsible for SDS. However, the precise genetic mechanism that leads to EFL1-induced SDS remains incompletely understood. Here we present three unrelated Korean SDS patients that carry biallelic pathogenic variants in EFL1 with biased allele frequencies, resulting from a bone marrow-specific somatic uniparental disomy (UPD) in chromosome 15. The recombination events generated cells that were homozygous for the relatively milder variant, allowing for the evasion of catastrophic physiological consequences. Still, the milder EFL1 variant was solely able to impair 80S ribosome assembly and induce SDS features in cell line and animal models. The loss of EFL1 resulted in a pronounced inhibition of terminal oligo-pyrimidine element-containing ribosomal protein transcript 80S assembly. Therefore, we propose a more accurate pathogenesis mechanism of EFL1 dysfunction that eventually leads to aberrant translational control and ribosomopathy.

Genetic Polymorphisms in miR-604A>G, miR-938G>A, miR-1302-3C>T and the Risk of Idiopathic Recurrent Pregnancy Loss

The purpose of this study was to investigate whether polymorphisms in five microRNAs (miRNAs), miR-604A>G, miR-608C>G, 631I/D, miR-938G>A, and miR-1302-3C>T, are associated with the risk of idiopathic recurrent pregnancy loss (RPL). Blood samples were collected from 388 patients with idiopathic RPL (at least two consecutive spontaneous abortions) and 227 control participants. We found the miR-604 AG and AG + GG genotypes of miR-604, the miR-938 GA and GA + AA genotypes of miR-938, and the miR-1302-3CT and CT + TT genotypes of miR-1302-3 are less frequent than the wild-type (WT) genotypes, miR-604AA, miR-938GG, and miR-1302-3CC, respectively, in RPL patients. Using allele-combination multifactor dimensionality reduction (MDR) analysis, we found that eight haplotypes conferred by the miR-604/miR-608/miR-631/miR-938/miR-1302-3 allele combination, A-C-I-G-T, A-C-I-A-C, G-C-I-G-C, G-C-I-G-T, G-G-I-G-C, G-G-I-G-T, G-G-I-A-C, G-G-D-G-C, three from the miR-604/miR-631/miR-938/miR-1302-3 allele combination, A-I-G-T, G-I-G-C, G-I-A-T, one from the miR-604/miR-631/miR-1302-3 allele combination, G-I-C, and two from the miR-604/miR-1302-3 allele combination, G-C and G-T, were less frequent in RPL patients, suggesting protective effects (all p < 0.05). We also identified the miR-604A>G and miR-938G>A polymorphisms within the seed sequence of the mature miRNAs and aligned the seed sequences with the 3′UTR of putative target genes, methylenetetrahydrofolate reductase (MTHFR) and gonadotropin-releasing hormone receptor (GnRHR), respectively. We further found that the binding affinities between miR-604/miR-938 and the 3′UTR of their respective target genes (MTHFR, GnRHR) were significantly different for the common (miR-604A, miR-938G) and variant alleles (miR-604G, miR-938A). These results reveal a significant association between the miR-604A>G and miR-938G>A polymorphisms and idiopathic RPL and suggest that miRNAs can affect RPL in Korean women.

The Effect of Photoperiod Genes and Flowering Time on Yield and Yield Stability in Durum Wheat

This study analysed the effect of flowering time as influenced by photoperiod sensitivity genes on yield and yield stability in durum wheat. Twenty-three spring genotypes harbouring different allele combinations at Ppd-A1 and Ppd-B1 were grown in 15 field experiments at three sites at latitudes from 41° to 19° N (Spain, Mexico-North and Mexico-South). Low temperature and solar radiation before flowering and long day length during grain-filling characteristic for the Spanish site resulted in high grain number/m2 (GN) and yield (GY), while a moderate GN combined with high solar radiation during grain-filling at Mexico-North led to heavier grains. Allele combination GS100-Ppd-A1a/Ppd-B1a reduced the flowering time up to nine days when compared with Ppd-A1b/Ppd-B1a. Differences in flowering time caused by Ppd-A1/Ppd-B1 allele combinations did not affect yield. Combinations GS105-Ppd-A1a/Ppd-B1b and Ppd-A1b/Ppd-B1b resulted in the highest GN, linked to spikelets/spike, which was higher in GS105-Ppd-A1a/Ppd-B1b due to more grains/spikelet. Flowering time caused by Eps had a minor effect on GN, spikes/m2 and grains/spike, but late flowering resulted in reduced grain weight and GY. Allele combinations harbouring alleles conferring a similar photoperiod sensitivity response at Ppd-A1 and Ppd-B1 resulted in greater yield stability than combinations that carry alleles conferring a different response. Allele combination GS100-Ppd-A1a/Ppd-B1a was the most suitable in terms of yield and yield stability of durum wheat cultivated under irrigation within the studied latitudes.

Base-specific mutational intolerance near splice-sites clarifies role of non-essential splice nucleotides

Variation in RNA splicing (i.e., alternative splicing) plays an important role in many diseases. Variants near 5′ and 3′ splice sites often affect splicing, but the effects of these variants on splicing and disease have not been fully characterized beyond the 2 “essential” splice nucleotides flanking each exon. Here we provide quantitative measurements of tolerance to mutational disruptions by position and reference allele-alternative allele combination. We show that certain reference alleles are particularly sensitive to mutations, regardless of the alternative alleles into which they are mutated. Using public RNA-seq data, we demonstrate that individuals carrying such variants have significantly lower levels of the correctly spliced transcript compared to individuals without them, and confirm that these specific substitutions are highly enriched for known Mendelian mutations. Our results propose a more refined definition of the “splice region” and offer a new way to prioritize and provide functional interpretation of variants identified in diagnostic sequencing and association studies.

Allelic variations at Dhn4 and Dhn7 are associated with frost tolerance in barley

The sequences of the closely linked barley dehydrin genes Dhn4 and Dhn7 are both known to vary allelically. Here we associated allelic constitution at Dhn4/7 with frost sensitivity across a panel of 30 diverse barley varieties. The combined presence of a 6 bp insertion in exon1 of Dhn4 and a 30 bp deletion in exon1 of Dhn7 was restricted to six-rowed winter and intermediate varieties characterised by relatively higher frost tolerance (12 genotypes; LT₅₀ from &ndash;14.2&deg;C to &ndash;15.6&deg;C). The alternative combination was present with one exception (sixrowed winter variety Alissa) only in spring and two-rowed winter varieties (17 genotypes; LT₅₀ from &ndash;10.0&deg;C to &ndash;14.3&deg;C). The genetic linkage between Dhn4 and Dhn7 identified e.g. in Dictoo and Morex varieties was verified by segregation analysis of F₂ plants from a cross between two genotypes carrying different allelic combination of Dhn4 and Dhn7 genes (two-rowed spring variety Akcent &times; six-rowed winter variety Okal). The potential of the former allelic combination as a marker for enhanced frost tolerance was tested in a sample of F₅ derivatives of a cross between the two-rowed winter type variety Monaco (Akcent allele combination) and the six-rowed winter type variety Okal. Plants with the Okal allele combination showed significantly higher frost tolerance than those with the alternative growth habit. The effect of ear type on frost tolerance was insignificant.