Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4, a cultivar widely cultivated in China, and a comprehensive database of genomic variations based on resequencing of 220 germplasms. Approximate 2.74 Gb contigs (N50 of 2.06 Mb), accounting for 88.39% of the estimated genome, were assembled, and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes. A total of 34,922 allelic genes were identified from the allele-aware genome. We observed the expansion of gene families, especially those related to the nitrogen metabolism, and the increase of repetitive elements including transposable elements, which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula. Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe, suggesting that geography may influence alfalfa genetic divergence during local adaption. Genome-wide association studies identified 101 single nucleotide polymorphisms (SNPs) associated with 27 agronomic traits. Two candidate genes were predicted to be correlated with fall dormancy and salt response. We believe that the allele-aware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.

A20 is a repressor of NF-κB and was recently shown to be frequently inactivated by deletions or mutations in several types of lymphomas including T-cell lymphoma. Little is known about the characteristics of A20 mutations in T-cell acute lymphoblastic leukemia (T-ALL). In this study, we analyzed A20 polymorphisms and characterized their features in 11 cases with T-ALL, 30 samples from healthy Chinese individuals, and 3 cells lines including CCRF-CEM, Molt-4, and Toledo cells. Two frequent A20 polymorphisms were found: a CCT deletion at position 12384 and a nucleotide exchange (A to C) at position 13751 (rs2307859 and rs661561). The homozygous form (CC) of rs661561 was detected in all 10 cases with detectable T-ALL, while only 80% (24/30) of the healthy controls had this genotype. We found one T-ALL case without the above frequent single-nucleotide polymorphisms (SNPs) in which a T to G mutation at position 12486 was found, which results in an amino acid exchange (Phe127Cys; rs2230926). Similar results were found in Molt-4 cells, which lack the frequent SNPs but have a heterozygous polymorphism at position 13749 (C > T) (rs5029948). Interestingly, the T-ALL case with the Phe127Cys mutation and Molt-4 cells demonstrated a high A20 copy number as measured by real-time polymerase chain reaction amplification with three primer sets that cover different regions of the A20 gene, corresponding to a high A20 and low NF-κB expression level. In conclusion, we characterized the features of A20 polymorphisms in T-ALL, and found that a low frequency A20 mutation, which was thought to be involved in malignant T-ALL development, might function differently in T cell lymphomas.

The potential relationship between Interleukin-6 (IL-6) gene polymorphisms and coronary artery disease (CAD) has been widely investigated. However, study findings on the -174 G/C and -572 G/C variants remain inconsistent and somewhat controversial. The present meta-analysis was conducted in an attempt to provide a more robust synthesis conclusion. PubMed and Embase were used to search for all relevant studies published on or before May 22, 2012. A total of 19 studies were ultimately included in the analysis. Overall combined risk was calculated with fixed or random-effects models. Subgroup and sensitivity analyses were performed. Among the included studies, no statistically significant differences were found between controls and CAD cases for the G allele contrasts of the -174 G/C and -572 G/C polymorphisms. The co-dominant genetic model was evaluated for the -174 G/C polymorphism. A significant association was detected using GG versus CC (OR = 0.801, 95 % CI: [0.652, 0.983], P = 0.034). However, the association was not obviously in subgroup analysis by ethnicity. The recessive genetic model was evaluated for the -572 G/C polymorphism. The relationship between -572 G/C polymorphism and CAD risk was only found to be significant in Asian populations (random-effects: OR = 1.908, 95 % CI: [1.016, 3.581], P = 0.044) using GG versus GC+CC. No obvious publication bias was found by Begg's funnel plots and the Egger's linear regression test (P = 0.315 for -174 G/C polymorphism and P = 0.118 for -572 G/C polymorphism). Our study indicated that the association between the IL-6 gene and CAD risk was mild and moderate for the -174 G/C and -572 G/C polymorphisms. However, this relationship requires additional investigation through well-designed studies with larger sample sizes.