Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution.  Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula.  In present study, 39 531 available coding sequences (CDSs) from M. truncatula were examined for codon usage bias (CUB).  Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB.  We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage.  These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively.  Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs.  The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content.  Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.

 

A two-year field experiment was conducted to evaluate the effects of plant density on tassel and ear differentiation, anthesis-silking interval (ASI), and grain yield formation of two types of modern maize hybrids (Zhongdan 909 (ZD909) as tolerant hybrid to crowding stress, Jidan 209 (JD209) and Neidan 4 (ND4) as intolerant hybrids to crowding stress) in Northeast China.  Plant densities of 4.50×10⁴ (D1), 6.75×104 (D2), 9.00×10⁴ (D3), 11.25×10⁴ (D4), and 13.50×10⁴ (D5) plants ha^–1 had no significant effects on initial time of tassel and ear differentiation of maize.  Instead, higher plant density delayed the tassel and ear development during floret differentiation and sexual organ formation stage, subsequently resulting in ASI increments at the rate of 1.2–2.9 days on average for ZD909 in 2013–2014, 0.7–4.2 days for JD209 in 2013, and 0.5–3.7 days for ND4 in 2014, respectively, under the treatments of D2, D3, D4, and D5 compared to that under the D1 treatment.  Total florets, silking florets, and silking rates of ear showed slightly decrease trends with the plant density increasing, whereas the normal kernels seriously decreased at the rate of 11.0–44.9% on average for ZD909 in 2013–2014, 2.0–32.6% for JD209 in 2013, and 9.7–28.3% for ND4 in 2014 with the plant density increased compared to that under the D1 treatment due to increased florets abortive rates.  It was also observed that 100-kernel weight of ZD909 showed less decrease trend compared that of JD209 and ND4 along with the plant densities increase.  As a consequence, ZD909 gained its highest grain yield by 13.7 t ha^–1 on average at the plant density of 9.00×104 plants ha^–1, whereas JD209 and ND4 reached their highest grain yields by 11.7 and 10.2 t ha^–1 at the plant density of 6.75×104 plants ha^–1, respectively.  Our experiment demonstrated that hybrids with lower ASI, higher kernel number potential per ear, and relative constant 100-kernel weight (e.g., ZD909) could achieve higher yield under dense planting in high latitude area (e.g., Northeast China).