Genome-Wide Association Study Identifies Candidate Genes Related to Seed Oil Composition and Protein Content in Gossypium hirsutum L.

Cotton (Gossypium spp.) is a leading natural fiber crop and an important source of vegetable protein and oil for humans and livestock. To investigate the genetic architecture of seed nutrients in upland cotton, a genome-wide association study (GWAS) was conducted in a panel of 196 germplasm resources under three environments using a CottonSNP80K chip of 77,774 loci. Relatively high genetic diversity (average gene diversity being 0.331) and phenotypic variation (coefficient of variation, CV, exceeding 3.9%) were detected in this panel. Correlation analysis revealed that the well-documented negative association between seed protein (PR) and oil may be to some extent attributable to the negative correlation between oleic acid (OA) and PR. Linkage disequilibrium (LD) was unevenly distributed among chromosomes and subgenomes. It ranged from 0.10–0.20 Mb (Chr19) to 5.65–5.75 Mb (Chr25) among the chromosomes and the range of Dt-subgenomes LD decay distances was smaller than At-subgenomes. This panel was divided into two subpopulations based on the information of 41,815 polymorphic single-nucleotide polymorphism (SNP) markers. The mixed linear model considering both Q-matrix and K-matrix [MLM(Q+K)] was employed to estimate the association between the SNP markers and the seed nutrients, considering the false positives caused by population structure and the kinship. A total of 47 SNP markers and 28 candidate quantitative trait loci (QTLs) regions were found to be significantly associated with seven cottonseed nutrients, including protein, total fatty acid, and five main fatty acid compositions. In addition, the candidate genes in these regions were analyzed, which included three genes, Gh_D12G1161, Gh_D12G1162, and Gh_D12G1165 that were most likely involved in the control of cottonseed protein concentration. These results improved our understanding of the genetic control of cottonseed nutrients and provided potential molecular tools to develop cultivars with high protein and improved fatty acid compositions in cotton breeding programs through marker-assisted selection

Effects of nitrogen fertilizer on protein synthesis, accumulation, and physicochemical properties in common buckwheat

Nitrogen (N) fertilization affects grain quality in common buckwheat (Fagopyrum esculentum Moench). But the effects of N fertilizer on various buckwheat protein parameters are not fully understood. This study aimed to investigate the synthesis, accumulation, and quality of buckwheat protein under four N application rates in the Loess Plateau, China. Optimal N application (180 kg N ha−1) improved yield, agronomic traits, and N transport and increased protein yield and protein component accumulation. Prolamin and glutelin accumulation first increased and then decreased with increasing N application. The relationships between the contents of protein components and the amount of applied N generally followed quadratic functions. Nitrate reductase and glutamine synthetase activities first increased and then decreased with increasing N levels. Optimal N fertilizer increased the waterholding capacity and thermal stability of buckwheat protein and reduced its emulsification capacity, but negligibly changed its oil-absorption capacity. Hydrophobic amino acids and glutelin content were the main factors affecting protein quality

Relationship of impulsivity and depression during early methamphetamine withdrawal in Han Chinese population

Objective: High level of impulsivity as well as depression is thought to be involved in the maintenance and development of methamphetamine (METH) addiction. However, the relationship between impulsivity and depression has not been studied thoroughly in METH dependence subjects, especially in early METH abstinent subjects. In this study, our objective is to explore the interplay between the depressive symptoms and impulsivity in early METH abstinent subjects.Methods: A total of 182 early abstinent METH dependent subjects (abstinence for 1-7 days) were recruited and the level of impulsivity was measured by the Barratt Impulsiveness Scale (BIS-11). Depressive symptoms and anxiety symptoms were assessed by the short 13-item Beck Depression Inventory (BDI-13) and Beck Anxiety Inventory (BAI) respectively.Results: Global impulsivity of BIS-11 was significantly correlated with depressive symptoms among early METH abstinent subjects (r = 0.283, p = 0.001). Moreover, all subscales of BIS-11 were also found to be correlated with depressive symptoms: correlation with attentional impulsivity (r = 0.202, p = 0.006); correlation with motor impulsivity (r = 0.267, p = 0.001); and correlation with non-planning impulsivity (r = 0.177, p = 0.017).Conclusions: This study showed a relationship between impulsivity and depression, which may further the comprehension of motivational elements contributing to the maintenance and development of METH use disorder. Future research would be dedicated to exploring underlying mechanisms of association between impulsivity and depression. (C) 2014 Elsevier Ltd. All rights reserved

Genome-wide analysis of codon usage bias in four sequenced cotton species

<div><p>Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, <i>G</i>. <i>arboreum</i> (A₂), <i>G</i>. <i>raimondii</i> (D₅), <i>G</i>. <i>hirsutum</i> (AD₁) and <i>G</i>. <i>barbadense</i> (AD₂) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.</p></div

The distribution of T3s, GC3s, GC and ENC of genes in 4 cotton species and 4 subgenomes.

<p>The distribution of T3s, GC3s, GC and ENC of genes in 4 cotton species and 4 subgenomes.</p

The optimal codons of 4 cotton species and 4 subgenomes.

<p>The optimal codons of 4 cotton species and 4 subgenomes.</p

The PR2-bias plots of 4 cotton species and 4 subgenomes.

<p>The PR2-bias plots of 4 cotton species and 4 subgenomes.</p

The ENC-plot of 4 cotton species and 4 subgenomes.

<p>The ENC-plot of 4 cotton species and 4 subgenomes.</p