Connection between polymorphisms in HTR2A , TPH2 , BDNF , TOMM40 genes and the successful mastering of human–computer interfaces Abstract The development of human–computer interfaces in different individuals occur with different efficiencies, this is due to the individual characteristics of the genotype determined by the single-nucleotide polymorphism (SNP) of a person. Here, we checked the connection between the success of the acquisition of the brain-computer, eye-tracking, electromyographic, and respiratory interfaces and SNP of the TOMM40, BDNF, HTR2A and TPH2 genes. Here, we show that the T-allele in rs6313 of the HTR2A gene is associated with an increase in the number of correctly submitted commands of the electromyographic and eye-tracking interfaces. This is probably due to the fact that, the T-allele carriers decrease expression of this serotonin receptor. The decreased expression of HTR2A may be a reason for an increase in the number of accurately submitted commands. It was shown that the TT genotype of rs4290270 polymorphism was associated with an increase in the accuracy of work with the myographic interface. In addition, the association of subjective interfaces work time with polymorphisms rs429358 and rs2030324 was noted. Thus, the genotypic characteristics of individuals can be a predictive sign for the degree of success of mastering human–computer interfaces, which can allow to expand the understanding of training the neural mechanisms when working with this class of devices.

Genetic diversity and population structure analysis of Asian and African aromatic rice ( Oryza sativa L.) genotypes Abstract Rice germplasms collected from different regions could be used as valuable resources for the future breeding programme. For the utilization of such collections, knowledge about the level and distribution of genetic diversity among these collections will facilitate the breeder. In this study, we report the phenotypic correlation, biochemical quality parameters and population genetic analysis of 35 rice accessions including 34 aromatic rice from different countries and a nonaromatic, Nagina 22, a well-known drought resistance variety. Further biochemical quality analysis, gel consistency test, molecular diversity analysis with 55 simple sequence repeat markers, population structure analysis and pair wise \(F_{\mathrm{ST}}\) analysis were also conducted to assess the genetic diversity. The collected rice genotypes showed significant variability in different agronomic traits, i.e. spikelet per panicle, branches per panicle etc. Results obtained from the above tests demonstrated the importance of regional genetic studies for understanding the diversification of aromatic rice in Asian and African rice.

Characterization of the complete chloroplast genome of Nitraria tangutorum , a desert shrub Abstract The chloroplast genome sequence of Nitraria tangutorum, a desert shrub, was sequenced using high-throughput sequencing technology and analysed phylogenetically in the present study. The chloroplast genome is 159,414 bp in length, including a large single copy region of 87,924 bp and small single copy region of 18,318 bp, and a pair of inverted repeat regions of 26,586 bp. The chloroplast genome contains 110 unique genes, including 77 protein-coding genes, four ribosomal RNA genes, and 29 tRNA genes. Most of these genes are present as a single copy and in two or more copies 19 genes occurred. Seventeen genes have one intron, and clpP and ycf3 genes contain two introns. A total of 81 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition to SSRs, 66 repeats were identified, including 41 tandem repeats, 10 palindromic repeats, and 15 forward repeats. The phylogenetic analysis based on 54 protein-coding genes demonstrated a close relationship between N. tangutorum and other plant species in Sapindales. The complete chloroplast genome sequence of N. tangutorum will provide important data for further study of taxonomy and systematics of the genus Nitraria.

The evolution study on Oryza rufipogon. dw by whole-genome sequencing Abstract The species of Oryza rufipogon. dw was first discovered at Dongxiang, Jiangxi in 1978. It is recognized as abundant in genetic resources with the characteristics of cold and insect resistance. A total of 100.15 Gb raw data was obtained from seven pair-end libraries by Illumina Hiseq4000 platform. Subsequently, a draft assembly genome of O. rufipogon. dw was generated with a final size of 422.7 Mb with a contig N50 of 15 kb and a scaffold N50 of 296.2 bb. The assembly genome size was higher than the estimated genome size (413 Mb) based on k-mer analysis. The identified repeat sequences accounted for 40.09% of the entire genome, and 32,521 protein-coding genes with an average of 4.59 exons per gene was annotated in five databases. Phylogenetic analysis using 1460 single-copy gene, O. rufipogon. dw was close with O. rufipogon by Bayes method. The wild rice species of O. rufipogon. dw divergence was estimated at \({\sim }0.3\) million years ago (Mya) from O. rufipogon, and \({\sim }0.6\ \hbox {Mya}\) from the O. sativa. The draft genome of O. rufipogon. dw provided an essential resource for its origin and evolution study.

Genetic analysis of the mandible morphology in DDD.Cg- $$A^{y}$$ A y /Sgn and C57BL/6J inbred mice Abstract Quantitative trait loci (QTL) mapping analysis was performed for the mandible morphology in DDD.Cg- \(A^{y}/\hbox {Sgn}\) and C57BL/6J inbred mice. The size and shape of the mandible was analysed by landmark-based geometric morphometrics as the centroid size and principal components (PCs), respectively. The \(A^{y}\) allele at the agouti locus significantly reduced the mandible size in DDD/Sgn background, and substantially altered the mandible shape in both strain backgrounds. Single-QTL scans, by including the agouti locus genotype ( \(A^{y}\) or non- \(A^{y}\) ) as an additive covariate, identified three significant QTL for the centroid size on chromosomes 5, 6 and 17, along with four suggestive QTL on chromosomes 2, 12, 18 and 19. These QTLs explained 46.85% of the centroid size variation in \(\hbox {F}_{2}\) mice. When the \(\hbox {F}_{2} A^{y}\) and \(\hbox {F}_{2}\) non- \(A^{y}\) mice were analysed separately, additional significant QTL were identified on chromosomes 12 and 15 in \(\hbox {F}_{2}\) non- \(A^{y}\) mice. Single-QTL scans also identified 15 significant QTL for the PC1, PC2 and PC3. When the agouti locus genotype was included as an interactive covariate, nine significant QTLs were identified. Unexpectedly, these agouti-interacting QTLs were identified for relatively minor PCs, for which no significant single-QTL were identified. Therefore, it was suggested that the alteration of the mandible shape in \(A^{y}\) mice was the consequence of interactions between the \(A^{y}\) allele and genes that themselves have relatively small phenotypic effect. Although further in vivo studies are required, we postulated Pkd1 as a possible candidate gene underlying QTL for the centroid size on chromosome 17.

Comparative analysis of camelid mitochondrial genomes Abstract Camelus dromedarius has played a pivotal role in both culture and way of life in the Arabian peninsula, particularly in arid regions where other domestic animals cannot be easily domesticated. Although, the mitochondrial genomes have recently been sequenced for several camelid species, wider phylogenetic studies are yet to be performed. The features of conserved gene elements, rapid evolutionary rate, and rare recombination make the mitochondrial genome a useful molecular marker for phylogenetic studies of closely related species. Here we carried out a comparative analysis of previously sequenced mitochondrial genomes of camelids with an emphasis on C. dromedarius, revealing a number of noticeable findings. First, the arrangement of mitochondrial genes in C. dromedarius is similar to those of the other camelids. Second, multiple sequence alignment of intergenic regions shows up to 90% similarity across different kinds of camels, with dromedary camels to reach 99%. Third, we successfully identified the three domains (termination-associated sequence, conserved domain and conserved sequence block) of the control region structure. The phylogenetic tree analysis showed that C. dromedarius mitogenomes were significantly clustered in the same clade with Lama pacos mitogenome. These findings will enhance our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Camelus, and provide more data for comparative mitogenomics in the family Camelidae.

Nucleotide sequence polymorphism in the RFL-PPR genes of potato Abstract Cytoplasmic male sterility (CMS) is widely used for hybrid seed production in cultivated Solanaceae species. However, there is very limited information about CMS-Rf genetic systems in potato (Solanum tuberosum). Studying the CMS-Rf systems in potato is both of theoretical and practical significance due to the emergence of a new revolutionary strategy of reinventing potato as a diploid inbred line-based crop to develop \(\hbox {F}_{{1}}\) hybrid seed potato breeding (Lindhout et al.2011; Jansky et al.2016). To search for potato Rf gene candidates, the comparative genetic approach was applied. Based on similarity to petunia Rf-PPR592 gene, 38 fragments were identified in five loci of the whole-genome nucleotide sequence of the accession DM 1-3 516 R44 S. tuberosum Phureja group (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The putative encoded mitochondrial proteins have 589–597 amino acid residues, similar to RF-PPR proteins of petunia and chili pepper and contain 14 or 15 PPR motifs. Primers have been developed flanking the most variable 782–865 bp regions of the selected loci, and polymorphism of the cloned fragments has been investigated in a subset of nine potato genotypes. The amplified fragments included seven or eight PPR motifs and lacked introns. The SNP frequencies ranged from 7.0 to 19.8% depending on the locus, while the ratio of nonsynonymous to synonymous substitutions varied between 0.9 and 2.1. Positions 1, 3 and 6 were the most variable in the studied PPR motifs. Our results demonstrated that the analysed sequences belong to the RFL-PPR gene subfamily and may be considered as Rf gene candidates in potato.

Construction, characteristics and high throughput molecular screening methodologies in some special breeding populations: a horticultural perspective Abstract Advanced marker technologies are widely used for evaluation of genetic diversity in cultivated crops, wild ancestors, landraces or any special plant genotypes. Developing agricultural cultivars requires the following steps: (i) determining desired characteristics to be improved, (ii) screening genetic resources to help find a superior cultivar, (iii) intercrossing selected individuals, (iv) generating genetically hybrid populations and screening them for agro-morphological or molecular traits, (v) evaluating the superior cultivar candidates, (vi) testing field performance at different locations, and (vii) certifying. In the cultivar development process valuable genes can be identified by creating special biparental or multiparental populations and analysing their association using suitable markers in given populations. These special populations and advanced marker technologies give us a deeper knowledge about the inherited agronomic characteristics. Unaffected by the changing environmental conditions, these provide a higher understanding of genome dynamics in plants. The last decade witnessed new applications for advanced molecular techniques in the area of breeding, with low costs per sample. These, especially, include next-generation sequencing technologies like reduced representation genome sequencing (genotyping by sequencing, restriction site-associated DNA). These enabled researchers to develop new markers, such as simple sequence repeat and single- nucleotide polymorphism, for expanding the qualitative and quantitative information on population dynamics. Thus, the knowledge acquired from novel technologies is a valuable asset for the breeding process and to better understand the population dynamics, their properties, and analysis methods.

In silico analysis of the structural and functional implications of SLC19A1 R27H polymorphism Abstract In view of the documented association of solute carrier family 19 member 1 (SLC19A1) G80A (R27H) polymorphism with the risk for different types of cancers and systemic lupus erythematosus (SLE), we have reanalysed the case–control study on breast cancer to ascertain the conditions in which this polymorphic variant exerts the risk of breast cancer. Association statistics have revealed that this polymorphism exerts the risk for breast cancer under the conditions of low folate intake, and in the absence of well-documented protective polymorphism in cytosolic serine hydroxymethyltransferase. To substantiate this observation, we have developed a homology model of SLC19A1 using glycerol-3-phosphate transporter (d1pw4a) as a template where 73% of the residues were modelled at 90% confidence while 162 residues were modelled ab initio. The wild and mutant proteins shared same topology in S3, S5, S6, S7, S11 and S12 transmembrane domains. The topology varied at S1 (28–43 residue vs 28–44 residue), S2 (66–87 residue vs 69–87 residue), S4 (117–140 residue vs 117–139 residue), S8 (305–325 residue vs 305–324 residue), S9 (336–356 residue vs 336–355 residue), and S10 (361–386 residue vs 361–385 residue) transmembrane domains between wild versus mutant proteins. S2 domain is shortened by three amino acid residues in the mutant while in other domains the difference corresponds to one amino acid residue. The 3DLigandSite analysis revealed that the metallic-ligand-binding sites at 273Trp, 277Asn, 379Leu, 439Phe and 442Leu are although unaffected, there is a loss of active sites corresponding to nonmetallic ligand binding. Tetrahydrofolate and methotrexate have lesser affinity towards the mutant protein than the wild protein. To conclude, the R27H polymorphism affects the secondary and tertiary structures of SLC19A1 with the significant loss in ligand-binding sites.

Genetics of fruit yield and its component traits under different fruiting habit backgrounds in chilli ( Capsicum annuum L.) Abstract The six basic generations (two parents, \(\hbox {F}_{1}\) , \(\hbox {F}_{2}\) and backcrosses) of 14 crosses developed from nine parents differing in fruits \(\hbox {node}^{-1}\) and fruit orientation were evaluated to decipher the genetics of three quantitative traits (average fruit weight, fruits \(\hbox {plant}^{-1}\) and green fruit yield \(\hbox {plant}^{-1})\) during the rainly season of 2016 and 2017. The magnitude and direction of the additive genetic effects [a], dominance genetic effects [d], magnitudes of additive genetic variance ( \({\upsigma }_{\mathrm{A}}^2 )\) and dominance genetic variance ( \({\upsigma }_{\mathrm{D}}^2 )\) varied with the genetic background of the crosses and traits. In the genetic background of crosses involving parents differing in fruit \(\hbox {node}^{-1}\) , the inheritance of average fruit weight, fruits \(\hbox {plant}^{-1}\) and fruit yield \(\hbox {plant}^{-1}\) were controlled by the genes with both additive and ambidirectional dominant effects. On the contrary, genes with only additive effects controlled the inheritance of average fruit weight, fruits \(\hbox {plant}^{-1}\) and fruit yield \(\hbox {plant}^{-1}\) in most genetic backgrounds of crosses involving parents differing in fruit orientation and those differing in both fruits \(\hbox {node}^{-1}\) and fruit orientation. Further, the genes controlling the inheritance of all the traits are dispersed among the parents used in the investigation. These results are discussed in relation to strategies to be used in breeding chilli.