Investigation of the genes associated with a male sterility mutant ( msm ) in Chinese cabbage ( Brassica campestris ssp. pekinensis ) using RNA-Seq Abstract In Chinese cabbage, hybrid seed production is performed using male sterility lines, an important approach to heterosis utilization. In this study, a stably inherited male sterile mutant msm was obtained from the ‘FT’-doubled haploid line of Chinese cabbage using isolated microspore culture combined with 60Co γ-ray mutagenesis. The genetic backgrounds of ‘FT’ and msm were highly consistent; however, compared with wild-type ‘FT’, msm exhibited completely degenerated stamens and no pollen phenotype. Other characters showed no significant differences. Cytological observations revealed that stamen abortion in msm begins during the tetrad period and that tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Genetic analysis indicated that the msm mutant phenotype is controlled by a single recessive nuclear gene. Comparative transcriptome analysis of ‘FT’ and msm flower buds using RNA-Seq technology revealed 1653 differentially expressed genes, among which, a large number associated with male sterility were detected, including 64 pollen development- and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes, and 16 transcription factor-related genes. An overwhelming majority of these genes were down-regulated in msm compared with ‘FT’. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, 24,476 single-nucleotide polymorphisms and 413,073 insertion–deletion events were specifically detected in msm. These results will facilitate elucidation of the regulatory mechanisms underlying male sterility in Chinese cabbage.

Quantitative trait loci for starch-corrected chip color after harvest, cold storage and after reconditioning mapped in diploid potato Abstract The objective of this study was to map the quantitative trait loci (QTLs) for chip color after harvest (AH), cold storage (CS) and after reconditioning (RC) in diploid potato and compare them with QTLs for starch-corrected chip color. Chip color traits AH, CS, and RC significantly correlated with tuber starch content (TSC). To limit the effect of starch content, the chip color was corrected for TSC. The QTLs for chip color (AH, CS, and RC) and the starch-corrected chip color determined with the starch content after harvest (SCAH), after cold storage (SCCS) and after reconditioning (SCRC) were compared to assess the extent of the effect of starch and the location of genetic factors underlying this effect on chip color. We detected QTLs for the AH, CS, RC and starch-corrected traits on ten potato chromosomes, confirming the polygenic nature of the traits. The QTLs with the strongest effects were detected on chromosomes I (AH, 0 cM, 11.5% of variance explained), IV (CS, 43.9 cM, 12.7%) and I (RC, 49.7 cM, 14.1%). When starch correction was applied, the QTLs with the strongest effects were revealed on chromosomes VIII (SCAH, 39.3 cM, 10.8% of variance explained), XI (SCCS, 79.5 cM, 10.9%) and IV (SCRC, 43.9 cM, 10.8%). Applying the starch correction changed the landscape of QTLs for chip color, as some QTLs became statistically insignificant, shifted or were refined, and new QTLs were detected for SCAH. The QTLs on chromosomes I and IV were significant for all traits with and without starch correction.

Phylogenetic relationship and genetic history of Central Asian Kazakhs inferred from Y-chromosome and autosomal variations Abstract The Xinjiang Uyghur Autonomous Region of China (XUARC) with 47 ethnic groups is a very colorful ethnic region of China, harboring abundant genetic and cultural diversity. The Kazakhs are the third largest ethnic group (7.02%) after Uyghur (46.42%) and Han (38.99%) in Xinjiang, but their genetic diversity and forensic characterization are poorly understood. In the current study, we genotyped 15 autosomal short tandem repeat (STR) loci and ten Y-STRs in 889 individuals (659 male and 230 female) collected from Kazak population of the Ili Kazak Autonomous Prefecture using AGCU Expressmarker 16 and 10Y-STR Kit (EX16 + 10Y). For autosomal STRs, we observed a total of 174 different alleles ranging from 6 to 34.2 repeat units and FGA showed the greatest power of discrimination (20 alleles) in Ili Kazakh population. We have not observed departures from Hardy–Weinberg equilibrium (HWE) after sequential Bonferroni correction and only found a minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The combined power of exclusion (CPE) was 0.99999998395 and combined power of discrimination (CPD) was 99.999999999999999798%. For Y-STRs, we observed a total of 496 different haplotypes in these ten Y-STR loci. The gene diversities ranged from 0.5023 (DYS391) to 0.8357 (DYS385a/b). The overall haplotype diversity (GD) was 0.9985 with random matching probability (RMP) of 0.0015. The results of population genetic analysis based on both autosomal and Y-chromosome STRs demonstrated that the genetic affinity among populations is generally consistent with ethnic, linguistic, and continental geographical classifications.

Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes Abstract The origin of supernumerary (B) chromosomes is clearly conditioned by their ancestry from the standard (A) chromosomes. Sequence similarity between A and B chromosomes is thus crucial to determine B chromosome origin. For this purpose, we compare here the DNA sequences from A and B chromosomes in the characid fish Characidium gomesi using two main approaches. First, we found 59 satellite DNA (satDNA) families constituting the satellitome of this species and performed FISH analysis for 18 of them. This showed the presence of six satDNAs on the B chromosome: one shared with sex chromosomes and autosomes, two shared with sex chromosomes, one shared with autosomes and two being B-specific. This indicated that B chromosomes most likely arose from the sex chromosomes. Our second approach consisted of the analysis of five repetitive DNA families: 18S and 5S ribosomal DNA (rDNA), the H3 histone gene, U2 snDNA and the most abundant satDNA (CgoSat01-184) on DNA obtained from microdissected B chromosomes and from B-lacking genomes. PCR and sequence analysis of these repetitive sequences was successful for three of them (5S rDNA, H3 histone gene and CgoSat01-184), and sequence comparison revealed that DNA sequences obtained from the B chromosomes displayed higher identity with C. gomesi genomic DNA than with those obtained from other Characidium species. Taken together, our results support the intraspecific origin of B chromosomes in C. gomesi and point to sex chromosomes as B chromosome ancestors, which raises interesting prospects for future joint research on the genetic content of sex and B chromosomes in this species.

Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection Abstract To provision the world sustainably, modern society must increase overall crop production, while conserving and preserving natural resources. Producing more with diminishing water resources is an especially daunting endeavor. Toward the goal of genetically improving drought resilience of cultivated Upland cotton (Gossypium hirsutum L.), this study addresses the genetics of differential yield components referred to as productivity and fiber quality traits under regular-water versus low-water (LW) field conditions. We used ten traits to assess water stress deficit, which included six productivity and four fiber quality traits on two recombinant inbred line (RIL) populations from reciprocally crossed cultivars, Phytogen 72 and Stoneville 474. To facilitate genetic inferences, we genotyped RILs with the CottonSNP63K array, assembled high-density linkage maps of over 7000 SNPs and then analyzed quantitative trait variations. Analysis of variance revealed significant differences for all traits (p < 0.05) in these RIL populations. Although the LW irrigation regime significantly reduced all traits, except lint percent, the RILs exhibited a broad phenotypic spectrum of heritable differences across the water regimes. Transgressive segregation occurred among the RILs, suggesting the possibility of genetic gain through phenotypic selection for drought resilience and perhaps through marker-based selection. Analyses revealed more than 150 quantitative trait loci (QTLs) associated with productivity and fiber quality traits (p < 0.005) on different genomic regions of the cotton genome. The multiple-QTL models analysis with LOD > 3.0 detected 21 QTLs associated with productivity and 22 QTLs associated with fiber quality. For fiber traits, strong clustering and QTL associations occurred in c08 and its homolog c24 as well as c10, c14, and c21. Using contemporary genome sequence assemblies and bioinformatically related information, the identification of genomic regions associated with responses to plant stress/drought elevates the possibility of using marker-assisted and omics-based selection to enhance breeding for drought resilient cultivars and identifying candidate genes and networks. RILs with different responses to drought indicated that it is possible to maintain high fiber quality under LW conditions or reduce the of LW impact on quality. The heritable variation among elite bi-parental RILs for productivity and quality under field drought conditions, and their association of QTLs, and thus specific genomic regions, indicate opportunities for breeding-based gains in water resource conservation, i.e., enhancing cotton’s agricultural sustainability.

A high-quality cucumber genome assembly enhances computational comparative genomics Abstract Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.

Single nucleotide polymorphisms in piRNA-pathway genes: an insight into genetic determinants of human diseases Abstract With the development of advanced high-throughput genotyping technologies, there has been a dramatic improvement in identifying millions of single nucleotide polymorphisms (SNPs) across the human genome. SNPs located within the genes involved in biogenesis and function of small regulatory RNAs such as PIWI-interacting RNAs (piRNAs) can alter physiological processes by affecting gene expression. The genetic variations within PIWI genes and their associated factors such as TDRDs, EIFs, and KIF17 etc. have shown significant association with dreadful human diseases such as Alzheimer’s disease, cancer, and schizophrenia. In this review, we have attempted to survey and summarize the association of all the genetic variants reported in different piRNA-pathway genes with diseases and discern their potential in clinical manifestations which will serve as a cornerstone for subsequent studies to decrypt the molecular mechanisms of SNPs in developing diseases.

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iN6-methylat (5-step): identifying DNA N 6 -methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule Abstract DNA N6-methyladenine is a non-canonical DNA modification that occurs in different eukaryotes at low levels and it has been identified as an extremely important function of life. Moreover, about 0.2% of adenines are marked by DNA N6-methyladenine in the rice genome, higher than in most of the other species. Therefore, the identification of them has become a very important area of study, especially in biological research. Despite the few computational tools employed to address this problem, there still requires a lot of efforts to improve their performance results. In this study, we treat DNA sequences by the continuous bags of nucleobases, including sub-word information of its biological words, which then serve as features to be fed into a support vector machine algorithm to identify them. Our model which uses this hybrid approach could identify DNA N6-methyladenine sites with achieved a jackknife test sensitivity of 86.48%, specificity of 89.09%, accuracy of 87.78%, and MCC of 0.756. Compared to the state-of-the-art predictor as well as the other methods, our proposed model is able to yield superior performance in all the metrics. Moreover, this study provides a basis for further research that can enrich a field of applying natural language-processing techniques in biological sequences.

Analysis of direct repeats and spacers of CRISPR/Cas systems type I-F in Brazilian clinical strains of Pseudomonas aeruginosa Abstract CRISPR/Cas is an adaptive immune system found in prokaryotes, with the main function of protecting these cells from invasion and possible death by mobile genetic elements. Pseudomonas aeruginosa is considered a model for type I-F CRISPR/Cas system studies. However, its CRISPR loci characteristics have not yet been thoroughly described, and its function has not yet been fully unraveled. The aims of this study were to find the frequency of the system in Brazilian clinical isolates; to identify the loci sequence, its spacer diversity and its origins; as well as to propose a unified spacer library to aid in future structural studies of the CRISPR loci of P. aeruginosa. We investigated types I-F and I-E gene markers to establish CRISPR/Cas typing, and observed two strains harboring both systems simultaneously, a very rare feature. Through amplification and sequencing of CRISPR loci related to type I-F system, we describe polymorphisms in DRs and 350 spacers, of which 97 are new. The spacers that were identified had their possible organisms or proteins of origin identified. Spacer arrays were grouped in five different CRISPR patterns and the plasticity was inferred by rearrangements in spacer arrays. Here, we perform the first detailed and focused description of CRISPR/Cas elements in Brazilian clinical strains of P. aeruginosa. Our findings reflect active and highly diverse CRISPR loci, and we suggest that CRISPR/Cas may also pose as a transcriptional regulatory mechanism. The structural and diversity features described here can provide insights into the function of CRISPR/Cas in this pathogen and help guide the development of new therapeutic strategies.