Construction of a foxtail millet linkage map and mapping of spikelet-tipped bristles 1(stb1) by using transposon display markers and simple sequence repeat markers with genome sequence information

We attempted genetic analysis and mapping of a gene responsible for the trait “spikelet-tipped bristles” (stb) in foxtail millet, Setaria italica (L.) P.Beauv., as the first step in positional cloning of the gene. This trait is important not only in grain yield such as grain number per panicle of this millet but also in the evolutionary development of the “bristle grass” clade including genera Setaria, Pennisetum and Cenchrus in subfamily Panicoideae. First of all, we confirmed that this trait is controlled by a single recessive gene, using two populations of F2 plants; one was a cross combination between two Taiwanese landraces and the other was a combination between a Taiwanese landrace and a Japanese landrace. Using the latter of the two F2 populations, with transposon display (TD) markers and simple sequence repeat (SSR) markers developed previously, we constructed a genetic map with 13 linkage groups and mapped the responsible gene (stb1) on chromosome 2. We also developed novel SSR markers by using foxtail millet genome sequence information, and we finally constructed nine linkage groups corresponding to nine chromosomes with a total length of 1287.5 cM, and mapped stb1 more precisely on chromosome 2. This work suggests that the foxtail millet genome sequences recently published are useful for developing genome-wide SSR markers for constructing linkage maps and mapping genes in this millet.     

High-throughput sequencing of <Emphasis Type="Italic">Prunus ferganensis</Emphasis> indicates that it is a geographical population of <Emphasis Type="Italic">P. persica</Emphasis>

Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.     

High-resolution mapping of the dull fruit skin gene D in cucumber (Cucumis sativus L.)

Dull/glossy fruit skin is a highly valuable external quality trait that affects the market value of cucumbers. In this study, genetic analysis showed that one single dominant gene, D (dull fruit skin), determines the dull fruit skin trait in cucumber. By combining bulked segregant analysis with 11 published polymorphic molecular markers on chromosome 5, the D/d gene was preliminarily mapped between markers SCZ69 and SSR16203, at genetic distances of 0.3 and 0.6 cM, respectively. Subsequently, a larger F2 (S06 × S94) population (842 individuals in total) was used for high-resolution mapping of the D/d gene. Finally, the D/d gene was fine-mapped between markers SSR37 and SSR112, at a physical distance of 244.9 kb (containing 31 candidate genes), using eight newly developed polymorphic simple sequence repeat (SSR) markers between SCZ69 and SSR16203. Based on semi-quantitative RT-PCR analysis, the possible candidate gene D was identified as Csa016880 or Csa016887. Meanwhile, validity analysis of the markers SSR37 and SSR112 was performed with 72 dull/glossy fruit lines, and showed that the two co-dominant SSR markers could be used for marker-assisted selection of the dull/glossy fruit trait in cucumber breeding. Moreover, this study will be helpful for cloning of the D gene in cucumber.     

Single-strand conformational polymorphism markers associated with a major QTL for fusarium head blight resistance in wheat

A major quantitative trait locus (QTL) associated with resistance to Fusarium head blight (FHB) was identified on chromosome 3BS between simple sequence repeat (SSR) markers Xgwm389 and Xgwm493 in wheat “Ning 7840”, a derivative from “Sumai 3”. However, the marker density of SSR in the QTL region was much lower than that required for marker-assisted selection (MAS) and map-based cloning. The objective of this study was to exploit new markers to increase marker density in this QTL region by using single-strand conformational polymorphism (SSCP) markers developed from wheat-expressed sequence tags (ESTs) on 3BS bin 8-0.78-1.0. Sixty-nine out of 85 SSCP primer pairs amplified PCR (polymerase chain reaction) products from the genomic DNA of “Chinese Spring”. Thirty-four primer pairs amplified PCR products that could form clear ssDNA (single strand DNA) bands through denaturation treatment. Ten SSCP markers had polymorphisms between Ning 7840 and “Clark”. Five of the ten polymorphic SSCP markers were located on chromosome 3B by nullitetrasomic analysis. Three SSCP markers (Xsscp6, Xsscp20, and Xsscp21) were mapped into the region between Xgwm493 and Xgwm533 and possessed a higher coefficient of determination (R²) than Xgwm493 and Xgwm533. The SSCP markers, Xsscp6, Xsscp20, and Xsscp21, can be used for map-based cloning of the QTL and for marker-assisted selection in FHB resistance breeding.     

The polyphyletic origin of the "Cheilostomata" (Bryszoa)

The relative appearance of the parietal muscles in the development of the zooids has been studied in several ctenostomatous and “cheilostomatous” species. A comparison of the different on-togenetical sequences demonstrated that a “cheilostomatous” type of organization of the zooids with a great probability has been achieved in minimum three times independentl and originated from different ctenostomatous sub-grous: the Membranidea from plesiomorgic victorelloids (ancestors of Bulbella with not yet developed peristomial tube), the Inoviceiata (Aetea) from advanced forms of victorelloids with reduced primary parietal muscles (perhaps stcies related to Pottsiella), and Penetrantia from arachnidioid or vesicularioid ancestors (?). Therefore, the classical orders ^α“Ctenostomata” and “Cheilostomata” represent only “stage groups” but no monohyletic systematical units. Because of the new concept and interpretation I propose a new name for the united group: Cteno-Cheilostomata, supra-ord. nov.     

Biochemical evidence bearing on the domestication of<Emphasis Type="Italic">Phaseolus</Emphasis> (Fabaceae) beans

The genusPhaseolus (Fabaceae) consists of some 50 species, all of which are distributed in the Americas. Four of these contain cultigens.P. vulgaris (common bean),P. lunatus (lima bean),P. acutifolius (tepary bean),P. coccineus subsp.coccineus (runner bean); andP. coccineus subsp.polyanthus (no English vernacular name). Biochemical markers—phaseolin seed storage protein and isozymes—have provided new evidence on the organization of the first three species. Domestication has possibly caused a strong reduction in genetic diversity inP. vulgaris andP. acutifolius. BothP. vulgaris andP. lunatus cultivars result from at least two independent domestications, in Mesoamerica and in the Andes. These two species consist of two gene pools, each of which includes wild ancestors and their respective cultivated descendants. Our findings suggest the need for additional emphasis on genetic conservation of wild ancestors and their use in breeding programs and for a comparison of inter-gene pool vs. intra-gene pool crosses in breeding programs.     

Novel genetic variants of sine oculis homeobox homolog 3 gene are associated with body weight and average daily gain in Bos taurus

Sine oculis homeobox homolog 3 (Six3) gene is responsible for normal mammalian pituitary development, and its genetic variations or deficiency will cause hypopituitarism, suggesting that this gene is a potential candidate gene for studying association with growth traits in animals. Herein, genetic variants within bovine Six3 gene was screened in 1031 individuals from four Chinese indigenous cattle breeds. Two novel polymorphisms (NC_007309:g.2515G>A and NC_007309:g.2607T>C) locating at positions nt1707 and nt1799 of intron 1 in bovine Six3 gene, were found, and could be genotyped by TaqI ACRS PCR-RFLP and Alw26I PCR-RFLP, respectively. The frequencies of allele “A” of TaqI locus varied from 0.004 to 0.309, as well as the frequencies of allele “C” of Alw26I locus waved from 0.025 to 0.340. Association analysis revealed no significant association of TaqI locus with growth traits in Nanyang breed. However, significant relationships between Alw26I locus and body weight (BW) and average daily gain (ADG) in Nanyang breed was found (p<0.05). The individuals with genotype TC had greater body weight and average daily gain than those with genotype TT at 18 months old. Furthermore, based on combinated genotypes from these two loci, diplotypes was found to be associated with growth traits (p<0.05).The individuals with dihaplotype GG-TC had greater body weight and average daily gain at 18 month-old than those of other dihaplotypes. Therefore, the TaqI and Alw26I genetic variants of bovine Six3 gene were recommended as DNA markers related to growth traits through marker-assisted selection for genetics and breeding in cattle.     

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

Genetic Diversity of Some Pear Cultivars and Genotypes Using Simple Sequence Repeat (SSR) Markers

The genetic diversity and relationships among 47 pear cultivars and genotypes (Pyrus spp.), including 4 Japanese pears (Pyrus pyrifolia), 40 European pears (Pyrus communis), 1 Chinese pear (Pyrus bretschneideri) as well as 2 wild relatives (Pyrus salicifolia and Pyrus mazandaranica) were studied using 28 microsatellite primer pairs. A total of 174 alleles were produced at the 28 SSR loci with their sizes ranging from 81 to 290?bp. The number of observed alleles for each locus ranged from 3 (TsuENH014 and TsuENH046) to 12 (NB103a), with an average of 6.21 alleles per locus. In some SSR loci, more than two alleles were amplified in some cultivars and genotypes, suggesting that duplication has occurred in those accessions. This information suggests that at least two genomic regions exist for these loci in the pear genome. The observed heterozygosity (H _o) values of amplified loci ranged from 0.17 (TsuENH006) to 0.97 (NB103a). Shannon's information index (I) value was observed to be highest (2.14) in the NB103a locus, while the TsuENH006 locus had the lowest value with an average of 1.37 among SSR loci. The Dice genetic similarity coefficient ranged from 0.29 (??Nijisseiki?? and P. mazandaranica) to 0.91 (??Chojuro?? and ??Nijisseiki??) among samples. UPGMA cluster analysis showed two major groups corresponding to the Japanese and European pears.     

Analysis and characterization of anthocyanins and carotenoids in Japanese blue tomato

Tomato (Solanum lycopersicum) is rich in anthocyanins, which are polyphenolic pigments. This study aimed to analyze and characterize the anthocyanin composition in cultivated blue tomato in Japan. The extracts of peel, seed, and pulp of tomatoes were purified following which anthocyanins and lycopene contents were analyzed using high-performance liquid chromatography and electrospray ionization mass spectrometry. Eleven types of anthocyanins were identified, including delphinidin, petunidin, and malvidin. Further, the antioxidant activity of anthocyanins was evaluated using 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt radical quenching assays and electron spin resonance. “Blue tomato” extracts exert antioxidant activity. Thus, we showed that petunidin was present in the “blue tomato” peel while lycopene was present in the peel and pulp. Additionally, the blue tomato peel extract was found to significantly inhibit H₂O₂-induced cell death in vitro. This is the first study on cell protective effects of Japanese blue tomato extract and petunidin in murine photoreceptor cells.     

The role of visual information in maintaining postural stability after the maximum exercise for the upper and lower limb muscles

The postural stability on a seesaw generating anterior–posterior instability with the eyes open (EO) and then the eyes closed (EC) in young healthy subjects (n = 28) before and 6 min after the maximum bicycle exercise (Wingate test) performed using lower limbs (“leg exercise”) or upper limbs (“hand exercise”) was investigated. It was found that “hand exercise” caused the same increase in average velocity (V, mm/s) and in the average range of sway of the centre of pressure (Qy, mm) as “leg exercise.” However, the duration of V recovery (EC: 2 min 30 s and 50 s; EO: 60 s and 40 s after “leg exercise” and “hand exercise,” respectively) and Qy (EC: 1 min 10 s and 30 s after “leg exercise” and “hand exercise,” respectively; EO: no changes from baseline) was shorter after “hand exercise.” In the presence of visual information, the increment in V decreased more than 2 times after “leg exercise” (+100.5% and + 40.5%, p < 0.01 for EC and EO, respectively) and after “hand exercise” (+73.0% and +30.3%, p < 0.01 for EC and EO, respectively). Moreover, Qy after both exercises remained at the initial level under EO conditions but significantly increased under EC conditions (+42.8%, p < 0.01 after “leg exercise” and +40.3%, p < 0.01 after “hand exercise”). Thus, the maximum exercise for the muscles of the upper limbs causes the same reduction in postural stability as analogous exercise for the muscles of the lower limbs, but the recovery period after “hand” exercise was shorter. The presence of visual information allows the baseline maintenance of postural stability and significantly reduces the strain of postural regulation while standing on a movable support after the maximum “leg exercise” and “hand exercise.”     

Genetic variation in wild Prunus L. subgen. Cerasus germplasm from Iran characterized by nuclear and chloroplast SSR markers

Key message

The selected material of Cerasus subgen. will be useful for conservation and management and important for Prunus breeding programs.

Abstract

Knowledge of relationships among the cultivated and wild species of Cerasus is important for recognizing gene pools in germplasm and developing effective conservation and management strategies. In this study, genetic and phylogenetic relationships of wild Cerasus subgenus species naturally growing in Iran, including P. avium (mazzard), P. mahaleb, P. brachypetala, P. incana, P. yazdiana, P. microcarpa subsp. microcarpa, P. microcarpa subsp. diffusa and P. pseudoprostrata and three commercial species, sweet cherry (P. avium), sour cherry (P. cerasus) and duke cherry (P. x gondouinii) was investigated based on 16 nuclear SSR and five chloroplast SSR. Very high level of polymorphism was detected among the studied species based these molecular markers, indicating high inter and intraspecific genetic variation. Inter and intraspecific genetic similarity coefficients varied from 0.00 to 1.00, indicating high genetic variation in studied germplasm. These two molecular markers types could distinguish differences between all species so that accessions of each species were placed into a single group. Based on molecular markers, a close correlation was observed between intraspecific variation and geographical distribution. Furthermore, based on nuSSR primers, most wild species showed 2–4 alleles and may be tetraploid. In conclusion, the conservation of these highly diverse native populations of Iranian wild Cerasus germplasm is recommended for future breeding activity.     

Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy

Children born to obese mothers are at increased risk for obesity, but the mechanisms behind this association are not fully understood. Our study aimed to investigate differences in the functions encoded by the microbiome of infants at 18 months of age when the transition from early infant-feeding to solid family foods is established. To investigate the impact of maternal prepregnancy body mass index on infants’ gut microbiome, faecal samples from infants born to normoweight (n = 21) and obese mothers (n = 18) were analysed by 16S rRNA gene sequencing and a functional-inference-based microbiome analysis. Our results indicated that Firmicutes was significantly enriched in infants born to normoweight mothers whereas Bacteroidetes was significantly enriched in infants born to obese women. In both microbiomes, the greatest number of genes (>50%) that were assigned a function encoded for proteins involved in “metabolism” among tier 1 KEGG Orthology (KO) categories. At lower KO functional categories, the microbiome of infants born to normoweight mothers was characterized by a significant enrichment in the abundances of “pentose phosphate pathway” (p = 0.037), “lysine biosynthesis” (p = 0.043), “glycerolipid metabolism” (p = 0.042), and “C5-branched dibasic acid metabolism” (p = 0.045). Notably, the microbiome of infants born to obese mothers was significantly enriched in “streptomycin biosynthesis” (p = 0.047), “sulphur metabolism” (p = 0.041), “taurine and hypotaurine metabolism” (p = 0.036), and “lipopolysaccharide biosynthesis” (p = 0.043). In summary, our study showed that maternal prepregnancy obesity may imprint a selective gut microbial composition during late infancy with distinct functional performances.     

Production of wheat-rye substitution lines and identification of chromosome composition of karyotypes using C-banding, GISH, and SSR markers

Based on the cross (Triticum aestivum L. × Secale cereale L.) × T. aestivum L., wheat-rye substitution lines (2n = 42) were produced with karyotypes containing, instead of a pair of homologous wheat chromosomes, a homeologous pair of rye chromosomes. The chromosome composition of these lines was described by GISH and C-banding methods, and SSR analysis. The results of genomic in situ hybridization demonstrated that karyotype of these lines included one pair of rye chromosomes each and lacked wheat-rye translocations. C-banding and SSR markers were used to identify rye chromosomes and determine the wheat chromosomes at which the substitution occurred. The lines were designated 1R(1D), 2R(2D)₂, 2R(2D)₃, 3R(3B), 6R(6A)₂. The chromosome composition of lines 1R(1A), 2R(W)₁, 5R(W), 5R(5A), and 6R(W)₁, which were earlier obtained according to the same scheme for crossing, was characterized using methods of telocentric analysis, GISH, C-banding, and SSR analysis. These lines were identified as 1R(1A), 2R(2D)₁, 5R(5D), 5R(5A), and 6R(6A)₁, C-banding of chromosomes belonging to line 1R(1A) revealed the presence of two translocated chromosomes (3DS.3DL-del. and 4AL.W) during simultaneous amplification of SSR markers located on 3DL and 4AS arms. The “combined” long arm of the newly derived chromosome 4A is assumed to be formed from the long arm of chromosome 4AS itself and a deleted segment 3DL. All examined lines are cytologically stable, except for 3R(3B), which does not affect the stability of rye 3R chromosome transfer. Chromosome identification and classification of the lines will permit them to be models for genetic studies that can be used thereafter as promising “secondary gene pools” for the purpose of plant breeding.     

microRNA-mediated <Emphasis Type="Italic">R</Emphasis> gene regulation: molecular scabbards for double-edged swords

Plant resistance (R) proteins are immune receptors that recognize pathogen effectors and trigger rapid defense responses, namely effector-triggered immunity. R protein-mediated pathogen resistance is usually race specific. During plant-pathogen coevolution, plant genomes accumulated large numbers of R genes. Even though plant R genes provide important natural resources for breeding disease-resistant crops, their presence in the plant genome comes at a cost. Misregulation of R genes leads to developmental defects, such as stunted growth and reduced fertility. In the past decade, many microRNAs (miRNAs) have been identified to target various R genes in plant genomes. miRNAs reduce R gene levels under normal conditions and allow induction of R gene expression under various stresses. For these reasons, we consider R genes to be double-edged “swords” and miRNAs as molecular “scabbards”. In the present review, we summarize the contributions and potential problems of these “swords” and discuss the features and production of the “scabbards”, as well as the mechanisms used to pull the “sword” from the “scabbard” when needed.     

Predictive factors of mortality in patients treated with tocilizumab for acute respiratory distress syndrome related to coronavirus disease 2019 (COVID-19)

COVID-19 patients (n = 34) suffering from ARDS were treated with tocilizumab (TCZ). Outcome was classified in two groups: “Death” and “Recovery”. Predictive factors of mortality were studied. Mean age was 75.3, mean oxygen (O₂) requirements 10.4 l/min. At baseline, all patients had multiple biological abnormalities (lymphopenia, increased CRP, ferritin, fibrinogen, D-dimer and liver enzymes). 24 patients (70.5%) recovered after TCZ therapy and 10 died (29.5%). Deceased subjects differed from patients in whom treatment was effective with regard to more pronounced lymphopenia (0.6 vs 1.0 G/l; p = 0.037), lower platelet number (156 vs 314 G/l; p = 0.0001), lower fibrinogen serum level (0.6 vs 1.0 G/l; p = 0.03), higher aspartate-amino-transferase (108 vs 57 UI/l; p = 0.05) and greater O₂ requirements (11 vs 8 l/min; p = 0.003).     

Identification of bioactive phytochemical from two Punica species using GC–MS and estimation of antioxidant activity of seed extracts

Punica species are medicinally important plants belonging to the family Lythraceae. The pomegranate is widely reported to exhibit antiviral, antioxidant, anticancer, anti-proliferative activities. In the present study the ethanolic extract of the peel seeds of two species of Punica (Punica granatum and Punica protopunica) were subjected to GC–MS analysis. Twenty-one and 14 compounds were identified in P. granatum and P. protopunica peel seeds, respectively. The main chemical constituents in P. granatum-peel seeds were propanoic acid, benzenedicarboxylic acid, methoxypropionic acid and methyl amine. The corresponding constituents of P. protopunica peel seeds were benzenedicarboxylic acid, benzoic acid and propanoic acid. Moreover, the antioxidant effects of the aqueous ethanolic extracts were estimated in vitro. The two tested extracts contained significantly different phenolic and total flavonoid contents in P. granatum than in P. protopunica. Different in vitro methods of antioxidant activity determination produced varying results. In malondialdehyde (MDA), hydrogen peroxide (H₂O₂) scavenging and 1,1-diphenyl-2-picrylhydrazyl (DPPH) assays, the two peel seed extracts exhibited very high antioxidant activities, with higher activity observed for the P. granatum extract.     

2′-(E)-O-p-coumaroylgalactaric acid and 2′-(E)-O-feruloylgalactaric acid in citrus

2′-(E)-O-p-Coumaroyl- and 2′-(E)-O-feruloylgalactaric acids, hitherto unknown in nature, have been isolated and identified from orange peel.