Auxin and CmAP1 regulate the reproductive development of axillary buds in Chinese chestnut (Castanea mollissima).

KEY MESSAGE: Auxin accumulation upregulates the expression of APETALA1 (CmAP1) and subsequently activates inflorescence primordium development in axillary buds of chestnut. The architecture of fruiting branches is a key determinant of chestnut yield. Normally, axillary buds at the top of mother fruiting branches develop into flowering shoots and bear fruits, and the lower axillary buds develop into vegetative shoots. Decapitation of the upper axillary buds induces the lower buds to develop into flowering shoots. How decapitation modulates the tradeoff between vegetative and reproductive development is unclear. We detected inflorescence primordia within both upper and lower axillary buds on mother fruiting branches. The level of the phytohormones 3-indoleacetic acid (IAA) and trans-zeatin (tZ) increased in the lower axillary buds in response to decapitation. Exogenous application of the synthetic analogues 1-naphthylacetic acid (NAA) or 6-benzyladenine (6-BA) blocked or promoted, respectively, the development of the inflorescence primordia in axillary buds. The transcript levels of the floral identity gene CmAP1 increased in axillary buds following decapitation. An auxin response element TGA-box is present in the CmAP1 promoter and influenced the CmAP1 promoter-driven expression of ß-glucuronidase (GUS) in floral organs in Arabidopsis, suggesting that CmAP1 is induced by auxin. We propose that decapitation releases axillary bud outgrowth from inhibition caused by apical dominance. During this process, decapitation-induced accumulation of auxin induces CmAP1 expression, subsequently promoting the reproductive development of axillary buds.

Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis.

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159-160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

Comparison of Physicochemical Properties of Starches from Nine Chinese Chestnut Varieties.

Chestnut is a popular food in many countries and is also an important starch source. In previous studies, physicochemical properties of starches have been compared among different Chinese chestnut varieties growing under different conditions. In this study, nine Chinese chestnut varieties from the same farm were investigated for starch physicochemical properties to exclude the effects of growing conditions. The dry kernels had starch contents from 42.7 to 49.3%. Starches from different varieties had similar morphologies and exhibited round, oval, ellipsoidal, and polygonal shapes with a central hilum and smooth surface. Starch had bimodal size distribution and the volume-weighted mean diameter ranged from 7.2 to 8.2 µm among nine varieties. The starches had apparent amylose contents from 23.8 to 27.3% but exhibited the same C-type crystalline structure and similar relative crystallinity, ordered degree, and lamellar structure. The gelatinization onset, peak, and conclusion temperatures ranged from 60.4 to 63.9 °C, from 64.8 to 68.3 °C, and from 70.5 to 74.5 °C, respectively, among nine starches; and the peak, hot, breakdown, final, and setback viscosities ranged from 5524 to 6505 mPa s, from 3042 to 3616 mPa s, from 2205 to 2954 mPa s, from 4378 to 4942 mPa s, and from 1326 to 1788 mPa s, respectively. The rapidly digestible starch, slowly digestible starch, and resistant starch ranged from 2.6 to 3.7%, from 5.7 to 12.7%, and from 84.4 to 90.7%, respectively, for native starch, and from 79.6 to 89.5%, from 1.3 to 3.8%, and from 7.1 to 17.4%, respectively, for gelatinized starch.

Comprehensive profiling of cell subsets of gastric cancer and liver metastasis based on single cell RNA-sequencing analysis.

Background: Liver metastasis (Li) is one of the most common distant metastatic sites for gastric cancer. A deeper understanding of its mechanism of action from a bioinformatics perspective may provide new insights. Therefore, the aim of this study was to use single cell RNA sequencing (scRNA-seq) to evaluate cell subtypes and understand the molecular mechanism of gastric cancer Li. Methods: The scRNA-seq data GSE163558 of gastric cancer and Li were downloaded from Gene Expression Omnibus (GEO). Single cell data were analyzed by various R packages such as Seurat, CellChat, gene set variation analysis (GSVA), monocle, gene set enrichment analysis (GSEA), and survival analysis and the results were plotted by ggplot2, R4.1.1. Protein expression was confirmed by immunohistochemistry in an additional patient cohort. Results: The genes APOD, CXCL5, and JUN are involved in epithelial cell metastasis. The infiltration of cytotoxic CD8 T cells was more frequent in gastric primary tumors (PTs) than in Lis. IL7R high natural killer (NK) cells that had high TXNIP and RIPOR2 expression were located at the site of Li and corresponded to a favorable prognosis. NK cells with high TNFAIP3 expression were located at the PT site and corresponded to a poor prognosis. Furthermore, the gene expression of myeloid cells was different depending on their localization in the PT site or Li. MHC-I signaling pathway was found to be activated in the PT compared to MHC-II at the site of Li, as revealed by cell-cell interaction, and HLA-E-CD94/NKG2A of NK cells was only activated in the PT and not in the Li. Conclusions: The present study revealed the difference between Li and gastric PT by scRNA-seq, demonstrating the impact of partial gene expression on patient prognosis. Our study provides new insights into gastric cancer and Li.

Corrigendum: Haplotype analysis of chloroplast genomes for jujube breeding.

[This corrects the article DOI: 10.3389/fpls.2022.841767.].

Characterization and identification of cold tolerant near-isogenic lines in rice.

To exploit the genetic mechanism of cold tolerance in rice, cold tolerant near-isogenic lines (NILs) were developed by backcrossing Kunmingxiaobaigu (KMXBG), reported to be the most cold-tolerant variety at the booting stage, as donor, with the cold sensitive Japanese commercial japonica variety, Towada. Comparisons of cold tolerance-related traits between five BC(6)F(5) NILs and recurrent parent Towada under cold treatment and normal temperatures at the booting stage showed that the differences between the NILs and Towada were significant only for spikelet fertility-related traits. Analyses of cold tolerance in the NILs at the budding (germination), seedling and booting stages indicated both correlated effects and differences. Lines 1913-4 and 1916-1 showed strong and stable tolerance at all three stages. Whole genome marker screening showed that the proportion of genetic background recovery was more than 98%. Seventeen markers from KMXBG were introgressed in two or more NILs, and cold tolerance genes were possibly present in these marker regions. The NILs should be excellent materials for both rice improvement and map-based cloning of cold tolerance QTLs.

Pan-genome analysis of three main Chinese chestnut varieties.

Chinese chestnut (Castanea mollissima Blume) is one of the earliest domesticated plants of high nutritional and ecological value, yet mechanisms of C. mollissima underlying its growth and development are poorly understood. Although individual chestnut species differ greatly, the molecular basis of the formation of their characteristic traits remains unknown. Though the draft genomes of chestnut have been previously released, the pan-genome of different variety needs to be studied. We report the genome sequence of three cultivated varieties of chestnut herein, namely Hei-Shan-Zhai-7 (H7, drought-resistant variety), Yan-Hong (YH, easy-pruning variety), and Yan-Shan-Zao-Sheng (ZS, early-maturing variety), to expedite convenience and efficiency in its genetics-based breeding. We obtained three chromosome-level chestnut genome assemblies through a combination of Oxford Nanopore technology, Illumina HiSeq X, and Hi-C mapping. The final genome assemblies are 671.99 Mb (YH), 790.99 Mb (ZS), and 678.90 Mb (H7), across 12 chromosomes, with scaffold N50 sizes of 50.50 Mb (YH), 65.05 Mb (ZS), and 52.16 Mb (H7). Through the identification of homologous genes and the cluster analysis of gene families, we found that H7, YH and ZS had 159, 131, and 91 unique gene families, respectively, and there were 13,248 single-copy direct homologous genes in the three chestnut varieties. For the convenience of research, the chestnut genome database was constructed. Based on the results of gene family identification, the presence/absence variations (PAVs) information of the three sample genes was calculated, and a total of 2,364, 2,232, and 1,475 unique genes were identified in H7, YH and ZS, respectively. Our results suggest that the GBSS II-b gene family underwent expansion in chestnut (relative to nearest source species). Overall, we developed high-quality and well-annotated genome sequences of three C. mollissima varieties, which will facilitate clarifying the molecular mechanisms underlying important traits, and shortening the breeding process.

Haplotype Analysis of Chloroplast Genomes for Jujube Breeding.

Jujube (family Rhamnaceae) is an important economic fruit tree in China. In this study, we reported 26 chloroplast (cp) sequences of jujube using Illumina paired-end sequencing. The sequence length of cp genome was 161, 367-161, 849 bp, which was composed of a large single-copy region (89053-89437 bp) and a small single-copy region (19356-19362 bp) separated by a pair of reverse repeat regions (26478-26533 bp). Each cp genome encodes the same 130 genes, including 112 unique genes, being quite conserved in genome structure and gene sequence. A total of 118 single base substitutions (SNPs) and 130 InDels were detected in 65 jujube accessions. Phylogenetic and haplotype network construction methods were used to analyze the origin and evolution of jujube and its sour-tasting relatives. We detected 32 effective haplotypes, consisting of 20 unique jujube haplotypes and 9 unique sour-jujube haplotypes. Compared with sour-jujube, jujube showed greater haplotype diversity at the chloroplast DNA level. To cultivate crisp and sweet fruit varieties featuring strong resistance, by combining the characteristics of sour-jujube and cultivated jujube, three hybrid combinations were suggested for reciprocal crosses: "Dongzao" × "Jingzao39," "Dongzao" × "Jingzao60," "Dongzao" × "Jingzao28." This study provides the basis for jujube species' identification and breeding, and lays the foundation for future research.

The complete chloroplast genome of Crataegus hupehensis Sarg. (Rosaceae), a medicinal and edible plant in China.

Crataegus hupehensis Sarg. is well-known for its medicinal and nutritive value. In this study, the complete chloroplast genome sequence of C. hupehensis was determined by using Illumina high-throughput sequencing approach. The complete chloroplast genome is 159,766 bp with 36.6% GC content. It contained a pair of inverted repeat regions of 26,385 bp, a large single-copy region of 87,852 bp, and a small single-copy region of 19,144 bp. It contained 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on chloroplast genomes indicated that C. hupehensisis was closely related to C. kansuensis and C. marshallii in the subfamily Maloideae. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Crataegus species.

Effects of green-manure and tillage management on soil microbial community composition, nutrients and tree growth in a walnut orchard.

This study characterized the effect of green manures (February orchid, hairy vetch, rattail fescue and a no-green-manure control) and the termination method (flail or disk) on nutrient contents, enzyme activities, microbial biomass, microbial community structure of rhizosphere soil and vegetative growth of walnut tree. All three selected green manures significantly enhanced the water content, organic C, total N and available P. The rattail fescue significantly decreased the mineral N. Total organic C, total N, mineral N and available P were significantly greater under flail than under disk. Hairy vetch and February orchid significantly improved levels of soil ß-glucosidase, N-acetyl-glucosaminidase and acid phosphatase activity, whereas rattail fescue improved only ß-glucosidase activity. All of the green manures significantly decreased phenoloxidase activity. ß-glucosidase, N-acetyl-glucosaminidase and acid phosphatase activities were significantly greater under flail relative to disk. The termination method had no significant effect on phenoloxidase activity. The different types of green manures and termination methods significantly altered the soil microbial biomass and microbial community structure. The green-manure treatments were characterized by a significantly greater abundance of Gram-positive (Gram +) bacteria, total bacteria and saprophytic fungi compared to the control. Hairy vetch significantly decreased the abundance of arbuscular mycorrhizal fungi (AMF) while February orchid and rattail fescue increased their abundance compared to the no-green-manure treatment. The abundance rates of Gram+ bacteria, actinomycetes, saprophytic fungi and AMF were significantly greater in soils under flail than under disk. In terms of vegetative growth of walnut tree, hairy vetch showed the greatest positive effects. The growth of walnut tree was significantly greater under flail relative to disk. Our results indicate that green-manure application benefits the rhizosphere soil micro-ecology, rhizosphere soil nutrient contents and tree growth. Overall, the hairy vetch and flail combined treatment is recommended for walnut orchards in northern China.

Chloroplast genome sequence of the wild Ziziphus jujuba Mill. var. spinosa from North China.

In this study, the complete chloroplast (cp) genome sequence of Ziziphus jujuba Mill. var. spinosa was mapped and determined based on Illumina sequencing data. The complete cp genome is 161,606 bp and contains a pair of inverted repeat regions of 26,479 bp each, a large single-copy region of 89,292 bp, and a small single-copy region of 19,356 bp. It harbors 112 unique genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on cp genomes indicates that the cp genome of wild Z. jujuba Mill. var. spinosa is similar to that of cultivated Z. jujuba and closely related to that of Z. incurva of the family Rhamnaceae.

Structural, thermal, and hydrolysis properties of large and small granules from C-type starches of four Chinese chestnut varieties.

Large and small granules were separated from C-type starches of four Chinese chestnut varieties growing in the same environment. They had similar amylose contents from 17.7% to 20.2% and showed C-type crystallinity. The large granules had relative crystallinity from 19.2% to 20.3%, ordered degree from 0.672 to 0.706, and lamellar peak intensity from 233.2 to 267.1, but small granules had relative crystallinity from 16.2% to 18.2%, ordered degree from 0.635 to 0.663, and lamellar peak intensity from 201.6 to 213.1. The gelatinization peak temperatures ranged from 62.6 to 65.7 °C in large granules but from 60.3 to 61.7 °C in small granules, and enthalpy variation did from 12.5 to 13.7 J/g in large granules but from 10.1 to 11.7 J/g in small granules. Both large and small granules showed biphasic hydrolysis. Though small granules had significantly higher hydrolysis rate than large granules, but they had similar total hydrolysis extent during whole hydrolysis. The granule size had significantly positive relationships with relative crystallinity, ordered degree, lamellar peak intensity, and gelatinization temperature and enthalpy variation, but was negatively correlated to hydrolysis rate. The principal component analysis was conducted to reveal the interrelationships among different starch properties and the variations among different starches.

Characterization of the complete chloroplast genome of the Pistacia vera L.

The complete chloroplast genome sequence of Pistacia vera was mapped and determined based on Illumina sequencing data. The complete chloroplast genome is 160,654 bp and contains a pair of inverted repeat regions of 26,596 bp each, a large single-copy region of 88,376 bp, and a small single-copy region of 19,086 bp. It harbors 113 genes, including 79 protein-coding genes,4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on chloroplast genomes indicates that Pistacia vera is closely related to that of Pistacia weinmanniifolia.

Changes in pore structure of coal caused by coal-to-gas bioconversion.

ABSTARCT: Microbial enhanced coalbed methane (ME-CBM) recovery is critically examined as a viable technology for natural gas recovery from coalbed methane (CBM) reservoirs. Since the majority of gas-in-place (GIP) is stored as an adsorbed phase in fine pores of coal matrix, the nano-pore structure directly influences gas storage and transport properties. Only limited studies have quantified the alteration of the nano-pore structure due to ME-CBM treatment. This study examines the evolution of the pore structure using a combination of small angle X-ray scattering (SAXS), low-pressure N2 and CO2 adsorption (LPGA) and high-pressure methane adsorption methods. The results show that the surface fractal dimension decreases for the two bioconverted coals compared to the untreated coal. After bio-treatment, the mesopore surface area and pore volume decrease with the average pore diameter increases, while the micropore surface area increases with pore volume decreases. Both inaccessible meso-/micropore size distributions decrease after bioconversion, while the accessible micropore size distribution increases, making a portion of closed micropore network accessible. In addition, the methane adsorption capacities increase after bio-treatment, which is confirmed by the increase of micropore surface area. A conceptual physical model of methanogenesis is proposed based on the evolution of the pore structure.

Fine Mapping of Two Additive Effect Genes for Awn Development in Rice (Oryza sativa L.).

Awns, important domestication and agronomic traits in rice (Oryza sativa L.), are conferred by polygenes and the environment. Near isogenic line (NIL) pairs BM33 and BM38 were constructed from crosses between awnless japonica cv Nipponbare as recurrent parent, and lines SLG or Funingxiaohongmang (awned japonica accessions), respectively, as donors. In order to study the genetic and molecular mechanism of awning, two unknown, independent genes with additive effects were identified in a cross between the NILs. To map and clone the two genes, a BC4F4 population of 8,103 individuals and a BC4F6 population of 11,206 individuals were constructed. Awn3-1 was fine mapped to a 101.13 kb genomic region between Indel marker In316 and SNP marker S9-1 on chromosome 3. Nine predicted genes in the interval were annotated in the Rice Annotation Project Database (RAP-DB), and Os03g0418600 was identified as the most likely candidate for Awn3-1 through sequence comparisons and RT-PCR assays. Awn4-2 was fine mapped to a 62.4 kb genomic region flanked by simple sequence repeat (SSR) marker M1126 and Indel maker In73 on chromosome 4L. This region contained the previously reported gene An-1 that regulates awn development. Thus, An-1 may be the candidate gene of Awn4-2. These results will facilitate cloning of the awn genes and thereby provide an understanding of the molecular basis of awn development.

Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes.

Introgression lines (ILs) are valuable materials for identifying quantitative trait loci (QTLs), evaluating genetic interactions, and marker assisted breeding. A set of 430 ILs (BC(5)F(3)) containing segments from upland tropical japonica cultivar IRAT109 in a lowland temperate japonica cultivar Yuefu background were developed. One hundred and seventy-six polymorphic markers were used to identify introgressed segments. No segment from IRAT109 was found in 160 lines. Introgressed segments of the other 270 lines covered 99.1% of the donor genome. The mean number of introgressed donor segments per individual was 3.3 with an average length of 14.4 cM. QTL analysis was conducted on basal root thickness (BRT) of the 270 ILs grown under irrigated lowland, upland and hydroponic conditions. A total of 22 QTLs affecting BRT were identified, six QTLs (qBRT3.1, qBRT3.2, qBRT6.1, qBRT8.2, qBRT9.1, and qBRT9.2) were consistently expressed under at least two environments (location and water regime), and qBRT7.2 was a new BRT QTL identified under lowland conditions. IL255 containing qBRT9.1 showed an increase of 10.09% and 7.07% BRT over cultivar Yuefu when grown under upland and lowland conditions, respectively. Using a population of 304 F(2:3) lines derived from the cross IL255×Yuefu, qBRT9.1 was validated and mapped to a 1.2 cM interval between RM24271 and RM566. The presence of qBRT9.1 explained 12% of BRT variation. The results provide upland rice ILs and BRT QTLs for analyzing the genetic basis of drought resistance, detecting favorable genes from upland rice, and rice drought resistance breeding.