The Yield and Diseases-Pest Performance of Breeding Materials for Tomatoes (Lycopersicon esculentum) Sourced from Different Exotic Sources

A study was conducted with 36 tomato germplasm [PGRC (19), The Netherlands (7), Japan (2), and Bangladesh (9)] with 3 check varieties in the research field of the Olericulture Division of Horticulture Research Centre (HRC), Bangladesh Agricultural Research Institute (BARI), Gazipur during the winter season of 2022-23 to identify promising tomato breeding germplasm. All the germplasm showed differences in most of the parameters studied. Considerable variation was observed for fruit yield per hectare varied from 39 to 144 tons, while the highest fruit yield per hectare was harvested from the germplasm viz., BD 7759B, BD 7757, BD 7751, BD 7301, QM, BD 7759A, BD 7762, QF, BD 7753, BD 8886, BD 10351, NL-1A, SLA-19. The number of locules, total soluble solids (TSS) and plant height at last harvest varied from 2 to 6.6, 2.6 to 5.9%, and 66 to 154cm, respectively. The TYLCV infection (%) and leaf-sucking pest infestation (%) were observed with a 1 to 20% range in the field condition in both cases. So, we can select that germplasm has zero per cent infestation. Considering the plant growth habit, earliness, different yield contributing horticultural traits, virus and pest infestation thirteen germplasm viz., BD 7759B, BD 7757, BD 7751, BD 7301, QM, BD 7759A, BD 7762, QF, BD 7753, BD 8886, BD 10351, NL-1A, SLA-19 were selected as breeding materials for further tomato improvement program.

Evaluation of UAV-derived multimodal remote sensing data for biomass prediction and drought tolerance assessment in bioenergy sorghum

Screening for drought tolerance is critical to ensure high biomass production of bioenergy sorghum in arid or semi-arid environments. The bottleneck in drought tolerance selection is the challenge of accurately predicting biomass for a large number of genotypes. Although biomass prediction by lowaltitude remote sensing has been widely investigated on various crops, the performance of the predictions are not consistent, especially when applied in a breeding context with hundreds of genotypes. In some cases, biomass prediction of a large group of genotypes benefited from multimodal remote sensing data;while in other cases, the benefits were not obvious. In this study, we evaluated the performance of single and multimodal data(thermal, RGB, and multispectral) derived from an unmanned aerial vehicle(UAV) for biomass prediction for drought tolerance assessments within a context of bioenergy sorghum breeding. The biomass of 360 sorghum genotypes grown under well-watered and water-stressed regimes was predicted with a series of UAV-derived canopy features, including canopy structure, spectral reflectance, and thermal radiation features. Biomass predictions using canopy features derived from the multimodal data showed comparable performance with the best results obtained with the single modal data with coefficients of determination(R2) ranging from 0.40 to 0.53 under water-stressed environment and0.11 to 0.35 under well-watered environment. The significance in biomass prediction was highest with multispectral followed by RGB and lowest with the thermal sensor. Finally, two well-recognized yieldbased drought tolerance indices were calculated from ground truth biomass data and UAV predicted biomass, respectively. Results showed that the geometric mean productivity index outperformed the yield stability index in terms of the potential for reliable predictions by the remotely sensed data.Collectively, this study demonstrated a promising strategy for the use of different UAV-based imaging sensors to quantify yield-based drought tolerance.

Mining and validation of novel genotyping-bysequencing(GBS)-based simple sequence repeats(SSRs)and their application for the estimation of the genetic diversity and population structure of coconuts(Cocos nucifera L.)in Thailand

Coconut(Cocos nucifera L.)is an important economic crop in tropical countries.However,the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut.Here,we present the results of simple sequence repeat(SSR)mining from a high-throughput genotyping-bysequencing(GBS)study of a collection of 38 coconut accessions.A total of 22,748 SSRs with di-,tri-,tetra-,penta-and hexanucleotide repeats of five or more were identified,2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions,and 315 loci were suitable for the development of SSR markers.One hundred loci were selected,and primer pairs for each SSR locus were designed and validated in 40 coconut accessions.The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus,with an average of 3.01 alleles.The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure,principal coordinate analysis(PCoA),and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand.The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding.The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.

Insect and Diseases Resistance in Tomato Entries

The study was conducted with 75 tomato entries at the farm of Olericulture Division, Horticulture Research Centre (HRC), Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh during the winter season of 2020-21 to evaluate insect and disease reaction. Among the various insect and diseases of tomatoes, the late blight, TYLCV, bacterial wilt infection and leaf miner, fruit borer infestation are most common in Bangladesh. The TYLCV infection was observed 0% to 27% infection, while 47 entries showed zero percent infection. The range of bacterial wilt infection was 0% to 10% and zero percent infection was observed in 62 entries. In case of leaf miner infestation and fruit borer infestation, the range was 0% to 43% and 0% to 10%, respectively. Considering tolerance to late blight, TYLCV, bacterial wilt infection and leaf miner, fruit borer infestation, fruit size, fruit shape, plant growth nature, cluster nature of fruit, type of fruit ten entries AVTO 1010, AVTO 1706, AVTO 1713, AVTO 1829, AVTO 1909, AVTO 1911, AVTO 1915, AVTO 1921, AVTO 1954 and SLA 011 were found zero percent late blight, TYLCV, bacterial wilt infection and leaf miner, fruit borer infestation. So, these ten entries can be selected for disease and insect tolerant tomato varieties development as well as developing disease and insect tolerant hybrid tomato varieties.

Establishment and Growth of Potato Micro-Cuttings in Sand Trays

Two separate experiments were conducted to evaluate the success of the establishment and growth of micro-cuttings of potato (5 - 6 cm tall) in sand trays [38 cm (L) × 28 cm (W) × 7.5 cm (H) plastic trays] under controlled environment (22?C ± 2?C, 60 - 75 μmosm–1?s–1 light energy for 16 h daily). In the first experiment, micro-cuttings of potato cv. Diamant were planted at six populations (500, 600, 700, 800, 900 and 1000 cuttings per tray) in treated sand (sun dry, 1% formaldehyde, 0.2% Dithane M-45 and control). The mortality percentage of micro-cuttings was nil for sun dry sand while formaldehyde and dithane M-45 treated sand had 1% - 4% against 15% in the control with the highest population density. Mortality of micro-cuttings in formaldehyde and dithane M-45 treated sand trays were found not to be related to pathogenic organism rather toxic effect of these two chemicals. Micro-cuttings in Sun dry and control treatments showed better growth performance than these in chemically treated sand trays. In the second experiment, urea @ 1, 2 and 3 g per tray was applied as solid form after 15 days of planting the micro-cuttings and as liquid form @ 0.5, 1 and 2% solution sprayed in the micro-cuttings repeatedly after 15, 30, 45 and 60 days of planting. The micro-cuttings which received urea as solid state died within 2 - 3 days and 2% urea solution was also detrimental. Urea solution @ 0.5% found to be very effective for vegetative growth of micro-cuttings in sand trays. The control was also good for vegetative growth but at a slower rate.

Effect of Maturity Indices on Growth and Quality of High Value Vegetables

The study took place at Bangladesh Agricultural Research Institute’s Olericulture Division’s research farm from March 2021 to February 2022 (BARI). In a protected net house, we investigated the impact of five different types of vegetables on various maturation stages, including tomato, broccoli, sweet pepper, cucumber, and netted melon. Vegetables cultivated under protected conditions in a transparent poly-film net house can improve quality, maturity, fruit size, and yield. When fruits and vegetables are picked before they are fully mature, they may stay green for longer, but they may not ripen to a satisfactory color and flavor, resulting in a loss of consumer confidence. Furthermore, because fruit continues to grow until the harvest, immature fruit will be smaller than mature fruit, reducing harvest yield. We tried to determine the right maturation stages in order to avoid product loss during our investigation. The tomato was found to be an appropriate size (6.5 cm length and 6.2 cm diameter), weight (84 g), TSS (4.5 percent), pH (4.3), “turning red”, and “tasty” at the week 5 stage, while the broccoli was found to be an appropriate size (12.0 cm length and 13.0 cm diameter), weight (360 g), and “green” color at the week 5 stage. At the week 6 stage, the nettled melon was found to be of appropriate size (15.2 cm length and 14.5 cm diameter), weight (800 g), TSS (10.8 percent), pH (6.3), “net fully developed” on the fruit skin and “much tasty,” while cucumber was found to be of appropriate size (8.8 - 10.8 cm length and 2.2 - 2.9 cm diameter), weight (61 - 88 g), TSS (3.8 - 4.1 percent), pH (6.3), “less powdery”. As a result, establishing the optimal maturity of our research will benefit both consumers and growers.

Overcoming seasonality in the tropics by growing tomato (<i>Lycopersicon esculentum Mill.</i>) varieties under cooled conditions

The main objective of this work was to overcome seasonality in tomato production under hot tropical summer conditions, as well as to evaluate the adaptability and productivity of cherry and normal size indeterminate tomato varieties. The tested varieties were the standard varieties, Chanoa, Merel, Sensie and Yusra and the cherry varieties, Tomi and Elitrro. The cherry variety Elitrro recorded the highest plant height followed by the normal Merel. The cherry varieties over-numbered the classic varieties for mean number of fruits per cluster and mean number of fruits per meter square. There was no significant difference between the best yielders, the classic varieties Chanoa (25.63 kg/m2) and Yusra (24.13 kg/m2) and the cherry variety Elitrro (24.00 kg/m2). Yusra recorded the highest fruit diameter (60-70 mm). The classic type tomatoes are well known and of high demand in Sudan that give Chanoa and Yusra better adoption chances. Our results clearly indicated that production of summer tomato under cooled plastic house conditions is a new technique that has the potential to overcome the seasonality of tomato production under Sudan and similar tropical condition.

Yield and Yield Contributing Performance of 75 Tomato Germplasm in Bangladesh

The study was conducted with 75 tomato germplasm/lines at the farm of Olericulture Division, Horticulture Research Centre (HRC), Bangladesh Agricultural Research Institute, Gazipur, Bangladesh during the winter season of 2020-21 to evaluate the WorldVeg tomato germplasm. The days to first harvest were varied from 106 to 116 days while twelve lines were harvested within 106 - 108 days. The number of fruits per plant varied from 11.7 to 71.3, while the range of single fruit weight was 16.4 - 186.6 g. Fruit yield per hectare was 15.7 - 150.4 t/ha where the highest fruit yield per hectare was obtained from the lines AVTO 1702 (150.40 t/ha), followed by AVTO 1409 (126.54 t/ha), AVTO 1010 (120.60 t/ha), AVTO 1712 (111.33 t/ha), AVTO 1711 (107.23 t/ha). The range of fruit length was observed 2.07 to 6.8 cm, while the fruit diameter was 1.9 to 7.4 cm. The range of pericarp thickness was 0.14 to 0.8 cm, while the range of number of locule was 2.0 to 8.2. The range of TSS level was 2.0% - 8.2%, while the shelf life of the tomato lines was recorded 5.2 to 10.3 days. Considering earliness, quantitative and qualitative characters, eleven WorldVeg Center tomato lines AVTO 1010, AVTO 1315, AVTO 1409, AVTO 1711, AVTO 1712, AVTO 1713, AVTO 1717, AVTO 1907, AVTO 1911, AVTO 1915 and AVTO 1921 were found promising. So, these eleven lines can be selected for further confirmation.

Effect of Different Nethouses on the Incidence of Insect on Vegetable Crops

In this study, the effects of different types of nethouses viz., NH1, NH2, and NH3, were investigated at the research farm of the Olericulture Division, Bangladesh Agricultural Research Institute (BARI) from Sep 2021 to Mar 2022 and compared to control (open field) in terms of the incidence of white fly, aphid, leaf miners, mites, and eggplant shoot and fruit borer (ESFB). This study included six vegetables 1) Tomato, 2) Eggplant, 3) Sweet pepper, 4) Broccoli, 5) Cucumber;6) Okra, as well as four nethouse treatments: 1) UV stabilized transparent polyethylene film with 60 mesh insect net along with green shade net (NH1);2) UV stabilized transparent polyethylene film with 60 mesh insect net (NH2);3) 60 mesh insect net (NH3);4) Open field infestation of white fly, aphid, leaf miners, mites, and ESFB was observed under open field conditions followed by NH1 conditions, while the lower infestation was observed in NH2 and NH3 for all vegetables. From the study, we found the use of stabilized transparent polyethylene film with a 60 mesh insect nethouse provided a negative effect on the presence of different types of notorious insects on vegetables. So, this type of protected nethouse will provide a new dimension to producing safe and quality vegetables in Bangladesh.

The Phytochemical and Antioxidant Characteristics of Fermented Jackfruit （Artocarpus heterophyllus L.） Leaves Using Single and Mixed Starter Culture

The phytochemical and antioxidant properties of fermented jackfruit leaves, using yeast and acetic acid bacteria, individually or in combination during 6 days of fermentation were investigated in the present study. Changes in pH, total reducing sugar, ethanol, acetic acid, total phenolics and flavanoids content were examined. A number of antioxidant activities such as ferric reducing antioxidant power （FRAP） and DPPH free radical scavenging activities were comparatively tested to determine the differences in the respective properties during the fermentation process. Results obtained demonstrated that there were differences in the phytochemical and antioxidant properties of fermented jackfruit leaves, depending on the fermentation starters. Fermented leaves using acetic acid bacteria alone, exhibited higher total reducing sugar （6.89 mg glucose/mL） compared to others. The ferric-reducing activities of fermented jackfruit leaves showed an increasing trend in the yeast fermentation process （5.96-10.12 mg ascorbic acid equivalent/mL）. Generally, all extracts of fermented jackfruit leaves exhibited stronger DPPH radical scavenging activity except in the total phenolics and flavonoids content, whereby it showed a decrease trend throughout the fermentation process.

Environmentally Induced Under-Development of Seeds in Garden Pea and Its Underlying Factors

Under-development of pea (Pisum sativum L.) seeds in normally developed pods, resulting in “unfilled pods”, has been a serious problem in the greenhouse cultivation in Wakayama Prefecture, one of the major regions of pea cultivation in Japan. This phenomenon appears to be induced by low temperature and low solar irradiation during pea growing season. This study examined the relationship between this seed under-development and sucrose-to-starch metabolism in developing seeds and pods after flowering. The starch content, ADP-glucose pyrophosphorylase (AGPase) and sucrose synthase activities of a pea cultivar, Kishuusui, were monitored through seed development in shading-treatment plot and in control plot. Results showed that the present treatment induced the depression of starch accumulation and AGPase activity in developing seeds compared with control, which might cause the occurrence of under-development of seeds and unfilled pods. Surplus carbohydrates from source organs might be stored in pod walls, as expected from higher starch level and AGPase activity in treated pod walls. The necessity of thermostable AGPase variants in pea to prevent the unfilled-pod problem was discussed.

Yield and Pest Performance of High-Temperature Tolerant Tomato (Lycopersicon esculentum) Lines for Year-Round Tomato Production in Bangladesh

The study was conducted at Olericulture Division, Bangladesh Agricultural Research Institute, Gazipur, Bangladesh during summer season of 2021 to see the performances of yield and yield-related components of twelve heat tolerant tomato hybrids. Significant variation was expressed for days to first harvest (101.0 - 108.0 days), while maximum number of fruits per plant was calculated in F1 2101 and F1 2201 (9.5), followed by F1 203, F1 2001, F1 2303, F1 2401 (9.0). The highest single fruit weight was estimated in F1 2501 (195.5 g), followed by F1 2101 (119.0 g), F1 2201 (113.8 g), while the range was 33.1 - 195.5 g. The range of fruit yield was 7.9 - 38.7 t/ha, while higher-yielding hybrids were viz., F1 203 (27.7 t/ha), F1 2101 (35.5 t/ha), F1 2201 (33.9 t/ha) and F1 2501 (28.7 t/ha). Maximum TSS was produced by F1 2501 (5.9%), followed by BARI Hybrid Tomato-8 (5.1%), F1 1101, F1 1903 (5.0%), with a range of 4.0% - 5.9%, while TYLCV infection and leaf sucking pest infestation varied from 0.0% - 10.0% and 3.3% - 16.7%, respectively. Thus, based on the performances of different yield and yield contributing traits, the hybrids, viz., F1 2101, F1 2201, F1 2501 may be selected to develop heat tolerant tomato hybrid varieties for the farmers of sub-tropical regions.

Isolation and Characterization of Beneficial Microorganisms in Organic, Semi-Organic and Conventional Fertilizer Treated Agricultural Field Soil and Comparison of Bacterial Richness

The effect of different farming systems on microbial communities in agricultural environment was investigated in the present study. Depending on the present farming trend, the microbial distribution in agricultural soils treated with organic, semi-organic and conventional fertilizers was analyzed. A total of 20 soil samples were collected from different types of agricultural fields of Bangladesh Agricultural Research Institute (BARI, Gazipur). Microorganisms playing beneficial roles in soil such as nitrogen fixation (e.g. Rhizobium sp., Azotobacter sp.), phosphate solubilization (e.g. Bacillus sp., Pseudomonas sp., Phosphobacteria) and auxin production (e.g. Pseudomonas sp., Serratia sp. and Bacillus sp.) were evaluated from each of the samples. The results revealed that agricultural fields treated with chemical fertilizers showed lower microbial count than that of organic fertilizer treated agricultural fields’ soil samples. In addition, organic fertilizers amended field soils have higher phytohormone (Auxin) activities, phosphate solubilization bacteria and other bacterial richness compared to chemical fertilizer applied field soil.

Isolation of Six Phosphate Dissolving Rhizosphere Bacteria （Bacillus subtilis） and Their Effects on the Growth, Phosphorus Nutrition and Yield of Maize （Zea mays L.） in Mali

The disadvantages of the long term application of Tilemsi natural phosphate （TNP） on maize （Zea mays L.） production has come out because of its low P availability. Some functional soil microbes, such as phosphate dissolving bacteria, have great potential in improvement of P solubility from TNP and P uptake by plants. The present study aimed to isolate and characterize typical phosphate dissolving bacterial strains （Bacillus subtilis） from Malian soils, and investigate their role in P uptake by maize grown in soils amended with TNP. The experimental design was a split plot with three main plots of fertilizers sources, i.e., natural phosphate, commercial fertilizer and without fertilizer, and with seven sub-plots of six microorganisms plus the control. The field experiment results have shown that the maize inoculated with the phosphate dissolving bacteria was improved in seed germination, plant growth, plant production （increase yield by 42%）, grain and aerial dry biomass （P） content of 34% and 64%, respectively. They have also shown that the locally available TNP can be used by the Malians farmers in maize culture and have comparable production to the one obtained with the costly imported commercial phosphate fertilizer, like the complex cereal. The project has provided information for the combined use of the Mali TNP and phosphate dissolving bacteria Bacillus subtilis subsp, subtilis （T）： DSM 10 in improvement of maize production in the country.

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the singlecell level

Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

STAG-CNS： An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species

One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences （CNSs） based on alignment have had relatively large minimum sequence lengths （≥15 bp） compared with the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS that can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed. Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ≤0.05. These CNSs exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNSs show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.

Ecophysiological responses of two closely related Magnoliaceae genera to seasonal changes in subtropical China

Aims Plants use a variety of hydraulic strategies to adapt to seasonal drought that differ by species and environmental conditions.The early-diverging Magnoliaceae family includes two closely related genera with contrasting leaf habits,Yulania(deciduous)and Michelia(evergreen),which naturally inhabit temperate and tropi-cal regions,respectively.Here,we evaluate the hydraulic strategy of species from both genera that have been ex situ conserved in a subtropical region to determine how they respond to the novel cool-dry season climatic pattern.Methods We measured ecophysiological traits in five Michelia and five Yulania species conserved in the South China Botanical Garden in both wet and dry season conditions and monitored the whole-year sap flow for four of these species.Important Findings We found that Magnoliaceae species that have been ex situ con-served in a subtropical climate did not suffer from excessive water stress due to the mild drought conditions of the dry season and the ecophysiological adjustments the species made to avoid this stress,which differed by leaf habit.Specifically,deciduous species com-pletely shed their leaves during the dry season,while evergreen species decreased their turgor loss points,dry mass based photo-synthetic rates,stomatal conductance and specific leaf areas(SLAs)compared to wet season measurements.In comparing the two dis-tinct leaf habits during the wet season,the leathery-leaved evergreen species had higher leaf hydraulic conductance and leaf to sapwood area ratios than the papery-leaved deciduous species,while the deciduous species had greater hydraulic conductivity calculated on both a stem and leaf area basis,dry mass based photosynthetic rates,leaf nutrients,SLAs and stomatal sizes than the evergreen species.Interestingly,species from both genera maintained similar sap flow in the wet season.Both photosynthetically active radia-tion and vapour pressure deficit affected the diurnal patterns of sap flow in the wet season,while only vapour pressure deficit played a dominant role in the dry season.This study reveals contrasting hydraulic strategies in Yulania and Michelia species under subtropi-cal seasonal conditions,and suggests that these ecophysiological adjustments might be affected more by leaf habit than seasonality,thus reflecting the divergent evolution of the two closely related genera.Furthermore,we show that Magnoliaceae species that are ex situ conserved in a subtropical climate are hydraulically sound,a finding that will inform future conservation efforts of this ancient family under the threat of climatic change.

Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia.This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria,as well as the initiation of nodule primordia from root cortical,endodermal,and pericycle cells,leading to the development of a new root organ,the nodule,where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant.Here,we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq(sNucRNA-seq)profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots.A gene expression map of the Medicago root was generated,comprising 25 clusters,which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes.A focus on root hair,cortex,endodermis,and pericycle cell types,showing the strongest differential regulation in response to a short-term(48 h)rhizobium inoculation,revealed not only known genes and functional pathways,validating the sNucRNA-seq approach,but also numerous novel genes and pathways,allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.

An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.

Analysis of solar radiation changes in Chinese solar greenhouses with different roof structures based on a solar radiation model

Chinese solar greenhouses(CSGs)are important agricultural production facilities.Under non-artificial heating conditions,solar radiation is the only CSGs energy source.It is highly important to optimally obtain solar energy in greenhouse construction and production.In this study,a solar radiation model for solar greenhouses was adopted to explore the quantities of solar radiation in greenhouses considering different front roof forms and angles.Herein,the solar radiation amounts corresponding to five roof forms,namely,double-section arc,parabolic,oval,arc,and linear roofs,are compared and analyzed during the four solar periods(beginning of spring,vernal equinox,beginning of winter,and winter solstice).It was found that the solar radiation of oval roof greenhouses on the ground was the largest and was 4.44%-23.68%higher than that of parabolic roofs.In addition,the cumulative sum of light on the linear roof greenhouse wall is also the largest and was 6.02%to 12.08%higher than the parabolic roof greenhouse in the four solar terms.Moreover,the solar radiation in CSGs was compared with front roof angles of 25°,30°,and 35°.It was observed that the solar radiation amount gradually increases with increasing angles.Notably,the variation at an angle of 35°influences the solar radiation of the paraboloidal CSGs ground and elliptical CSGs north wall to the greatest extent,which increased by 8.23%and 12.74%,respectively.This study confirms the role of front roof form and inclination angle in enhancing the greenhouse solar radiation level.