Pub Date : 2022-06-07DOI: 10.1186/s40529-022-00349-6
J. Long, Wang Xing, Yuguang Wang, Zedong Wu, Wenjing Li, Yinbin Zou, Jiaping Sun, Fushun Zhang, Z. Pi
{"title":"Comparative proteomic analysis on chloroplast proteins provides new insights into the effects of low temperature in sugar beet","authors":"J. Long, Wang Xing, Yuguang Wang, Zedong Wu, Wenjing Li, Yinbin Zou, Jiaping Sun, Fushun Zhang, Z. Pi","doi":"10.1186/s40529-022-00349-6","DOIUrl":"https://doi.org/10.1186/s40529-022-00349-6","url":null,"abstract":"","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65691174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nitrogen is an essential macronutrient for plant growth and development. Crops with a high nitrogen input usually have high yields. However, outbreaks of brown planthoppers (Nilaparvata lugens; BPH) frequently occur on rice farms with excessive nitrogen inputs. Rice plants carrying BPH resistance genes are used for integrated pest management. Thus, the impact of nitrogen on the resistance of rice near-isogenic lines (NILs) with BPH resistance genes was investigated. We tested these NILs using a standard seedbox screening test and a modified bulk seedling test under different nitrogen treatments. The amount of nitrogen applied had an impact on the resistance of some lines with BPH resistance genes. In addition, three NILs (NIL-BPH9, NIL-BPH17, and NIL-BPH32) were further examined for antibiosis and antixenosis under varying nitrogen regimes. The N. lugens nymph population growth rate, honeydew excretion, female fecundity, and nymph survival rate on the three NILs were not affected by different nitrogen treatments except the nymph survival rate on NIL-BPH9 and the nymph population growth rate on NIL-BPH17. Furthermore, in the settlement preference test, the preference of N. lugens nymphs for IR24 over NIL-BPH9 or NIL-BPH17 increased under the high-nitrogen regime, whereas the preference of N. lugens nymphs for IR24 over NIL-BPH32 was not affected by the nitrogen treatments. Our results indicated that the resistance of three tested NILs did not respond to different nitrogen regimes and that NIL-BPH17 exerted the most substantial inhibitory effect on N. lugens growth and development.
{"title":"Effect of nitrogen fertilizer on the resistance of rice near-isogenic lines with BPH resistance genes","authors":"Lin, Shau-Ching, Li, Yi, Hu, Fang-Yu, Wang, Chih-Lu, Kuang, Yun-Hung, Sung, Chang-Lin, Tsai, Shin-Fu, Yang, Zhi-Wei, Li, Charng-Pei, Huang, Shou-Horng, Liao, Chung-Ta, Hechanova, Sherry Lou, Jena, Kshirod K., Chuang, Wen-Po","doi":"10.1186/s40529-022-00347-8","DOIUrl":"https://doi.org/10.1186/s40529-022-00347-8","url":null,"abstract":"Nitrogen is an essential macronutrient for plant growth and development. Crops with a high nitrogen input usually have high yields. However, outbreaks of brown planthoppers (Nilaparvata lugens; BPH) frequently occur on rice farms with excessive nitrogen inputs. Rice plants carrying BPH resistance genes are used for integrated pest management. Thus, the impact of nitrogen on the resistance of rice near-isogenic lines (NILs) with BPH resistance genes was investigated. We tested these NILs using a standard seedbox screening test and a modified bulk seedling test under different nitrogen treatments. The amount of nitrogen applied had an impact on the resistance of some lines with BPH resistance genes. In addition, three NILs (NIL-BPH9, NIL-BPH17, and NIL-BPH32) were further examined for antibiosis and antixenosis under varying nitrogen regimes. The N. lugens nymph population growth rate, honeydew excretion, female fecundity, and nymph survival rate on the three NILs were not affected by different nitrogen treatments except the nymph survival rate on NIL-BPH9 and the nymph population growth rate on NIL-BPH17. Furthermore, in the settlement preference test, the preference of N. lugens nymphs for IR24 over NIL-BPH9 or NIL-BPH17 increased under the high-nitrogen regime, whereas the preference of N. lugens nymphs for IR24 over NIL-BPH32 was not affected by the nitrogen treatments. Our results indicated that the resistance of three tested NILs did not respond to different nitrogen regimes and that NIL-BPH17 exerted the most substantial inhibitory effect on N. lugens growth and development.","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138515253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-23DOI: 10.1186/s40529-022-00346-9
Hale, Amanda R., Ruegger, Paul M., Rolshausen, Philippe, Borneman, James, Yang, Jiue-in
Potato taste defect (PTD) of coffee is characterized by a raw potato like smell that leads to a lower quality taste in the brewed coffee, and harms the commercial value of some East African coffees. Although several causes for PTD have been proposed, none of them have been confirmed. Recently, high throughput sequencing techniques and bioinformatic analysis have shown great potential for identifying putative causal agents of plant diseases. Toward the goal of determining the cause of PTD, we examined raw coffee beans from Rwanda exhibiting varying PTD scores using an Illumina-based sequence analysis of the fungal rRNA ITS region. Six fungal amplicon sequence variants (ASVs) with high relative abundances correlated with coffee taste scores. Four of these ASVs exhibited negative correlations – Aspergillus versicolor, Penicillium cinnamopurpureum, Talaromyces radicus, and Thermomyces lanuginosus – indicating that they might be causing PTD. Two of these fungi exhibited positive correlations – Kazachstania humilis and Clavispora lusitaniae – indicating that they might be inhibiting organisms that cause PTD. This study addressed PTD causality from a new angle by examining fungi with high throughput sequencing. To our knowledge, this is the first study characterizing fungi associated with PTD, providing candidates for both causality and biocontrol.
{"title":"Fungi associated with the potato taste defect in coffee beans from Rwanda","authors":"Hale, Amanda R., Ruegger, Paul M., Rolshausen, Philippe, Borneman, James, Yang, Jiue-in","doi":"10.1186/s40529-022-00346-9","DOIUrl":"https://doi.org/10.1186/s40529-022-00346-9","url":null,"abstract":"Potato taste defect (PTD) of coffee is characterized by a raw potato like smell that leads to a lower quality taste in the brewed coffee, and harms the commercial value of some East African coffees. Although several causes for PTD have been proposed, none of them have been confirmed. Recently, high throughput sequencing techniques and bioinformatic analysis have shown great potential for identifying putative causal agents of plant diseases. Toward the goal of determining the cause of PTD, we examined raw coffee beans from Rwanda exhibiting varying PTD scores using an Illumina-based sequence analysis of the fungal rRNA ITS region. Six fungal amplicon sequence variants (ASVs) with high relative abundances correlated with coffee taste scores. Four of these ASVs exhibited negative correlations – Aspergillus versicolor, Penicillium cinnamopurpureum, Talaromyces radicus, and Thermomyces lanuginosus – indicating that they might be causing PTD. Two of these fungi exhibited positive correlations – Kazachstania humilis and Clavispora lusitaniae – indicating that they might be inhibiting organisms that cause PTD. This study addressed PTD causality from a new angle by examining fungi with high throughput sequencing. To our knowledge, this is the first study characterizing fungi associated with PTD, providing candidates for both causality and biocontrol.","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138515241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-19DOI: 10.1186/s40529-022-00345-w
A. Omer, M. S. Osman, Alia A. Badawy
{"title":"Inoculation with Azospirillum brasilense and/or Pseudomonas geniculata reinforces flax (Linum usitatissimum) growth by improving physiological activities under saline soil conditions","authors":"A. Omer, M. S. Osman, Alia A. Badawy","doi":"10.1186/s40529-022-00345-w","DOIUrl":"https://doi.org/10.1186/s40529-022-00345-w","url":null,"abstract":"","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45654676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N-acetylglucosaminidase (NAGase) could liberate N-acetylglucosamine (GlcNAc) from GlcNAc-containing oligosaccharides. Trichoderma spp. is an important source of chitinase, particularly NAGase for industrial use. nag1 and nag2 genes encoding NAGase, are found in the genome in Trichoderma spp. The deduced Nag1 and Nag2 shares ~ 55% homology in Trichoderma virens. Most studies were focus on Nag1 and nag1 previously. The native NAGase (TvmNAG2) was purified to homogeneity with molecular mass of ~ 68 kDa on SDS-PAGE analysis, and identified as Nag2 by MALDI/MS analysis from an isolate T. virens strain mango. RT-PCR analyses revealed that only nag2 gene was expressed in liquid culture of T. virens, while both of nag1 and nag2 were expressed in T. virens cultured on the plates. TvmNAG2 was thermally stable up to 60 °C for 2 h, and the optimal pH and temperature were 5.0 and 60–65 °C, respectively, using p-nitrophenyl-N-acetyl-β-D-glucosaminide (pNP-NAG) as substrate. The hydrolytic product of colloidal chitin by TvmNAG2 was suggested to be GlcNAc based on TLC analyses. Moreover, TvmNAG2 possesses antifungal activity, inhibiting the mycelium growth of Sclerotium rolfsii. And it was resistant to the proteolysis by papain and trypsin. The native Nag2, TvmNAG2 was purified and identified from T. virens strain mango, as well as enzymatic properties. To our knowledge, it is the first report with the properties of native Trichoderma Nag2.
n -乙酰氨基葡萄糖酶(NAGase)能从含GlcNAc的低聚糖中释放n -乙酰氨基葡萄糖(GlcNAc)。木霉是几丁质酶的重要来源，特别是工业用的长酶。在木霉基因组中发现了编码NAGase的nag1和nag2基因，推断出nag1和nag2基因在木霉中同源性约为55%。以往的研究多集中在Nag1和Nag1上。通过SDS-PAGE分析，从芒果T. virens分离株中纯化到同源的天然NAGase (TvmNAG2)，分子量为~ 68 kDa，通过MALDI/MS分析鉴定为Nag2。RT-PCR分析显示，在培养液中，野田鼠只表达nag2基因，而在培养皿中，野田鼠同时表达nag1和nag2基因。以对硝基苯基-n -乙酰基-β- d -氨基葡萄糖(pNP-NAG)为底物，TvmNAG2在60℃下热稳定2 h，最佳pH和温度分别为5.0和60 - 65℃。TLC分析表明，TvmNAG2水解胶体甲壳素的产物为GlcNAc。此外，TvmNAG2具有抗真菌活性，可抑制罗氏菌丝体的生长。对木瓜蛋白酶和胰蛋白酶的蛋白水解具有抗性。从芒果T. virens菌株中纯化鉴定了原生Nag2, TvmNAG2，并对其酶学性质进行了研究。据我们所知，这是第一次报道天然木霉Nag2的性质。
{"title":"Purification, identification and characterization of Nag2 N-acetylglucosaminidase from Trichoderma virens strain mango","authors":"Huang, Jheng-Hua, Zeng, Feng-Jin, Guo, Jhe-Fu, Huang, Jian-Yuan, Lin, Hua-Chian, Lo, Chaur-Tsuen, Chou, Wing-Ming","doi":"10.1186/s40529-022-00344-x","DOIUrl":"https://doi.org/10.1186/s40529-022-00344-x","url":null,"abstract":"N-acetylglucosaminidase (NAGase) could liberate N-acetylglucosamine (GlcNAc) from GlcNAc-containing oligosaccharides. Trichoderma spp. is an important source of chitinase, particularly NAGase for industrial use. nag1 and nag2 genes encoding NAGase, are found in the genome in Trichoderma spp. The deduced Nag1 and Nag2 shares ~ 55% homology in Trichoderma virens. Most studies were focus on Nag1 and nag1 previously. The native NAGase (TvmNAG2) was purified to homogeneity with molecular mass of ~ 68 kDa on SDS-PAGE analysis, and identified as Nag2 by MALDI/MS analysis from an isolate T. virens strain mango. RT-PCR analyses revealed that only nag2 gene was expressed in liquid culture of T. virens, while both of nag1 and nag2 were expressed in T. virens cultured on the plates. TvmNAG2 was thermally stable up to 60 °C for 2 h, and the optimal pH and temperature were 5.0 and 60–65 °C, respectively, using p-nitrophenyl-N-acetyl-β-D-glucosaminide (pNP-NAG) as substrate. The hydrolytic product of colloidal chitin by TvmNAG2 was suggested to be GlcNAc based on TLC analyses. Moreover, TvmNAG2 possesses antifungal activity, inhibiting the mycelium growth of Sclerotium rolfsii. And it was resistant to the proteolysis by papain and trypsin. The native Nag2, TvmNAG2 was purified and identified from T. virens strain mango, as well as enzymatic properties. To our knowledge, it is the first report with the properties of native Trichoderma Nag2.","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138515249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-05-16DOI: 10.1186/s40529-022-00343-y
Sabah Merrium, Zulfiqar Ali, Muhammad Habib-Ur-Rahman, Sadia Hakeem, Muhammad Arslan Khalid
Background: Plants use different mechanisms to transport the collected fog water. Leaf traits of wheat play an important role in directing fog water through leaf rolling and leaf angle into the root zone, where it can be stored for consumption. Wheat leaf traits can enhance fog capturing under drought stress. To examine this, 200 wheat genotypes were characterized for leaf rolling and leaf angle under optimal conditions in the field using a randomized complete block design. Seven different phenotypic combinations for leaf traits were observed. A core set of 44 genotypes was evaluated under drought stress.
Results: Results show that variability for leaf traits existed among genotypes. An association was found between leaf rolling and leaf angle, moisture capturing, physiological parameters, and yield contributing traits using correlation. Physiological parameters, especially water use efficiency, were positively correlated with grain yield and moisture capturing at both growth stages. The genotypes (G11 at tillering and G24 at booting phonological phases) with inward to twisting type rolling and erect to semi-erect leaf angle capture more water (12-20%) within the root zone. Twenty-one genotypes were selected based on moisture capturing efficiency and evaluated for leaf surface wettability. Association was found between fog capturing and wettability. This shows that it was due to the leaf repellency validated from static contact angle measurements.
Conclusion: These results will give insights into fog capturing and the development of drought-tolerant crops in the semi-arid and arid regions.
{"title":"Leaf rolling and leaf angle improve fog capturing and transport in wheat; adaptation for drought stress in an arid climate.","authors":"Sabah Merrium, Zulfiqar Ali, Muhammad Habib-Ur-Rahman, Sadia Hakeem, Muhammad Arslan Khalid","doi":"10.1186/s40529-022-00343-y","DOIUrl":"https://doi.org/10.1186/s40529-022-00343-y","url":null,"abstract":"<p><strong>Background: </strong>Plants use different mechanisms to transport the collected fog water. Leaf traits of wheat play an important role in directing fog water through leaf rolling and leaf angle into the root zone, where it can be stored for consumption. Wheat leaf traits can enhance fog capturing under drought stress. To examine this, 200 wheat genotypes were characterized for leaf rolling and leaf angle under optimal conditions in the field using a randomized complete block design. Seven different phenotypic combinations for leaf traits were observed. A core set of 44 genotypes was evaluated under drought stress.</p><p><strong>Results: </strong>Results show that variability for leaf traits existed among genotypes. An association was found between leaf rolling and leaf angle, moisture capturing, physiological parameters, and yield contributing traits using correlation. Physiological parameters, especially water use efficiency, were positively correlated with grain yield and moisture capturing at both growth stages. The genotypes (G11 at tillering and G24 at booting phonological phases) with inward to twisting type rolling and erect to semi-erect leaf angle capture more water (12-20%) within the root zone. Twenty-one genotypes were selected based on moisture capturing efficiency and evaluated for leaf surface wettability. Association was found between fog capturing and wettability. This shows that it was due to the leaf repellency validated from static contact angle measurements.</p><p><strong>Conclusion: </strong>These results will give insights into fog capturing and the development of drought-tolerant crops in the semi-arid and arid regions.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71478044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The root drugs of the family Apocynaceae are medicinally important and used in Indian Systems of Medicine (ISM). There is often a problem of misidentification and adulteration of genuine samples with other samples in the market trade. Keeping in view the adulteration problem of raw drug material, comparative macroscopic and microscopic (qualitative and quantitative) characterisation and chemical analysis (TLC and LC–MS profiling) of a total of 14 economically important root drugs of family Apocynaceae were done for practical and rapid identification. A total of 33 qualitative botanical characteristics of root samples were subjected to Principal Component Analysis (PCA) and Cluster analysis to identify taxonomically significant characteristics in the distinction of root drug samples at the species level. Comparative qualitative and quantitative data on morphological, macroscopic, and microscopic characters were generated for the studied 14 species. Despite the similarity in some root characters, a combined study involving the surface, anatomical, and powder features helped distinguish root samples at the species level. The relative relationship between selected species was represented as clustering or grouping in the dendrogram. PCA analysis determined significant characters leading to species grouping and identification. Results showed that clustering of xylem vessels in cross-section, pore size, and distribution in the cut root, the shape of starch grains, the thickness of cork zone were among the most notable characters in species distinction. Chemical profiling revealed unique fingerprints and content of chemical compounds, which were significant in identification of root drug samples. The comparative botanical standards and chemical profiles developed in the present study can be used as future reference standards for the quick, easy, and correct identification of root drug samples to be used in the herbal drug industry. Further, the identified significant microscopic characters have the potential for taxonomic studies in species delimitation.
{"title":"Comparative morpho-anatomical standardization and chemical profiling of root drugs for distinction of fourteen species of family Apocynaceae","authors":"Kumar, Pankaj, Bhushan, Anil, Gupta, Prasoon, Gairola, Sumeet","doi":"10.1186/s40529-022-00342-z","DOIUrl":"https://doi.org/10.1186/s40529-022-00342-z","url":null,"abstract":"The root drugs of the family Apocynaceae are medicinally important and used in Indian Systems of Medicine (ISM). There is often a problem of misidentification and adulteration of genuine samples with other samples in the market trade. Keeping in view the adulteration problem of raw drug material, comparative macroscopic and microscopic (qualitative and quantitative) characterisation and chemical analysis (TLC and LC–MS profiling) of a total of 14 economically important root drugs of family Apocynaceae were done for practical and rapid identification. A total of 33 qualitative botanical characteristics of root samples were subjected to Principal Component Analysis (PCA) and Cluster analysis to identify taxonomically significant characteristics in the distinction of root drug samples at the species level. Comparative qualitative and quantitative data on morphological, macroscopic, and microscopic characters were generated for the studied 14 species. Despite the similarity in some root characters, a combined study involving the surface, anatomical, and powder features helped distinguish root samples at the species level. The relative relationship between selected species was represented as clustering or grouping in the dendrogram. PCA analysis determined significant characters leading to species grouping and identification. Results showed that clustering of xylem vessels in cross-section, pore size, and distribution in the cut root, the shape of starch grains, the thickness of cork zone were among the most notable characters in species distinction. Chemical profiling revealed unique fingerprints and content of chemical compounds, which were significant in identification of root drug samples. The comparative botanical standards and chemical profiles developed in the present study can be used as future reference standards for the quick, easy, and correct identification of root drug samples to be used in the herbal drug industry. Further, the identified significant microscopic characters have the potential for taxonomic studies in species delimitation.","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138515242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-04-06DOI: 10.1186/s40529-022-00341-0
Erick Gutiérrez, I. Trejo
{"title":"Tree and shrub recruitment under environmental disturbances in temperate forests in the south of Mexico","authors":"Erick Gutiérrez, I. Trejo","doi":"10.1186/s40529-022-00341-0","DOIUrl":"https://doi.org/10.1186/s40529-022-00341-0","url":null,"abstract":"","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65691125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-04-01DOI: 10.1186/s40529-022-00340-1
N. Pradhan, Xuli Fan, Francesco Martini, Huayang Chen, Hong Liu, Jiangyun Gao, U. Goodale
{"title":"Correction to: Seed viability testing for research and conservation of epiphytic and terrestrial orchids","authors":"N. Pradhan, Xuli Fan, Francesco Martini, Huayang Chen, Hong Liu, Jiangyun Gao, U. Goodale","doi":"10.1186/s40529-022-00340-1","DOIUrl":"https://doi.org/10.1186/s40529-022-00340-1","url":null,"abstract":"","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65691099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1’s blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
{"title":"Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution","authors":"Panibe, Jerome P., Wang, Long, Lee, Yi-Chen, Wang, Chang-Sheng, Li, Wen-Hsiung","doi":"10.1186/s40529-022-00336-x","DOIUrl":"https://doi.org/10.1186/s40529-022-00336-x","url":null,"abstract":"Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1’s blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138519693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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