Pub Date : 2021-01-01DOI: 10.5376/MPB.2021.12.0002
Yang Xiujuan, Xin-Rong He, Yunxia Zhao, Jing-Hao Gao, Wang Xuemei
Chinese sesame state field trial began in 1983. Since then, 44 varieties have been recommended or approved by state sesame certification committee. Most of the listed varieties have been widely utilized in agricultural production. In this review, we summarize the main achievements in the past 40 years and point out existing problems in sesame regional field test after a brief retrospection in China. The advancement of sesame breeding was also summarized and highlighted by the performance of some representative new sesame varieties recommended by the national field trial. Then, the problems in sesame breeding and state field trial were discussed. Finally, we provided some suggestions for the sesame breeding and state field trial that may be of interest of the sesame community in future.
{"title":"Progress and Perspective on Chinese State Field Trials for Sesame New Varieties in the Past 40 Years","authors":"Yang Xiujuan, Xin-Rong He, Yunxia Zhao, Jing-Hao Gao, Wang Xuemei","doi":"10.5376/MPB.2021.12.0002","DOIUrl":"https://doi.org/10.5376/MPB.2021.12.0002","url":null,"abstract":"Chinese sesame state field trial began in 1983. Since then, 44 varieties have been recommended or approved by state sesame certification committee. Most of the listed varieties have been widely utilized in agricultural production. In this review, we summarize the main achievements in the past 40 years and point out existing problems in sesame regional field test after a brief retrospection in China. The advancement of sesame breeding was also summarized and highlighted by the performance of some representative new sesame varieties recommended by the national field trial. Then, the problems in sesame breeding and state field trial were discussed. Finally, we provided some suggestions for the sesame breeding and state field trial that may be of interest of the sesame community in future.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87229548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-01DOI: 10.5376/mpb.2021.12.0030
M. Tan, Yuxin Shi, Haisu Zheng, L. Shao, Peimin He
{"title":"Development of Polymorphic SSR Markers in Vallisneria Based on RAD seq","authors":"M. Tan, Yuxin Shi, Haisu Zheng, L. Shao, Peimin He","doi":"10.5376/mpb.2021.12.0030","DOIUrl":"https://doi.org/10.5376/mpb.2021.12.0030","url":null,"abstract":"","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90489077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pitaya is a burgeoningly tropical fruit, there are two common varieties, red peel with red pulp and red peel with white pulp. To investigate the reason of different colors in two kinds of pitaya, explore differencially expressed genes (DEGs), in this study, we profiled transcriptome in flesh of two varieties (Hylocereu polyrhizus and Hylocereu undatus) in green stage and mature stage respectively. 53 240 reads with high quality were obtained. Analysing the DEGs, we found there were bigger differences in different stage rather than different variety. Gene ontology (GO) functional analysis and KEGG pathway analysis were adopted in R1 VS R3 and W3 VS W3. Through GO analysis, we found many genes enriched in protein binding transcription factor activity in molecule founction. Through KEGG pathway analysis, we found most genes were enriched in biosynthesis of secondary metabolism, amino acid and nucleic acid metabolism, and tyrosine metabolism. In addintion, tyrosine was the precursor of betalaines. In conclusion, the development of Hylocereu polyrhizus accompanying by the synthesis of a large amount of betalaines, tyrosine played a key role as a precursor, and the synthesis of this pigment required a mass of amino acids, enzymes, and transcription factors. Betalaines synthesis pathway has not cleared yet, this study explored key genes related to betalaines synthesis and provided useful information for optimizing the betalaines synthesis pathway, which was the basis of later experiments.
火龙果是一种新兴的热带水果，有两种常见的品种，红皮带红果肉和红皮带白果肉。为了探究两种火龙果颜色不同的原因，探讨差异表达基因(DEGs)，本研究分别对两种火龙果(Hylocereu polyrhizus和Hylocereu undatus)在青期和成熟期果肉的转录组进行了分析。获得53240条高质量reads。结果表明，不同生育期的差异大于品种间的差异。在R1 VS R3和W3 VS W3中采用基因本体(GO)功能分析和KEGG通路分析。通过氧化石墨烯分析，我们在分子功能上发现了许多富含蛋白结合转录因子活性的基因。通过KEGG通路分析，我们发现大多数基因富集于次生代谢、氨基酸和核酸代谢、酪氨酸代谢的生物合成中。此外，酪氨酸是甜菜碱的前体。综上所述，多根水合木的发育伴随大量甜菜碱和酪氨酸的合成，而酪氨酸的合成需要大量的氨基酸、酶和转录因子。甜菜碱的合成途径尚未明确，本研究探索了甜菜碱合成的关键基因，为优化甜菜碱的合成途径提供了有用的信息，为后续的实验奠定了基础。
{"title":"Differential Expression Analysis of Genes Related to Flesh Color in Hylocereu polyrhizus and Hylocereu undatus","authors":"Pan-Yang Guo, Hua Tang, Chengli Liu, Shuang-shuang Wei, Jiaquan Huang","doi":"10.5376/MPB.2021.12.0006","DOIUrl":"https://doi.org/10.5376/MPB.2021.12.0006","url":null,"abstract":"Pitaya is a burgeoningly tropical fruit, there are two common varieties, red peel with red pulp and red peel with white pulp. To investigate the reason of different colors in two kinds of pitaya, explore differencially expressed genes (DEGs), in this study, we profiled transcriptome in flesh of two varieties (Hylocereu polyrhizus and Hylocereu undatus) in green stage and mature stage respectively. 53 240 reads with high quality were obtained. Analysing the DEGs, we found there were bigger differences in different stage rather than different variety. Gene ontology (GO) functional analysis and KEGG pathway analysis were adopted in R1 VS R3 and W3 VS W3. Through GO analysis, we found many genes enriched in protein binding transcription factor activity in molecule founction. Through KEGG pathway analysis, we found most genes were enriched in biosynthesis of secondary metabolism, amino acid and nucleic acid metabolism, and tyrosine metabolism. In addintion, tyrosine was the precursor of betalaines. In conclusion, the development of Hylocereu polyrhizus accompanying by the synthesis of a large amount of betalaines, tyrosine played a key role as a precursor, and the synthesis of this pigment required a mass of amino acids, enzymes, and transcription factors. Betalaines synthesis pathway has not cleared yet, this study explored key genes related to betalaines synthesis and provided useful information for optimizing the betalaines synthesis pathway, which was the basis of later experiments.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90981934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-01DOI: 10.5376/MPB.2021.12.0018
D. He, Weiping Zhang, Wei Lin, Jiale Chen, Peng He, Dawei Zhang, M. Yan
Anthocyanins are important substances accounting for the leaf color in Brassica juncea and PAP1 gene is one of the key transport factors in the anthocyanin synthesis pathway. In this study, homologous cloning technology was used to clone the PAP1 gene sequences of Brassica juncea with different leaf colors. Specific primers were designed according to the gene sequences of Brassica rapa with high homology for PCR amplification. The PAP1 gene of Brassica juncea is 1 348 bp~1 669 bp long, and the coding region sequence is 744 bp~753 bp, including 3 exons and 2 introns. Two MYB blinding domains are found in PAP1 protein at the site of 9~59 and 62~110 amino acids. Phylogenetic analysis showed that the PAP1 gene of Brassica juncea had high homology with the related genes of Brassica rapa and Brassica rapa subsp. rapa, but had low homology with Arabidopsis thaliana. Compared gene sequences in Brassica juncea with different leaf colors, there are no differences between the coding sequence of purple and red leaf Brassica juncea, but the encoded protein have 22 amino acid differences from green leaves. We also observed the lower expression level of PAP1 and its related target genes such as DFR, TT19 in green leaves, which may lead to the differences of leaf color in Brassica juncea. This study provides a reference for exploring the function of PAP1 gene and the formation mechanism of different leaf color of Brassica juncea.
{"title":"Cloning and Expression Analysis of PAP1 in Brassica juncea","authors":"D. He, Weiping Zhang, Wei Lin, Jiale Chen, Peng He, Dawei Zhang, M. Yan","doi":"10.5376/MPB.2021.12.0018","DOIUrl":"https://doi.org/10.5376/MPB.2021.12.0018","url":null,"abstract":"Anthocyanins are important substances accounting for the leaf color in Brassica juncea and PAP1 gene is one of the key transport factors in the anthocyanin synthesis pathway. In this study, homologous cloning technology was used to clone the PAP1 gene sequences of Brassica juncea with different leaf colors. Specific primers were designed according to the gene sequences of Brassica rapa with high homology for PCR amplification. The PAP1 gene of Brassica juncea is 1 348 bp~1 669 bp long, and the coding region sequence is 744 bp~753 bp, including 3 exons and 2 introns. Two MYB blinding domains are found in PAP1 protein at the site of 9~59 and 62~110 amino acids. Phylogenetic analysis showed that the PAP1 gene of Brassica juncea had high homology with the related genes of Brassica rapa and Brassica rapa subsp. rapa, but had low homology with Arabidopsis thaliana. Compared gene sequences in Brassica juncea with different leaf colors, there are no differences between the coding sequence of purple and red leaf Brassica juncea, but the encoded protein have 22 amino acid differences from green leaves. We also observed the lower expression level of PAP1 and its related target genes such as DFR, TT19 in green leaves, which may lead to the differences of leaf color in Brassica juncea. This study provides a reference for exploring the function of PAP1 gene and the formation mechanism of different leaf color of Brassica juncea.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87616170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-31DOI: 10.5376/MPB.2020.11.0030
Yongfeng Lou, X. Song, Huayu Sun, Z. Gao
To explore the role of Growth regulating-factor (GRF) in the growth of bamboo shoots, one GRF gene was isolated from moso bamboo ( Phyllostachys edulis ) by RT-PCR. Bioinformatics methods were used for gene sequence analysis, and the expression pattern of the GRF gene in bamboo shoots at different development stages was analyzed by qRT-PCR. Simultaneously, ectopic expression in Arabidopsis was conducted to validate the gene function. The result showed that the isolated gene from moso bamboo was 1 164 bp, encoding 387 amino acids, which was named as PeGRF1 . Protein sequence analysis showed that PeGRF1 had the complete typical domains (WRC and QLQ) of GRF family. The phylogenetic analysis demonstrated that PeGRF1 were clustered closer to the GRFs of monocotyledonous plants such as Oryza sativa , indicating they had close relationship. PeGRF1 expressed predominantly in young bamboo shoots. Meanwhile, the expression level of PeGRF1 was significantly higher during rapid growth stage than that during slow growth stage of bamboo shoots, and the expression level of PeGRF1 in the upper and middle of bamboo shoots was significantly higher than that in the base. Overexpression of PeGRF1 could increase the plant height of transgenic Arabidopsis . Taken together, our results demonstrated that PeGRF1 was involved in development of bamboo shoots, which provided references for elucidating the biological functions of GRF genes in bamboo.
{"title":"Cloning and Primary Functional Analysis of PeGRF1 in Phyllostachys edulis","authors":"Yongfeng Lou, X. Song, Huayu Sun, Z. Gao","doi":"10.5376/MPB.2020.11.0030","DOIUrl":"https://doi.org/10.5376/MPB.2020.11.0030","url":null,"abstract":"To explore the role of Growth regulating-factor (GRF) in the growth of bamboo shoots, one GRF gene was isolated from moso bamboo ( Phyllostachys edulis ) by RT-PCR. Bioinformatics methods were used for gene sequence analysis, and the expression pattern of the GRF gene in bamboo shoots at different development stages was analyzed by qRT-PCR. Simultaneously, ectopic expression in Arabidopsis was conducted to validate the gene function. The result showed that the isolated gene from moso bamboo was 1 164 bp, encoding 387 amino acids, which was named as PeGRF1 . Protein sequence analysis showed that PeGRF1 had the complete typical domains (WRC and QLQ) of GRF family. The phylogenetic analysis demonstrated that PeGRF1 were clustered closer to the GRFs of monocotyledonous plants such as Oryza sativa , indicating they had close relationship. PeGRF1 expressed predominantly in young bamboo shoots. Meanwhile, the expression level of PeGRF1 was significantly higher during rapid growth stage than that during slow growth stage of bamboo shoots, and the expression level of PeGRF1 in the upper and middle of bamboo shoots was significantly higher than that in the base. Overexpression of PeGRF1 could increase the plant height of transgenic Arabidopsis . Taken together, our results demonstrated that PeGRF1 was involved in development of bamboo shoots, which provided references for elucidating the biological functions of GRF genes in bamboo.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81550652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-21DOI: 10.5376/mpb.2020.11.0026
Hongfang Zhu, Dandan Xi, Xiaofeng Li, Lu Gao, Yuying Zhu
Temperature is a main environmental factor that affects anthocyanin biosynthesis and accumulation in purple pakchoi (Brassica campestris ssp. Chinensis Makino.). Purple pakchoi is one of the most popular vegetables with high content of anthocyanin in China. Recently, we found that the purple color of purple pakchoi cultivar, "ziyi", deepened after 10-day low temperature(5°C, LT) treatment with increased anthocyanin content compared to plants after 20°C (normal temperature, NT, control) treatment. Contractly, the color of pakchoi treated with 10-day heat temperature (35°C, HT) became lighter with decreased anthocyanin content than that of control. The transcriptiom analysis revealed a total of 51008 unigenes from plants treated with NT，LT, and HT by RNA-seq. A total of 4321 and 8455 differentially expressed genes (DEGs) were identified from HT and LT compared to NT, respectively. Among these DEGs, 173 unigenes were downregulated in LT and upregulated in HT compared to NT. 218 unigenes were upregulated in LT and downregulated in HT. Further Gene Ontology enrichment analysis revealed a series of candidate genes that may be involve in temperature-mediated anthocyanin accumulation, including structural genes and 20 transcription factors. Collectively, our study provide a global view of transcriptiomic resources in response to temperature-induced anthocyanin accumulation in purple pakchoi.
{"title":"RNA-Seq Reveals Transcription Factors Involved in Temperature-mediated Anthocyanin Accumulation and Biosynthesis in Purple Pakchoi (Brassica campestris ssp. Makino.)","authors":"Hongfang Zhu, Dandan Xi, Xiaofeng Li, Lu Gao, Yuying Zhu","doi":"10.5376/mpb.2020.11.0026","DOIUrl":"https://doi.org/10.5376/mpb.2020.11.0026","url":null,"abstract":"Temperature is a main environmental factor that affects anthocyanin biosynthesis and accumulation in purple pakchoi (Brassica campestris ssp. Chinensis Makino.). Purple pakchoi is one of the most popular vegetables with high content of anthocyanin in China. Recently, we found that the purple color of purple pakchoi cultivar, \"ziyi\", deepened after 10-day low temperature(5°C, LT) treatment with increased anthocyanin content compared to plants after 20°C (normal temperature, NT, control) treatment. Contractly, the color of pakchoi treated with 10-day heat temperature (35°C, HT) became lighter with decreased anthocyanin content than that of control. The transcriptiom analysis revealed a total of 51008 unigenes from plants treated with NT，LT, and HT by RNA-seq. A total of 4321 and 8455 differentially expressed genes (DEGs) were identified from HT and LT compared to NT, respectively. Among these DEGs, 173 unigenes were downregulated in LT and upregulated in HT compared to NT. 218 unigenes were upregulated in LT and downregulated in HT. Further Gene Ontology enrichment analysis revealed a series of candidate genes that may be involve in temperature-mediated anthocyanin accumulation, including structural genes and 20 transcription factors. Collectively, our study provide a global view of transcriptiomic resources in response to temperature-induced anthocyanin accumulation in purple pakchoi.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88413987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-18DOI: 10.5376/MPB.2020.11.0021
Liu Wei, Huo Chensi, Wang Guoping, Shang Yongjin, Fan Xinping
Key genes in strawberry fruit development play an important role in the development and maturation of strawberry fruit, and are also important in molecular breeding and genetic improvement. UPL probes was used to quantitatively analyze the expression of strawberry genes FaNCED1 , FaPG , FaEXP5 and FaDFR at different stages of fruit development and in different organs. The results showed that FaPG and FaEXP5 significantly increased expression in the late stage of fruit development. And FaPG had significant fruit-specific expression. At every stage of fruit development, FaDFR showed a higher level of expression than other genes. This study provides some theoretical reference for the development and utilization of key genes in strawberry fruit development.
{"title":"Comparison of Expression Activity of Key Genes in Strawberry Fruit Development","authors":"Liu Wei, Huo Chensi, Wang Guoping, Shang Yongjin, Fan Xinping","doi":"10.5376/MPB.2020.11.0021","DOIUrl":"https://doi.org/10.5376/MPB.2020.11.0021","url":null,"abstract":"Key genes in strawberry fruit development play an important role in the development and maturation of strawberry fruit, and are also important in molecular breeding and genetic improvement. UPL probes was used to quantitatively analyze the expression of strawberry genes FaNCED1 , FaPG , FaEXP5 and FaDFR at different stages of fruit development and in different organs. The results showed that FaPG and FaEXP5 significantly increased expression in the late stage of fruit development. And FaPG had significant fruit-specific expression. At every stage of fruit development, FaDFR showed a higher level of expression than other genes. This study provides some theoretical reference for the development and utilization of key genes in strawberry fruit development.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87963570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-18DOI: 10.5376/mpb.2020.11.0020
Yue Zuo, Yong-hua Xu
The dormancy and germination of seeds are determined by the balance between the embryo growth potential and the binding force imposed by the seed coat. The germination of different seeds is not synchronized, and the stimulus required to promote germination varies greatly. Before germination, the seeds need to undergo water absorption, reactivate metabolic activities and redifferentiate embryonic tissues to mobilize nutrients stored in seeds and initiate meristematic activities. The transition from dry seeds to seedlings is highly sensitive to different environmental conditions, especially light, temperature and water. This response to environmental signals is regulated by one or more hormones. Various plant hormones regulate seed germination through highly complex interactions. Among them, the role of GA (gibberellin) and ABA (Abscisic acid) in regulating seed germination is particularly critical. This article reviewed the mechanisms by which GA and ABA control seed dormancy at the molecular level, and discussed the way they interact with other hormones. Finally, the development direction of plant hormone research on seed germination is prospected.
{"title":"Research Progress on the Mechanism of GA and ABA during Seed Germination","authors":"Yue Zuo, Yong-hua Xu","doi":"10.5376/mpb.2020.11.0020","DOIUrl":"https://doi.org/10.5376/mpb.2020.11.0020","url":null,"abstract":"The dormancy and germination of seeds are determined by the balance between the embryo growth potential and the binding force imposed by the seed coat. The germination of different seeds is not synchronized, and the stimulus required to promote germination varies greatly. Before germination, the seeds need to undergo water absorption, reactivate metabolic activities and redifferentiate embryonic tissues to mobilize nutrients stored in seeds and initiate meristematic activities. The transition from dry seeds to seedlings is highly sensitive to different environmental conditions, especially light, temperature and water. This response to environmental signals is regulated by one or more hormones. Various plant hormones regulate seed germination through highly complex interactions. Among them, the role of GA (gibberellin) and ABA (Abscisic acid) in regulating seed germination is particularly critical. This article reviewed the mechanisms by which GA and ABA control seed dormancy at the molecular level, and discussed the way they interact with other hormones. Finally, the development direction of plant hormone research on seed germination is prospected.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"9 6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82697103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-09-18DOI: 10.5376/mpb.2020.11.0022
Hua Xiaofang, Bi Chuyun, Bi-fang Huang, Ming Xu, Zhijian Yang, Shiqiang Lin, Xuanyang Chen
The plant MYB is a transcription factor family large in number and with important functions. In this study, the MYB family genes were screened and identified via bioinformatic methods from the raw sequence of sweet potato ( Ipomoea batatas ) genome and the gene structure and function of R2R3-MYB were analyzed. The results showed that there were 88 R2R3-MYB genes with intact R2 and R3 conservative domains, which contained 8 and 9 highly conserved basic amino acids. The results of MEME analysis showed that there were 10 conserved motifs within the I. batatas R2R3-MYB protein sequences. For the I. batatas R2R3-MYB protein sequences, over 80% contained motif 1, motif 2, motif 3, motif 4, motif 5 and motif 7. The R2R3-MYB genes were distributed unevenly across the 15 chromosomes. The number of R2R3-MYB genes in chromosome No.5 was 15, which was the largest; the numbers of R2R3-MYB genes in chromosome No. 4 and 13 were both only 2, which was the smallest. Analysis of the sequence alignment showed that there were 6 pairs of interchromosomal duplication and there were 20 pairs of intrachromosomal duplication, 19 of which existed in clusters. The function prediction and categorization via sequence analysis showed that 44 R2R3-MYB genes of the I. batatas could be categorized to the 13 subgroups of the A. thaliana R2R3-MYB genes, which were involved in the responses to biotic stress and abiotic stress, anthocyanin biosynthesis, anther development, etc. Further analysis showed that 36 R2R3-MYB genes might play important roles in dealing with biotic stress and abiotic stress, 9 of which showed significant up/down-regulation under Fusarium oxysporum f. sp. batatas stress and 27 of which showed significant up/down-regulation under low temperature stress. The domains of I. batatas R2R3-MYB transcription factors were highly conservative, which contained highly conserved motifs within R2 and R3 domains. The phylogenetic tree and transcriptomics data analysis showed that some R2R3-MYB genes might play roles in growth and development, metabolism regulation, biotic stress and abiotic stress, which lent support to I. batatas breeding.
{"title":"Identification and Analysis of R2R3-MYB Genes in Sweet Potato Genome","authors":"Hua Xiaofang, Bi Chuyun, Bi-fang Huang, Ming Xu, Zhijian Yang, Shiqiang Lin, Xuanyang Chen","doi":"10.5376/mpb.2020.11.0022","DOIUrl":"https://doi.org/10.5376/mpb.2020.11.0022","url":null,"abstract":"The plant MYB is a transcription factor family large in number and with important functions. In this study, the MYB family genes were screened and identified via bioinformatic methods from the raw sequence of sweet potato ( Ipomoea batatas ) genome and the gene structure and function of R2R3-MYB were analyzed. The results showed that there were 88 R2R3-MYB genes with intact R2 and R3 conservative domains, which contained 8 and 9 highly conserved basic amino acids. The results of MEME analysis showed that there were 10 conserved motifs within the I. batatas R2R3-MYB protein sequences. For the I. batatas R2R3-MYB protein sequences, over 80% contained motif 1, motif 2, motif 3, motif 4, motif 5 and motif 7. The R2R3-MYB genes were distributed unevenly across the 15 chromosomes. The number of R2R3-MYB genes in chromosome No.5 was 15, which was the largest; the numbers of R2R3-MYB genes in chromosome No. 4 and 13 were both only 2, which was the smallest. Analysis of the sequence alignment showed that there were 6 pairs of interchromosomal duplication and there were 20 pairs of intrachromosomal duplication, 19 of which existed in clusters. The function prediction and categorization via sequence analysis showed that 44 R2R3-MYB genes of the I. batatas could be categorized to the 13 subgroups of the A. thaliana R2R3-MYB genes, which were involved in the responses to biotic stress and abiotic stress, anthocyanin biosynthesis, anther development, etc. Further analysis showed that 36 R2R3-MYB genes might play important roles in dealing with biotic stress and abiotic stress, 9 of which showed significant up/down-regulation under Fusarium oxysporum f. sp. batatas stress and 27 of which showed significant up/down-regulation under low temperature stress. The domains of I. batatas R2R3-MYB transcription factors were highly conservative, which contained highly conserved motifs within R2 and R3 domains. The phylogenetic tree and transcriptomics data analysis showed that some R2R3-MYB genes might play roles in growth and development, metabolism regulation, biotic stress and abiotic stress, which lent support to I. batatas breeding.","PeriodicalId":32255,"journal":{"name":"Journal of Plant Molecular Breeding","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84327915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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