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Lin Y, Xiang Y, Wei S, Zhang Q, Liu Y, Zhang Z, Tang S. Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape. Ecol Evol 2024; 14:e70094. [PMID: 39091326 PMCID: PMC11291554 DOI: 10.1002/ece3.70094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.
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Affiliation(s)
- Yanfang Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
- Wuzhou No. 18 Middle SchoolWuzhouChina
| | - Yingying Xiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Sujian Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Yanhua Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
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Zhang S, Yu Z, Sun L, Liang S, Xu F, Li S, Zheng X, Yan L, Huang Y, Qi X, Ren H. T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality. HORTICULTURE RESEARCH 2024; 11:uhae033. [PMID: 38495030 PMCID: PMC10940123 DOI: 10.1093/hr/uhae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/23/2024] [Indexed: 03/19/2024]
Abstract
Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.
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Affiliation(s)
- Shuwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Zheping Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Li Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Senmiao Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Sujuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Xiliang Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
| | - Lijv Yan
- Linhai Specialty and Technology Extension Station, 219 Dongfang Avenue, Linhai 317000, Zhejiang, China
| | - Yinghong Huang
- Jiangsu Taihu Evergreen Fruit Tree Technology Promotion Center, Dongshan Town, Wuzhong District, Suzhou 215107, Jiangsu, China
| | - Xingjiang Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
- Xianghu Laboratory, 168 Gengwen Road, Xiaoshan District, Hangzhou 311231, Zhejiang, China
| | - Haiying Ren
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 298 Desheng Road, Shangcheng District, Hangzhou 310021, Zhejiang, China
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Guo D, Wang R, Fang J, Zhong Y, Qi X. Development of sex-linked markers for gender identification of Actinidia arguta. Sci Rep 2023; 13:12780. [PMID: 37550389 PMCID: PMC10406875 DOI: 10.1038/s41598-023-39561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/27/2023] [Indexed: 08/09/2023] Open
Abstract
The fruit of the dioecious plant Actinidia arguta has become a great attraction recently. It has long been difficult to distinguish the genders of hybrid seedlings before flowering, therefore increasing the expenditures of breeding. To produce reliable molecular marker for gender identification, this research utilized whole-genome re-sequencing of 15 males and 15 females from an 8-year-old cross population to develop gender specific markers. P51 and P11 were identified as sex-linked markers after verification. Both of these markers, according to the PCR results, only amplified a single band in male samples. These two markers were tested in 97 hybrids (52 females and 45 males) and 31 wild individuals (13 females and 18 males), with an accuracy of 96.88% and 96.09%, correspondingly. This research also verified the universalities of the two markers in Actinidia chinensis samples, and it could be inferred from the PCR results that neither marker was applicable to A. chinensis samples. The BLAST results of the two markers demonstrated that the two markers were closely aligned with different parts of the Y male-specific region of A. chinensis genome, thus they were likely to be useful for the research on the mechanism of sex determination of A. arguta. The two male-linked makers, P51 and P11, have already been used in sex-identification of A. arguta seedlings.
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Affiliation(s)
- Dandan Guo
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Ran Wang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Jinbao Fang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yunpeng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Xiujuan Qi
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
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Xue L, Huang X, Zhang Z, Lin Q, Zhong Q, Zhao Y, Gao Z, Xu C. An Anthocyanin-Related Glutathione S-Transferase, MrGST1, Plays an Essential Role in Fruit Coloration in Chinese Bayberry ( Morella rubra). FRONTIERS IN PLANT SCIENCE 2022; 13:903333. [PMID: 35755659 PMCID: PMC9213753 DOI: 10.3389/fpls.2022.903333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/20/2022] [Indexed: 05/31/2023]
Abstract
Chinese bayberry (Morella rubra) is a fruit tree economically important in China and accumulates abundant amounts of anthocyanins in fruit as it ripens. Owing to the fact that all anthocyanin containing fruit tissues in Chinese bayberry are edible and anthocyanins can provide various health benefits in human body, the mechanisms underpinning anthocyanin accumulation in this fruit are worthy of investigation. It has been known that in plants anthocyanins are synthesized in the cytoplasmic surface of the endoplasmic reticulum and subsequently transported into the vacuole for storage, and glutathione S-transferases (GSTs) have been verified to be involved in this process. But the characterization and functionalization of the GST counterpart in Chinese bayberry is not available. The GST anthocyanin transporter MrGST1 was discovered to be related with anthocyanin accumulation in fruit from distinct developmental stages of "Biqi," a staple cultivar that accumulates over 1 mg/g anthocyanins in ripe fruit. The expression of MrGST1 was well associated with anthocyanin accumulation either in fruit collected at six developmental stages or in ripe fruit from 12 cultivars. MrGST1 was found to be responsible for the transport of anthocyanins but not proanthocyanidins when the Arabidopsis tt19 mutant was functionally complemented. Transient ectopic expression of MrGST1 in combination with MrMYB1.1 and MrbHLH1 dramatically boosted pigmentation in Nicotiana tabacum leaves in contrast to MrMYB1.1 and MrbHLH1. The promoter of MrGST1 comprised eight MYB binding sites (MBSs) according to cis-element analysis. Data from yeast one-hybrid assay and dual-luciferase tests demonstrated that MrMYB1.1 exerted considerable transactivation effect on the MrGST1 promoter by recognizing the MBS4, the fourth MBS from the ATG start site. Our results together provided molecular evidence for the contribution of MrGST1 in regulating anthocyanin accumulation in Chinese bayberry fruit.
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Affiliation(s)
- Lei Xue
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, China
| | - Xiaorong Huang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, China
| | - Zehuang Zhang
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qihua Lin
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qiuzhen Zhong
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yun Zhao
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhongshan Gao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, China
| | - Changjie Xu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, China
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Transcriptome Analysis and Identification of a Female-Specific SSR Marker in Pistacia chinensis Based on Illumina Paired-End RNA Sequencing. Genes (Basel) 2022; 13:genes13061024. [PMID: 35741786 PMCID: PMC9222763 DOI: 10.3390/genes13061024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023] Open
Abstract
Pistacia chinensis Bunge (P. chinensis), a dioecious plant species, has been widely found in China. The female P. chinensis plants are more important than male plants in agricultural production, as their seeds can serve as an ideal feedstock for biodiesel. However, the sex of P. chinensis plants is hard to distinguish during the seedling stage due to the scarcity of available transcriptomic and genomic information. In this work, Illumina paired-end RNA sequencing assay was conducted to unravel the transcriptomic profiles of female and male P. chinensis flower buds. In total, 50,925,088 and 51,470,578 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 83,370 unigenes with a mean length of 1.3 kb were screened. Overall, 64,539 unigenes (77.48%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG, and GO databases, 71 of which were putatively related to the floral development of P. chinensis. Additionally, 21,662 simple sequence repeat (SSR) motifs were identified in 17,028 unigenes of P. chinensis, and the mononucleotide motif was the most dominant type of repeats (52.59%) in P. chinensis, followed by dinucleotide (22.29%), trinucleotide (20.15%). The most abundant repeats were AG/CT (13.97%), followed by AAC/GTT (6.75%) and AT/TA (6.10%). Based on these SSR, 983 EST-SSR primers were designed, 151 of which were randomly chosen for validation. Of these validated EST-SSR markers, 25 SSR markers were found to be polymorphic between male and female plants. One SSR marker, namelyPCSSR55, displayed excellent specificity in female plants, which could clearly distinguish between male and female P. chinensis. Altogether, our findings not only reveal that the EST-SSR marker is extremely effective in distinguishing between male and female P. chinensis but also provide a solid framework for sex determination of plant seedlings.
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Lin Q, Zhong Q, Zhang Z. A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry ( Morella rubra) with different flesh colors. PeerJ 2022; 10:e13466. [PMID: 35669961 PMCID: PMC9165596 DOI: 10.7717/peerj.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/28/2022] [Indexed: 01/14/2023] Open
Abstract
The Chinese bayberry (Morella rubra Sieb. et Zucc.) is grown commercially in China and other Asian countries for its flavorful and appealing fruit. Here, two bayberry varieties differing in both color and flavor, namely, BDK ('Baidongkui') and DK ('Dongkui'), in China were compared. A total of 18 anthocyanins, three proanthocyanidins, and 229 primary metabolites were identified in the pulp of the two varieties; these were analyzed and compared using ultra-performance liquid chromatography-tandem mass spectrometry. The DK pulp showed higher concentrations of all 18 anthocyanins compared with BDK, apart from peonidin-3,5-O-diglucoside which was not detected in BDK and which was responsible for the formation of pink pulp in BDK. Principal component analysis and cluster analysis of the primary metabolites indicated that the two bayberry varieties had distinct metabolite profiles with approximately 37% (85/229) of the primary metabolome being significantly different. Of these, 62 metabolites were down-regulated and 23 metabolites were up-regulated in BDK relative to DK. Our results suggested that the flavor of the BDK fruit was different from DK, which could be explained by the reduced saccharide, organic acid, amino acid, and proanthocyanidin contents. These findings enhance our understanding of the metabolites responsible for color and taste differences in the Chinese bayberry.
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Zhang S, Yu Z, Sun L, Ren H, Zheng X, Liang S, Qi X. An overview of the nutritional value, health properties, and future challenges of Chinese bayberry. PeerJ 2022; 10:e13070. [PMID: 35265403 PMCID: PMC8900607 DOI: 10.7717/peerj.13070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/15/2022] [Indexed: 01/12/2023] Open
Abstract
Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development.
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Affiliation(s)
- Shuwen Zhang
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
| | - Zheping Yu
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
| | - Li Sun
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
| | - Haiying Ren
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
| | - Xiliang Zheng
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
| | - Senmiao Liang
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
| | - Xingjiang Qi
- Zhejiang Academy of Agricultural Sciences, Institute of Horticulture, Hangzhou, Jianggan, China
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Comparative Transcriptome Analysis Reveals Sex-Biased Expression of Hormone-Related Genes at an Early Stage of Sex Differentiation in Red Bayberry (Morella rubra). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular mechanism of sex development and differentiation in the economically important dioecious fruit tree, red bayberry (Morella rubra), was revealed using next-generation transcriptome sequencing (NGS), and comparative analyses were used to identify differentially expressed genes (DEGs) in female and male flower buds. A total of 7,029 of these DEGs were identified at two early development stages. KEGG pathway enrichment analysis revealed that plant hormone signal transduction was significantly overrepresented, and 91 genes related to hormones were identified. An analysis of 7,029 DEGs revealed 161 hormone-related genes, with the 42 related to auxin and 26 related to ethylene being the most highly represented. A total of 62 genes were significantly up-regulated in females and 29 were in males, with 18 of them specifically expressed in females and 10 in males. A total of 415 transcription factors were identified, with 129 genes up-regulated in females and 53 in males. Moreover, 38 had female-specific expression and 18 had male-specific expression. Using weighted gene co-expression network analysis (WGCNA), two modules were found to be associated with sexual type. In the module coded light-green, there were five genes related to hormones, one to flower development and ten transcription factors with four genes specifically expressed in the males and four in females. The hub gene in the light-green module is MR0TCONS_00017483.1 (ACO), which is involved in ethylene biosynthesis and had male-specific expression. Among the transcription factors, three of the four male-specific expressed genes involved in flavonoid biosynthesis, including the MYB gene MR1TCONS_00020658.1 and two BHLH genes, MR6G001563.1 and MR8G020751.1, played important roles in male floral differentiation. In the dark-cyan module, six hormone-related genes, five transcription factors and three flower development genes were identified with the hub gene MR1G019545.1 (ETR1), which participates in the ethylene signaling pathway, and MR4G023618.1, which encodes the C3H zinc finger transcription factor. These results indicate that ethylene is the key hormone that interacts with other hormones and transcription factors to regulate sex differentiation in the red bayberry, which also provides new insights into the mechanism of sex determination and differentiation in the red bayberry.
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Wang Y, Yang Q, Zhu Y, Zhao L, Ju P, Wang G, Zhou C, Zhu C, Jia H, Jiao Y, Jia H, Gao Z. MrTPS3 and MrTPS20 Are Responsible for β-Caryophyllene and α-Pinene Production, Respectively, in Red Bayberry ( Morella rubra). FRONTIERS IN PLANT SCIENCE 2022; 12:798086. [PMID: 35069655 PMCID: PMC8777192 DOI: 10.3389/fpls.2021.798086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/06/2021] [Indexed: 05/24/2023]
Abstract
Red bayberry is a sweet, tart fruit native to China and grown widely in the south. The key organic compounds forming the distinctive aroma in red bayberry, are terpenoids, mainly β-caryophyllene and α-pinene. However, the key genes responsible for different terpenoids are still unknown. Here, transcriptome analysis on samples from four cultivars, during fruit development, with different terpenoid production, provided candidate genes for volatile organic compound (VOC) production. Terpene synthases (TPS) are key enzymes regulating terpenoid biosynthesis, and 34 TPS family members were identified in the red bayberry genome. MrTPS3 in chromosome 2 and MrTPS20 in chromosome 7 were identified as key genes regulating β-caryophyllene and α-pinene synthesis, respectively, by qRT-PCR. Subcellular localization and enzyme activity assay showed that MrTPS3 was responsible for β-caryophyllene (sesquiterpenes) production and MrTPS20 for α-pinene (monoterpenes). Notably, one amino acid substitution between dark color cultivars and light color cultivars resulted in the loss of function of MrTPS3, causing the different β-caryophyllene production. Our results lay the foundation to study volatile organic compounds (VOCs) in red bayberry and provide potential genes for molecular breeding.
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Affiliation(s)
- Yan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qinsong Yang
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yifan Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lan Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Pengju Ju
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoyun Wang
- Yuyao Agriculture Technology Extension Center, Ningbo, China
| | - Chaochao Zhou
- Yuyao Agriculture Technology Extension Center, Ningbo, China
| | - Changqing Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Huijuan Jia
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Jiao
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, China
| | - Huimin Jia
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Zhongshan Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Zhang S, Yu Z, Qi X, Wang Z, Zheng Y, Ren H, Liang S, Zheng X. Construction of a High-Density Genetic Map and Identification of Leaf Trait-Related QTLs in Chinese Bayberry ( Myrica rubra). FRONTIERS IN PLANT SCIENCE 2021; 12:675855. [PMID: 34194452 PMCID: PMC8238045 DOI: 10.3389/fpls.2021.675855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.
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Affiliation(s)
| | | | - Xingjiang Qi
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Wang Y, Jia HM, Shen YT, Zhao HB, Yang QS, Zhu CQ, Sun DL, Wang GY, Zhou CC, Jiao Y, Chai CY, Yan LJ, Li XW, Jia HJ, Gao ZS. Construction of an anchoring SSR marker genetic linkage map and detection of a sex-linked region in two dioecious populations of red bayberry. HORTICULTURE RESEARCH 2020; 7:53. [PMID: 32257239 PMCID: PMC7109115 DOI: 10.1038/s41438-020-0276-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/02/2020] [Accepted: 02/12/2020] [Indexed: 05/21/2023]
Abstract
Red bayberry (Morella rubra) is an evergreen fruit tree found in southern China whose whole-genome sequence has recently been published. We updated the linkage map of the species by adding 118 SSR markers and the female-specific marker MrFT2_BD-SEX. The integrated map included eight linkage groups and spanned 491 cM. Eleven sex-associated markers were identified, six of which were located in linkage group 8, in agreement with the previously reported location of the sex-determining region. The MrFT2_BD-SEX marker was genotyped in 203 cultivated accessions. Among the females of the accessions, we found two female-specific alleles, designated W-b (151 bp) and W-d (129 bp). We previously found that 'Dongkui', a female cultivar, could produce viable pollen (we refer to such plants 'Dongkui-male') and serve as the paternal parent in crosses. The genotypes of the MrFT2_BD-SEX marker were W-b/Z in 'Biqi' and W-d/Z in 'Dongkui-male'. The progeny of a cross between these parents produced a 3:1 female (W-) to male (ZZ) ratio and the expected 1:1:1:1 ratio of W-b/W-d: W-b/Z: W-d/Z: Z/Z. In addition, the flowering and fruiting phenotypes of all the F1 progeny fit their genotypes. Our results confirm the existence of ZW sex determination and show that the female phenotype is controlled by a single dominant locus (W) in a small genomic region (59 kb and less than 3.3 cM). Furthermore, we have produced a homozygous "super female" (WW) that should produce all-female offspring in the F2 generation, providing a foundation for commercial use and presenting great potential for use in modern breeding programs.
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Affiliation(s)
- Yan Wang
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Hui-Min Jia
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Yu-Tong Shen
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Hai-Bo Zhao
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Qin-Song Yang
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Chang-Qing Zhu
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - De-Li Sun
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Guo-Yun Wang
- Yuyao Forestry Technology Extension Center, 315400 Ningbo, China
| | - Chao-Chao Zhou
- Yuyao Forestry Technology Extension Center, 315400 Ningbo, China
| | - Yun Jiao
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, China
| | - Chun-Yan Chai
- Cixi Forestry Technology Extension Center, 315300 Cixi, China
| | - Li-Ju Yan
- Linhai Forestry Technology Extension Center, 317000 Taizhou, China
| | - Xiong-Wei Li
- Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, 201403 Shanghai, China
| | - Hui-Juan Jia
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
| | - Zhong-Shan Gao
- Fruit Science Institute, College of Agriculture and Biotechnology, Zhejiang University, 310058 Hangzhou, China
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12
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Wu B, Zhong Y, Wu Q, Chen F, Zhong G, Cui Y. Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:563452. [PMID: 33013982 PMCID: PMC7509436 DOI: 10.3389/fpls.2020.563452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/24/2020] [Indexed: 05/16/2023]
Abstract
High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.
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Affiliation(s)
- Bo Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
| | - Yun Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
| | - Qianqian Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
| | - Fangyong Chen
- Citrus Research Institute of Zhejiang, Huangyan, China
- *Correspondence: Fangyong Chen, ; Guangyan Zhong,
| | - Guangyan Zhong
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, & Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences (IFTR-GDAAS), Guangzhou, China
- *Correspondence: Fangyong Chen, ; Guangyan Zhong,
| | - Yiping Cui
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, & Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
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13
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Zhao HB, Jia HM, Wang Y, Wang GY, Zhou CC, Jia HJ, Gao ZS. Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit development and ripening in red bayberry (Morella rubra). Gene 2019; 717:144045. [PMID: 31425741 DOI: 10.1016/j.gene.2019.144045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023]
Abstract
The MADS-box gene family encodes transcription factors and plays an important role in plant growth and the development of flower and fruit. A perennial dioecious plant, the red bayberry genome has been published recently, providing the opportunity to analyze the MADS-box gene family and its role in fruit development and ripening. Here, we identified 54 MADS-box genes in the red bayberry genome, and classified them into two types based on phylogenetic analysis. Thirteen Type I MADS-box genes were subdivided into three subfamilies and 41 Type II MADS-box genes into 13 subfamilies. A total of 46 MADS-box genes were distributed across eight red bayberry chromosomes, and the other eight genes were located on the unmapped scaffolds. Transcriptome analysis suggested that the expression of most Type II genes was higher than Type I in five female tissues. Moreover, 26 MADS-box genes were expressed during red bayberry fruit development and ten of them showed high expression. qRT-PCR showed that the expression of MrMADS01 (SEP, MIKCC), with differences between the pale pink and red varieties, increased significantly at the final ripening stage, suggesting it may participate in ripening as positive regulator and related to anthocyanin biosynthesis. These results provide some clues for future study of MADS-box genes in red bayberry, especially in ripening process.
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Affiliation(s)
- Hai-Bo Zhao
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hui-Min Jia
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; current address: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 201602, China.
| | - Yan Wang
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Yun Wang
- Agriculture Extensions and Services Station, Bureau of Agriculture and Rural Affairs, Yuyao, Ningbo 315400, China
| | - Chao-Chao Zhou
- Agriculture Extensions and Services Station, Bureau of Agriculture and Rural Affairs, Yuyao, Ningbo 315400, China
| | - Hui-Juan Jia
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhong-Shan Gao
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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14
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Jia H, Jia H, Cai Q, Wang Y, Zhao H, Yang W, Wang G, Li Y, Zhan D, Shen Y, Niu Q, Chang L, Qiu J, Zhao L, Xie H, Fu W, Jin J, Li X, Jiao Y, Zhou C, Tu T, Chai C, Gao J, Fan L, van de Weg E, Wang J, Gao Z. The red bayberry genome and genetic basis of sex determination. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:397-409. [PMID: 29992702 PMCID: PMC6335074 DOI: 10.1111/pbi.12985] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/01/2018] [Accepted: 07/04/2018] [Indexed: 05/12/2023]
Abstract
Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.
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Affiliation(s)
- Hui‐Min Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hui‐Juan Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | | | - Yan Wang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hai‐Bo Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wei‐Fei Yang
- Hangzhou 1 Gene LtdHangzhouChina
- Forestry Technology Extension CenterYuyaoNingboChina
- Present address:
Annoroad Gene Tech. Co., LtdBeijingChina
| | - Guo‐Yun Wang
- Forestry Technology Extension CenterYuyaoNingboChina
| | - Ying‐Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | - Yu‐Tong Shen
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qing‐Feng Niu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular GeneticsCenter of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Le Chang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jie Qiu
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Lan Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Han‐Bing Xie
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wan‐Yi Fu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jing Jin
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xiong‐Wei Li
- Forest & Fruit Tree InstituteShanghai Academy of Agricultural SciencesShanghaiChina
| | - Yun Jiao
- Institute of ForestryNingbo Academy of Agricultural ScienceNingboChina
| | | | - Ting Tu
- Shunmei Breeding and Propagation Centre for Chinese BayberryYuyaoChina
| | | | | | - Long‐Jiang Fan
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Eric van de Weg
- Plant Breeding‐Wageningen University and ResearchWageningenThe Netherlands
| | | | - Zhong‐Shan Gao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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15
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Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018; 653:80-90. [DOI: 10.1016/j.gene.2018.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
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16
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Mei L, Dong N, Li F, Li N, Yao M, Chen F, Tang L. Transcriptome analysis of female and male flower buds of Idesia polycarpa Maxim. var. vestita Diels. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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Guo LN, Gao XF. Genetic diversity and population structure of Indigofera szechuensis complex (Fabaceae) based on EST-SSR markers. Gene 2017; 624:26-33. [DOI: 10.1016/j.gene.2017.04.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
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18
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Fu YP, Liang Y, Dai YT, Yang CT, Duan MZ, Zhang Z, Hu SN, Zhang ZW, Li Y. De Novo Sequencing and Transcriptome Analysis of Pleurotus eryngii subsp. tuoliensis (Bailinggu) Mycelia in Response to Cold Stimulation. Molecules 2016; 21:molecules21050560. [PMID: 27196889 PMCID: PMC6273410 DOI: 10.3390/molecules21050560] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022] Open
Abstract
Cold stimulation of Bailinggu's mycelia is the main factor that triggers primordia initiation for successful production of fruiting bodies under commercial cultivation. Yet, the molecular-level mechanisms involved in mycelia response to cold stimulation are still unclear. Here, we performed comparative transcriptomic analysis using RNA-Seq technology to better understand the gene expression regulation during different temporal stages of cold stimulation in Bailinggu. A total of 21,558 Bailinggu mycelia unigenes were de novo assembled and annotated from four libraries (control at 25 °C, plus cold stimulation treatments at -3 °C for a duration of 1-2 days, 5-6 days, and 9-10 days). GO and KEGG pathway analysis indicated that functional groups of differentially expressed unigenes associated with cell wall and membrane stabilization, calcium signaling and mitogen-activated protein kinases (MAPK) pathways, and soluble sugars and protein biosynthesis and metabolism pathways play a vital role in Bailinggu's response to cold stimulation. Six hundred and seven potential EST-based SSRs loci were identified in these unigenes, and 100 EST-SSR primers were randomly selected for validation. The overall polymorphism rate was 92% by using 10 wild strains of Bailinggu. Therefore, these results can serve as a valuable resource for a better understanding of the molecular mechanisms associated with Bailinggu's response to cold stimulation.
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Affiliation(s)
- Yong-Ping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Agriculture, Jilin Agricultural University, Changchun 130118, China.
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA.
| | - Yuan Liang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yue-Ting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Agriculture, Jilin Agricultural University, Changchun 130118, China.
| | - Chen-Tao Yang
- China National GeneBank, Environmental Genomics, BGI, Shenzhen 518083, China.
| | - Ming-Zheng Duan
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Agriculture, Jilin Agricultural University, Changchun 130118, China.
| | - Zhuo Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Agriculture, Jilin Agricultural University, Changchun 130118, China.
| | - Song-Nian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhi-Wu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, College of Agriculture, Jilin Agricultural University, Changchun 130118, China.
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19
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Zhai F, Mao J, Liu J, Peng X, Han L, Sun Z. Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them. FRONTIERS IN PLANT SCIENCE 2016; 7:330. [PMID: 27047511 PMCID: PMC4796010 DOI: 10.3389/fpls.2016.00330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/04/2016] [Indexed: 05/31/2023]
Abstract
Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation.
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Affiliation(s)
- Feifei Zhai
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Jinmei Mao
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
- Research Institute of Economic Forest, Xinjiang Academy of ForestryXinjiang, China
| | - Junxiang Liu
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Xiangyong Peng
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Lei Han
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Zhenyuan Sun
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
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20
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Yang L, Gong F, Xiong E, Wang W. Proteomics: a promising tool for research on sex-related differences in dioecious plants. FRONTIERS IN PLANT SCIENCE 2015; 6:954. [PMID: 26583026 PMCID: PMC4631940 DOI: 10.3389/fpls.2015.00954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/19/2015] [Indexed: 05/07/2023]
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