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Wang D, Cheng B, Zhang J. High-density genetic map and quantitative trait loci map of skin color in hawthorn ( Crataegus pinnatifida bge. Var. major N.E.Br.). Front Genet 2024; 15:1405604. [PMID: 38873113 PMCID: PMC11169616 DOI: 10.3389/fgene.2024.1405604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/09/2024] [Indexed: 06/15/2024] Open
Abstract
Fruit skin color is an important trait of the hawthorn tree, which has an important influence on fruit quality. Crataegus pinnatifida Bge. var. Major N.E.Br. Is one of the most widely cultivated varieties in China and has a long history of medicinal use. In recent years, it has attracted the attention of the world due to its nutritional and medicinal values. Skin color is the focus of breeders and food processors. At present, skin color-related genes have still not been mapped. In this study, "Shandong Da Mianqiu" (♀, red skin color), "Da Huang Mianzha" (♂, yellow skin color) and 131 F1 hybrids were used to construct genetic map of hawthorn by RAD-seq, and QTL mapping was performed by combining these features with the hue angle and the observed color. In this study, 13,260 SNP was assigned to 17 linkage groups, with an integrated map covering 2,297.75 cM was constructed. A total of 5 QTLs related to hawthorn skin color were detected on LG1, LG3 and LG15. Whether hue angle or pericarp color acts as phenotype for QTL mapping, the candidate genes include bHLH086, WD repeat regions and Myb-like. bHLH, WD and Myb play an important role in the color regulation of Hawthorn skin color. These results lay a solid foundation for QTL mapping and molecular marker-assisted breeding of hawthorn.
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Affiliation(s)
- Dongsheng Wang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Beibei Cheng
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Qinhuangdao, China
| | - Jijun Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, China
- Hebei Higher Institute Application Technology Research and Development Center of Horticultural Plant Biological Breeding, Qinhuangdao, China
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Iqbal S, Bai Y, Hayat F, Coulibaly D, Khalil-Ur-Rehman M, Shi T, Gao Z. Comprehensive transcriptomic and metabolomic analysis revealed distinct flavonoid biosynthesis regulation during abnormal pistil development in Japanese apricot. Genomics 2022; 114:110451. [PMID: 35988654 DOI: 10.1016/j.ygeno.2022.110451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 08/06/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Japanese apricot is an imperative stone fruit plant with numerous processing importance. The failure of reproductive system is the most common cause of fruit loss, through which pistil abortion is the fundamental one. To understand this mechanism, we used a combination of transcriptomic and metabolomic approaches to investigate the biochemical and molecular basis of flavonoid biosynthesis. Due to the regulated expression of flavonoid pathway-related genes in plants, flavonoid biosynthesis is largely regulated at the transcriptional level. A total of 2272 differently expressed genes and 215 differential metabolites were found. The expression of the genes and metabolites encoding flavonoid biosynthesis was lower in abnormal pistils that are in line with the flavonoid quantification from abnormal pistils. Besides, a couple of genes were also detected related to MYB, MADS, NAC and bHLH transcription factors. Remarkably, we found 'hydroxycinnamoyl transferase (LOC103323133)' and flavonoid related metabolite '2-hydroxycinnamic acid' was lower expressed in abnormal pistil, proposing the cause of pistil abortion. Collectively, the present study delivers inclusive transcriptional and metabolic datasets that proposed valuable prospects to unravel the genetic mechanism underlying pistil abortion.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Faisal Hayat
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Daouda Coulibaly
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | | | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Iqbal S, Hayat F, Mushtaq N, Khalil-ur-Rehman M, Khan U, Yasoob TB, Khan MN, Ni Z, Ting S, Gao Z. Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening. PLANTS 2022; 11:plants11151898. [PMID: 35893602 PMCID: PMC9332017 DOI: 10.3390/plants11151898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
Auxin/indole-3-acetic acid (Aux/IAA) is a transcriptional repressor in the auxin signaling pathway that plays a role in several plant growth and development as well as fruit and embryo development. However, it is unclear what role they play in Japanese apricot (Prunus mume) fruit development and maturity. To investigate the role of Aux/IAA genes in fruit texture, development, and maturity, we comprehensively identified and expressed 19 PmIAA genes, and demonstrated their conserved domains and homology across species. The majority of PmIAA genes are highly responsive and expressed in different hormone treatments. PmIAA2, PmIAA5, PmIAA7, PmIAA10, PmIAA13, PmIAA18, and PmIAA19 showed a substantial increase in expression, suggesting that these genes are involved in fruit growth and maturity. During fruit maturation, alteration in the expression of PmIAA genes in response to 1-Methylcyclopropene (1-MCP) treatment revealed an interaction between auxin and ethylene. The current study investigated the response of Aux/IAA development regulators to auxin during fruit ripening, with the goal of better understanding their potential application in functional genomics.
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Affiliation(s)
- Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
- Correspondence: (S.I.); (Z.G.); Tel./Fax: +86-025-8439-5724 (S.I. & Z.G.)
| | - Faisal Hayat
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
| | - Naveed Mushtaq
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
| | - Muhammad Khalil-ur-Rehman
- Department of Horticultural Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Ummara Khan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Talat Bilal Yasoob
- Department of Animal Sciences, Ghazi University, Dera Ghazi Khan 32200, Pakistan;
| | | | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
| | - Shi Ting
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
- Correspondence: (S.I.); (Z.G.); Tel./Fax: +86-025-8439-5724 (S.I. & Z.G.)
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Farneti B, Khomenko I, Ajelli M, Emanuelli F, Biasioli F, Giongo L. Ethylene Production Affects Blueberry Fruit Texture and Storability. FRONTIERS IN PLANT SCIENCE 2022; 13:813863. [PMID: 35401635 PMCID: PMC8990881 DOI: 10.3389/fpls.2022.813863] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Ethylene, produced endogenously by plants and their organs, can induce a wide array of physiological responses even at very low concentrations. Nevertheless, the role of ethylene in regulating blueberry (Vaccinium spp.) ripening and storability is still unclear although an increase in ethylene production has been observed in several studies during blueberry ripening. To overcome this issue, we evaluated the endogenous ethylene production of a Vaccinium germplasm selection at different fruit ripening stages and after cold storage, considering also textural modifications. Ethylene and texture were further assessed also on a bi-parental full-sib population of 124 accessions obtained by the crossing between "Draper" and "Biloxi", two cultivars characterized by a different chilling requirement and storability performances. Our results were compared with an extensive literature research, carried out to collect all accessible information on published works related to Vaccinium ethylene production and sensitivity. Results of this study illustrate a likely role of ethylene in regulating blueberry shelf life. However, a generalisation valid for all Vaccinium species is not attainable because of the high variability in ethylene production between genotypes, which is strictly genotype-specific. These differences in ethylene production are related with blueberry fruit storage performances based on textural alterations. Specifically, blueberry accessions characterized by the highest ethylene production had a more severe texture decay during storage. Our results support the possibility of tailoring ad hoc preharvest and postharvest strategies to extend blueberry shelf life and quality according with the endogenous ethylene production level of each cultivar.
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Affiliation(s)
- Brian Farneti
- Berries Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Iuliia Khomenko
- Sensory Quality Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Matteo Ajelli
- Berries Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Francesco Emanuelli
- Berries Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Franco Biasioli
- Sensory Quality Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Lara Giongo
- Berries Genetics and Breeding Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
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Analysis of Selected Variants of DRD2 and ANKK1 Genes in Combat Athletes. Genes (Basel) 2021; 12:genes12081239. [PMID: 34440413 PMCID: PMC8393533 DOI: 10.3390/genes12081239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 12/01/2022] Open
Abstract
The level of physical activity is conditioned by many different factors, including, among others, the personality traits of a person. Important is the fact that personality traits are a moderately heritable factor and on the basis of the analysis of several genes, various lifetime outcomes can be predicted. One of the most important pathways influencing personality traits is connected to the dopaminergic system; hence, we decided to analyze the DRD2 PROM. rs1799732, DRD2 rs1076560, DRD2 Tag1D rs1800498, DRD2 Ex8 rs6276, DRD2Tag1B rs1079597 and ANKK1 Tag1A rs180049. The research group included 258 male athletes (mean age = 26.02; SD = 8.30), whereas the control group was 284 healthy male volunteers matched for age (mean age = 22.89; SD = 4.78), both of Caucasian origin and without history of substance dependency or psychosis. Genomic DNA was extracted from venous blood using standard procedures. Genotyping was conducted with the real-time PCR method. Differences in the frequency of the DRD2Tag1B rs1079597 gene polymorphism were found between people practicing combat sports and the control group, and the DRD2 PROM. rs1799732, DRD2 rs1076560, DRD2 Tag1D rs1800498, DRD2 Ex8 rs6276, DRD2Tag1B rs1079597 and ANKK1 Tag1A rs1800497 genotypes and allele frequencies in the studied sample did not differ between the analyzed groups. Hence, we considered these polymorphic places as an interesting area for the further search for unambiguous associations between personality traits and attitude towards physical effort.
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Iqbal S, Pan Z, Hayat F, Bai Y, Coulibaly D, Ali S, Ni X, Shi T, Gao Z. Comprehensive transcriptome profiling to identify genes involved in pistil abortion of Japanese apricot. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1191-1204. [PMID: 34177144 PMCID: PMC8212332 DOI: 10.1007/s12298-021-01019-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/08/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Flower development exists as a key period in the angiosperms life cycle and the proper development is considered with its reproductive success. Pistil abortion is one of the widely distributed aspects of berry plants and its basic mechanism in Japanese apricot is quite unclear and needs thorough investigation. The present study was carried out to get a deep insight into the pistil abortion mechanism in Japanese apricot using a transcriptomic approach. A large number of DEGs were identified from different development stages of normal and abortive pistils. Pair-wise comparison analysis was performed as LY1 vs DQD1, LY2 vs DQD2, and LY3 vs DQD3 and produced 3590, 2085, and 2286 transcripts, respectively. The Gene Ontology (GO) showed that different metabolic processes, plant hormones, developmental processes, and photosystem-related genes were involved in pistil abortion. The pathway analysis revealed significant enrichment of plant hormone's signal transduction and circadian rhythm pathways. Furthermore, transcription factors such as MYB, MADS-box, and NAC family showed lower expression in abortive pistils. The current study presents a new strategy for advanced research and understanding of the pistil abortion process in Japanese apricot and provides a possible reference for other deciduous fruit trees.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50 Zhongling Street, Nanjing, 210014 China
| | - Zhenpeng Pan
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Faisal Hayat
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Daouda Coulibaly
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Sajid Ali
- Department of Horticulture, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Pakistan
| | - Xiaopeng Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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Iqbal S, Pan Z, Wu X, Shi T, Ni X, Bai Y, Gao J, Khalil-Ur-Rehman M, Gao Z. Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot. THE PLANT GENOME 2020; 13:e20052. [PMID: 33217203 DOI: 10.1002/tpg2.20052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIP-Seq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars 'Daqiandi' (DQD) and 'Longyan' (LY), which showed that the majority of DNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhenpeng Pan
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Wu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai An, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography Shenzhen University, Shenzhen, China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaopeng Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Khalil-Ur-Rehman
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Shi P, Xu Z, Zhang S, Wang X, Ma X, Zheng J, Xing L, Zhang D, Ma J, Han M, Zhao C. Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch]. BMC PLANT BIOLOGY 2020; 20:438. [PMID: 32967617 PMCID: PMC7510285 DOI: 10.1186/s12870-020-02557-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/19/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted. RESULTS A high-density single nucleotide polymorphism (SNP)-based peach linkage map was constructed using specific locus amplified fragment sequencing (SLAF-seq). This genetic map consisted of 7998 SLAF markers, spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers. A total of 40 QTLs and 885 annotated candidate genes were detected for 10 fruit-related traits, including fruit weight (FW), fruit diameter (FD), percentage of red skin colour (PSC), eating quality (EQ), fruit flavour (FV), red in flesh (RF), red around pit (RP), adherence to pit (AP), fruit development period (FDP) and fruit fibre content (FFC). Eighteen QTLs for soluble solid content (SSC) were identified along LGs 1, 4, 5, and 6 in 2015 and 2016, and 540 genes were annotated in QTL intervals. Thirty-two QTLs for fruit acidity content (FA) were detected on LG1, and 2, 4, 5, 6, and 1232 candidate genes were identified. The expression profiles of 2 candidate genes for SSC and 4 for FA were analysed in parents and their offspring. CONCLUSIONS We constructed a high-density genetic map in peach based on SLAF-seq, which may contribute to the identification of important agronomic trait loci. Ninety QTLs for 12 fruit-related traits were identified, most of which overlapped with previous reports, and some new QTLs were obtained. A large number of candidate genes for fruit-related traits were screened and identified. These results may improve our understanding of the genetic control of fruit quality traits and provide useful information in marker-assisted selection for fruit quality in peach breeding programmes.
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Affiliation(s)
- Pei Shi
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ze Xu
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shaoyu Zhang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xianju Wang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaofei Ma
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jicheng Zheng
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Libo Xing
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Dong Zhang
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Juanjuan Ma
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Mingyu Han
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Caiping Zhao
- College of horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
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Analyzing Differentially Expressed Genes and Pathways Associated with Pistil Abortion in Japanese Apricot via RNA-Seq. Genes (Basel) 2020; 11:genes11091079. [PMID: 32942711 PMCID: PMC7565994 DOI: 10.3390/genes11091079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Reproduction is a critical stage in the flower development process, and its failure causes serious problems affecting fruit quality and yield. Pistil abortion is one of the main factors in unsuccessful reproduction and occurs in many fruit plants. In Japanese apricot, the problem of pistil abortion is very common and affects fruit quality and plant yield; however, its molecular mechanism is not clearly understood. Therefore, in the current study, we used RNA-Seq to identify the differentially expressed genes (DEGs) and pathways actively involved in pistil abortion. A total of 3882 differentially expressed genes were found after cutoff and pairwise comparison analysis. According to KEGG pathway analysis, plant hormone signaling transduction and metabolic pathways were found most significantly enriched in this study. A total of 60 transcription factor families such as MADS-box, NAC and TCP showed their role in this process. RT-qPCR assays confirmed that the expression levels were consistent with RNA-Seq results. This study provides an alternative to be considered for further studies and understanding of pistil abortion processes in Japanese apricot, and it provides a reference related to this issue for other deciduous fruit crops.
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Iqbal S, Ni X, Bilal MS, Shi T, Khalil-ur-Rehman M, Zhenpeng P, Jie G, Usman M, Gao Z. Identification and expression profiling of sugar transporter genes during sugar accumulation at different stages of fruit development in apricot. Gene 2020; 742:144584. [DOI: 10.1016/j.gene.2020.144584] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/11/2022]
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Lu N, Zhang M, Xiao Y, Han D, Liu Y, Zhang Y, Yi F, Zhu T, Ma W, Fan E, Qu G, Wang J. Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F 1 population of Catalpa bungei × Catalpa duclouxii Dode. BMC PLANT BIOLOGY 2019; 19:596. [PMID: 31888555 PMCID: PMC6937828 DOI: 10.1186/s12870-019-2207-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/17/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies. RESULTS Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis. CONCLUSIONS This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.
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Affiliation(s)
- Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Donghua Han
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037 Jiangsu People’s Republic of China
| | - Ying Liu
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Erqin Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People’s Republic of China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
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