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Zi Y, Zhang M, Yang X, Zhao K, Yin T, Wen K, Li X, Liu X, Zhang H. Identification of the sweet orange (Citrus sinensis) bHLH gene family and the role of CsbHLH55 and CsbHLH87 in regulating salt stress. THE PLANT GENOME 2024:e20502. [PMID: 39215542 DOI: 10.1002/tpg2.20502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/01/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Salt stress is one of the primary environmental stresses limiting plant growth and production and adversely affecting the growth, development, yield, and fruit quality of Citrus sinensis. bHLH (basic helix-loop-helix) genes are involved in many bioregulatory processes in plants, including growth and development, phytohormone signaling, defense responses, and biosynthesis of specific metabolites. In this study, by bioinformatics methods, 120 CsbHLHgenes were identified, and phylogenetic analysis classified them into 18 subfamilies that were unevenly distributed on nine chromosomes. The cis-acting elements of the CsbHLH genes were mainly hormone-related cis-acting elements. Seventeen CsbHLH genes exhibited significant differences in expression under salt stress. Six CsbHLH genes with significant differences in expression were randomly selected for quantitative real-time polymerase chain reaction (qRT-PCR) validation. The qRT-PCR results showed a strong correlation with the transcriptome data. Phytohormones such as jasmonic acid (JA) are essential for biotic and abiotic stress responses in plants, and CsbHLH55 and CsbHLH87 are considered candidate target genes for sweet orange MYC2 transcription factors involved in the JA signaling pathway. These genes are the main downstream effectors in the JA signaling pathway and can be activated to participate in the JA signaling pathway. Activation of the JA signaling pathway inhibits the production of reactive oxygen species and improves the salt tolerance of sweet orange plants. The CsbHLH55 and CsbHLH87 genes could be candidate genes for breeding new transgenic salt-resistant varieties of sweet orange.
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Affiliation(s)
- Yinqiang Zi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Mengjie Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Ke Wen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xulin Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
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Chen P, Liu J, Tang Q, Zhou T, Guo L, Xu Y, Chai L, Xu Q, Deng Z, Li X. Genetic Identification of Medicinal Citrus Cultivar 'Local Juhong' Using Molecular Markers and Genomics. Genes (Basel) 2024; 15:719. [PMID: 38927655 PMCID: PMC11203252 DOI: 10.3390/genes15060719] [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: 04/25/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
The citrus cultivar 'Local Juhong', which has historically been used as a traditional Chinese medicinal material, originated in Yuanjiang County, Hunan Province.Its parental type and genetic background are indistinct as of yet. Morphological observation shows that 'Local Juhong' has a slight oblateness in fruit shape, a relatively smooth pericarp, a fine and slightly raised oil vacuole, and an inward concave at the blossom end. The tree form and fruit and leaf morphology of 'Local Juhong' are similar to those of 'Huangpi' sour orange. To reveal the genetic background of 'Local Juhong', 21 citrus accessions were evaluated using nuclear and chloroplast SSR markers and whole-genome SNP information. 'Local Juhong' was grouped with mandarins and sub-grouped with 'Miyagawa Wase' and 'Yanxi Wanlu' in a nuclear SSR analysis, which indicated that its pollen parent might be mandarins. It was closely clustered with orange and pummelo in the chloroplast SSR analysis. The genomic sequence similarity rate of 'Local Juhong' with mandarin and pummelo heterozygosity was 70.88%; the main part was the heterozygosity, except for the unknown (19.66%), mandarin (8.73%), and pummelo (3.9%) parts. Thus, 'Local Juhong' may be an F1 hybrid with pummelo as the female parent and mandarin as the male parent, sharing sisterhood with 'Huangpi' sour orange.
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Affiliation(s)
- Peng Chen
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (P.C.); (J.L.); (T.Z.); (L.G.); (Y.X.)
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
- Yuelushan Laboratory, Changsha 410125, China
| | - Jingbo Liu
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (P.C.); (J.L.); (T.Z.); (L.G.); (Y.X.)
- Yuelushan Laboratory, Changsha 410125, China
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Tie Zhou
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (P.C.); (J.L.); (T.Z.); (L.G.); (Y.X.)
- Yuelushan Laboratory, Changsha 410125, China
| | - Lingxia Guo
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (P.C.); (J.L.); (T.Z.); (L.G.); (Y.X.)
- Yuelushan Laboratory, Changsha 410125, China
| | - Yuanyuan Xu
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (P.C.); (J.L.); (T.Z.); (L.G.); (Y.X.)
- Yuelushan Laboratory, Changsha 410125, China
| | - Lijun Chai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; (L.C.); (Q.X.)
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; (L.C.); (Q.X.)
| | - Ziniu Deng
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Xianxin Li
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (P.C.); (J.L.); (T.Z.); (L.G.); (Y.X.)
- Yuelushan Laboratory, Changsha 410125, China
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Savadi S, Muralidhara BM, Venkataravanappa V, Adiga JD. Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB. FRONTIERS IN PLANT SCIENCE 2023; 14:1242025. [PMID: 37670858 PMCID: PMC10475544 DOI: 10.3389/fpls.2023.1242025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12-<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, "Cashew Microsatellite Database (CMDB)," was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.
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Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur, Karnataka, India
| | - B. M. Muralidhara
- ICAR-Indian Institute of Horticultural Research (IIHR), CHES, Madikeri, Karnataka, India
| | - V. Venkataravanappa
- ICAR-Indian Institute of Horticultural Research (IIHR), CHES, Madikeri, Karnataka, India
| | - J. D. Adiga
- ICAR- Directorate of Cashew Research (DCR), Puttur, Karnataka, India
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Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep 2023; 13:10919. [PMID: 37407627 DOI: 10.1038/s41598-023-37024-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
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Affiliation(s)
- Jagveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- Department of Fruit Science, College of Horticulture & Forestry, Acharya Narendra Deva University of Agricultural & Technology, Kumarganj, 224229, India
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Vishal Sharma
- National Agri-Food Biotechnology Institute, Sector-81, SAS Nagar, Mohali, Punjab, 140308, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173229, India
| | - Popat Nanaso Gaikwad
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurupkar Singh Sidhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Nimarpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Taveena Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - H S Rattanpal
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, 141004, India
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Itoo H, Shah RA, Qurat S, Jeelani A, Khursheed S, Bhat ZA, Mir MA, Rather GH, Zargar SM, Shah MD, Padder BA. Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut ( Juglans regia L.). 3 Biotech 2023; 13:136. [PMID: 37124992 PMCID: PMC10130282 DOI: 10.1007/s13205-023-03563-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03563-6.
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Affiliation(s)
- H. Itoo
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Rafiq Ahmad Shah
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - S. Qurat
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Afnan Jeelani
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Sheikh Khursheed
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Zahoor A. Bhat
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - M. A. Mir
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - G. H. Rather
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - M. D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
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Meena RK, Kashyap P, Shamoon A, Dhyani P, Sharma H, Bhandari MS, Barthwal S, Ginwal HS. Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus. Funct Integr Genomics 2023; 23:103. [PMID: 36973584 DOI: 10.1007/s10142-023-01033-z] [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: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (FST = 0.119), severe inbreeding (FIS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.
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Affiliation(s)
- Rajendra K Meena
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India.
| | - Priyanka Kashyap
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Payal Dhyani
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Hansraj Sharma
- ICFRE - Bamboo & Rattan Centre, Aizawl, 796007, Mizoram, India
- ICFRE-Rain Forest Research Institute, Jorhat, 785001, Assam, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
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Zhao M, Shu G, Hu Y, Cao G, Wang Y. Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding. BMC Genomics 2023; 24:136. [PMID: 36944913 PMCID: PMC10029318 DOI: 10.1186/s12864-023-09156-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Repetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account for only 0.03% of the genome, they have been widely used in maize genetic research and breeding as highly informative codominant DNA markers. The genome-wide distribution and polymorphism of SSRs are not well studied due to the lack of high-quality genome DNA sequence data. RESULTS In this study, using data from high-quality de novo-sequenced maize genomes of five representative maize inbred lines, we revealed that SSRs were more densely present in telomeric region than centromeric region, and were more abundant in genic sequences than intergenic sequences. On genic sequences, tri- and hexanucleotide motifs were more abundant in CDS sequence and some mono- and dinucleotide motifs were more abundant in UTR sequences. Median length and chromosomal density of SSRs were both narrowly range-bound, with median length of 14-18 bp and genome-wide average density of 3355.77 bp/Mbp. LTR-RTs of < 0.4 Mya had higher SSR density (4498-4992 bp/Mbp). The genome-specific and motif-specific SSR polymorphism were studied. Their potential breeding applications were discussed. CONCLUSIONS We found that the median length of SSR sequences of different SSR motifs was nearly constant. SSR density in genic regions was much higher than intergenic regions. In addition, SSR density at LTR-RTs of different evolutionary ages varied in a narrow range. The SSRs and their LTR-RT carriers evolved at an equal rate. All these observations indicated that SSR length and density were under control of yet unknown evolutionary forces. The chromosome region-specific and motif-specific SSR polymorphisms we observed supported the notion that SSR polymorphism was invaluable genome resource for developing highly informative genome and gene markers in maize genetic research and molecular breeding.
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Affiliation(s)
- Meiqi Zhao
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoping Shu
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China
| | - Yanhong Hu
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China
| | - Gangqiang Cao
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yibo Wang
- Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001, China.
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, China.
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, 450001, China.
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Malhotra EV, Jain R, Bansal S, Mali SC, Sharma N, Agrawal A. Development of a new set of genic SSR markers in the genus Gentiana: in silico mining, characterization and validation. 3 Biotech 2021; 11:430. [PMID: 34527507 DOI: 10.1007/s13205-021-02969-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/19/2021] [Indexed: 11/26/2022] Open
Abstract
Gentiana is an important genus of around 360 medicinally important species, majority of which are not well characterized. Despite its importance, very few genomic resources are available for Gentiana L. Till date, the number of informative and robust simple sequence repeat (SSR)-based markers is limited and very few efforts have been made for their development. A set of robust, freely accessible and informative SSR markers for Gentiana is a pre-requisite for any molecular systematic as well as improvement studies in this group of pharmacologically valuable plants. In view of the importance of these plants, Expressed Sequence Tag (EST) sequences of 18 Gentiana species were surveyed for the development of a large set of non-redundant SSR markers. A total of 5808 perfect SSR with an average length of 17 bp and relative abundance of 214 loci/Mb were identified in the analysed 47,487 EST sequences using Krait software. Mapping of the ESTs resulted in gene ontology annotations of 49.14% of the sequences. Based on these perfect SSRs, 2902 primer pairs were designed, and 60 markers were randomly selected and validated on a set of Gentiana kurroo Royle accessions. Among the screened markers, 39 (65%) were found to be cross-species transferable. This is the first report of the largest set of functional, novel genic SSR markers in Gentiana, which will be a valuable resource for future characterization, genotype identification, conservation and genomic studies in the various species of this group of important medicinal plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02969-4.
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Affiliation(s)
- Era Vaidya Malhotra
- Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rishu Jain
- Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sangita Bansal
- Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Suresh Chand Mali
- Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neelam Sharma
- Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Anuradha Agrawal
- Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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citSATdb: Genome-Wide Simple Sequence Repeat (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement. Genes (Basel) 2020; 11:genes11121486. [PMID: 33321957 PMCID: PMC7764524 DOI: 10.3390/genes11121486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 11/17/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are popular co-dominant markers that play an important role in crop improvement. To enhance genomic resources in general horticulture, we identified SSRs in the genomes of eight citrus species and characterized their frequency and distribution in different genomic regions. Citrus is the world's most widely cultivated fruit crop. We have implemented a microsatellite database, citSATdb, having the highest number (~1,296,500) of putative SSR markers from the genus Citrus, represented by eight species. The database is based on a three-tier approach using MySQL, PHP, and Apache. The markers can be searched using multiple search parameters including chromosome/scaffold number(s), motif types, repeat nucleotides (1-6), SSR length, patterns of repeat motifs and chromosome/scaffold location. The cross-species transferability of selected markers can be checked using e-PCR. Further, the markers can be visualized using the Jbrowse feature. These markers can be used for distinctness, uniformity, and stability (DUS) tests of variety identification, marker-assisted selection (MAS), gene discovery, QTL mapping, and germplasm characterization. citSATdb represents a comprehensive source of markers for developing/implementing new approaches for molecular breeding, required to enhance Citrus productivity. The potential polymorphic SSR markers identified by cross-species transferability could be used for genetic diversity and population distinction in other species.
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Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, Sheng O, Mayer C, Yi G, Deng G. Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana. Genes (Basel) 2020; 11:genes11121479. [PMID: 33317074 PMCID: PMC7763637 DOI: 10.3390/genes11121479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
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Affiliation(s)
- Manosh Kumar Biswas
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- Correspondence: (M.K.B.); (G.D.)
| | - Mita Bagchi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- The College of Economics and Managements, South China Agricultural University, Guangzhou 510640, China
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, West Bengal 700064, India;
| | - Jennifer Ann Harikrishna
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yuxuan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany;
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Correspondence: (M.K.B.); (G.D.)
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11
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Spatial Structure and Genetic Variation of a Mangrove Species (Avicennia marina (Forssk.) Vierh) in the Farasan Archipelago. FORESTS 2020. [DOI: 10.3390/f11121287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Avicennia marina (Forssk.) Vierh is distributed in patches along the Farasan archipelago coast and is the most common mangrove species in the Red Sea. However, to date, no studies have been directed towards understanding its genetic variation in the Farasan archipelago. In this investigation, genetic variations within and among natural populations of Avicennia marina in the Farasan archipelago were studied using 15 microsatellite markers. The study found 142 alleles on 15 loci in nine populations. The observed (Ho) and expected (He) heterozygosity values were 0.351 and 0.391, respectively, which are much lower than those of earlier studies on A. marina in the Arabian Gulf. An inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (FST = 0.301) was similar to other mangrove species. Our findings suggest that the sea current direction and coastal geomorphology might affect genetic dispersal of A. marina. The more isolated populations with fewer connections by sea currents exhibited lower genetic variation and differentiation between populations. The genetic clustering of populations fell into three main groups—Group 1 (populations of Farasan Alkabir Island), Group 2 (populations of Sajid Island), and Group 3 (mix of one population of Farasan Alkabir Island and a population of Zifaf Island). More genetic variation and less genetic differentiation occurred when the population was not isolated and had a direct connection with sea currents. Both of these factors contributed to limited propagule dispersal and produced significant structures among the population. It is expected that the results of this research will be useful in determining policy and species-conservation strategies and in the rehabilitation of A. marina mangrove stands on the Farasan islands in an effort to save this significant natural resource.
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12
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Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species. Sci Rep 2020; 10:18621. [PMID: 33122761 PMCID: PMC7596044 DOI: 10.1038/s41598-020-75553-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/05/2020] [Indexed: 01/06/2023] Open
Abstract
Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5'-UTR and 3'-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.
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13
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Biswas MK, Darbar JN, Borrell JS, Bagchi M, Biswas D, Nuraga GW, Demissew S, Wilkin P, Schwarzacher T, Heslop-Harrison JS. The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Sci Rep 2020; 10:15312. [PMID: 32943659 PMCID: PMC7498607 DOI: 10.1038/s41598-020-71984-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/24/2020] [Indexed: 12/25/2022] Open
Abstract
Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79-0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html , downloadable from Figshare).
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Affiliation(s)
- Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - Jaypal N Darbar
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Mita Bagchi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Gizachew Woldesenbet Nuraga
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK. .,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China.
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Manee MM, Al-Shomrani BM, Al-Fageeh MB. Genome-wide characterization of simple sequence repeats in Palmae genomes. Genes Genomics 2020; 42:597-608. [PMID: 32246355 PMCID: PMC7181556 DOI: 10.1007/s13258-020-00924-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/10/2020] [Indexed: 11/17/2022]
Abstract
Background Microsatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars. Objective This is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species. Methods We identified and compared perfect SSRs with 1–6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, Elaeis oleifera, and Elaeis guineensis. Results A total of 118241, 328189, 450753, 176608, and 70694 SSRs were identified, respectively. The six repeat types were not evenly distributed across the five genomes. Mono- and dinucleotide SSRs were the most abundant, and GC content was highest in tri- and hexanucleotide SSRs. Conclusion We envisage that this analysis would further substantiate more in-depth computational, biochemical, and molecular studies on the roles SSRs may play in the genome organization of the palm species. The current study contributes a detailed characterization of simple sequence repeats in palm genomes. Electronic supplementary material The online version of this article (10.1007/s13258-020-00924-w) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manee M Manee
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Center of Excellence for Genomics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Badr M Al-Shomrani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohamed B Al-Fageeh
- National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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15
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Exploration and Exploitation of Novel SSR Markers for Candidate Transcription Factor Genes in Lilium Species. Genes (Basel) 2018; 9:genes9020097. [PMID: 29443955 PMCID: PMC5852593 DOI: 10.3390/genes9020097] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/07/2018] [Accepted: 02/12/2018] [Indexed: 11/29/2022] Open
Abstract
Lilies (Lilium sp.) are commercially important horticultural crops widely cultivated for their flowers and bulbs. Here, we conducted large-scale data mining of the lily transcriptome to develop transcription factor (TF)-associated microsatellite markers (TFSSRs). Among 216,768 unigenes extracted from our sequence data, 6966 unigenes harbored simple sequence repeats (SSRs). Seventy-one SSRs were associated with TF genes, and these were used to design primers and validate their potential as markers. These 71 SSRs were accomplished with 31 transcription factor families; including bHLH, MYB, C2H2, ERF, C3H, NAC, bZIP, and so on. Fourteen highly polymorphic SSRs were selected based on Polymorphic Information Content (PIC) values and used to study genetic diversity and population structure in lily accessions. Higher genetic diversity was observed in Longiflorum compared to Oriental and Asiatic populations. Lily accessions were divided into three sub-populations based in our structure analysis, and an un-rooted neighbor-joining tree effectively separated the accessions according to Asiatic, Oriental, and Longiflorum subgroups. Finally, we showed that 46 of the SSR-associated genes were differentially expressed in response to Botrytis elliptica infection. Thus, our newly developed TFSSR markers represent a powerful tool for large-scale genotyping, high-density and comparative mapping, marker-aided backcrossing, and molecular diversity analysis of Lilium sp.
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16
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Ahmed MM, Shen C, Khan AQ, Wahid MA, Shaban M, Lin Z. A comparative genomics approach revealed evolutionary dynamics of microsatellite imperfection and conservation in genus Gossypium. Hereditas 2017; 154:12. [PMID: 28529469 PMCID: PMC5437633 DOI: 10.1186/s41065-017-0034-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
Background Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood. Results Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites. Moreover, comparative genomics approach aided in exploration of microsatellites conservation footprints in Gossypium evolution. Based on our results, motif imperfection in repeat length was found intricately related to genomic abundance of imperfect microsatellites among 13 genomes. Microsatellite decay estimation depicted slower decay of long motif repeats which led to predominant abundance of 5-nt repeat motif in Gossypium species. Short motif repeats exhibited rapid decay through the evolution of Gossypium lineage ensuing drastic decrease of 2-nt repeats, of which, “AT” motif type dilapidated in cultivated tetraploids of cotton. Conclusion The outcome could be a directive to explore comparative evolutionary footprints of simple non-coding genetic elements i.e., repeat elements, through the evolution of genus-specific characteristics in cotton genomes. Electronic supplementary material The online version of this article (doi:10.1186/s41065-017-0034-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Muhammad Atif Wahid
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
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17
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Filho JAF, de Brito LS, Leão AP, Alves AA, Formighieri EF, Júnior MTS. In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms. Bioinform Biol Insights 2017; 11:1177932217702388. [PMID: 28469420 PMCID: PMC5402704 DOI: 10.1177/1177932217702388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/02/2017] [Indexed: 11/16/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.
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Affiliation(s)
- Jaire Alves Ferreira Filho
- Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.,Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil.,Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | | | | | - Manoel Teixeira Souza Júnior
- Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.,Embrapa Agroenergia, Parque Estação Biológica (PqEB), Brasília, Brazil
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18
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Massaiti Kuboyama Kubota T, Bebeachibuli Magalhães A, Nery da Silva M, Ribeiro Villas Boas P, Novelli VM, Bastianel M, Sagawa CHD, Cristofani-Yaly M, Marcondes Bastos Pereira Milori D. Laser-induced Fluorescence Spectroscopy (LIFS) for Discrimination of Genetically Close Sweet Orange Accessions ( Citrus sinensis L. Osbeck). APPLIED SPECTROSCOPY 2017; 71:203-214. [PMID: 27402688 DOI: 10.1177/0003702816658668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Although there is substantial diversity among cultivated sweet oranges genotypes with respect to morphological, physiological, and agronomic traits, very little variation at DNA level has been observed. It is possible that this low DNA molecular variability is due to a narrow genetic basis commonly observed in this citrus group. The most different morphological characters observed were originated through mutations, which are maintained by vegetative propagation. Despite all molecular tools available for discrimination between these different accessions, in general, low polymorphism has been observed in all groups of sweet oranges and they may not be identified by molecular markers. In this context, this paper describes the results obtained by using laser-induced fluorescent spectroscopy (LIFS) as a tool to discriminate sweet orange accessions ( Citrus sinensis L. Osbeck) including common, low acidity, pigmented, and navel orange groups, with very little variation at DNA level. The findings showed that LIFS combined with statistical methods is capable to discriminate different accessions. The basic idea is that citrus leaves have multiple fluorophores and concentration depends on their genetics and metabolism. Thus, we consider that the optical properties of citrus leaves may be different, depending on variety. The results have shown that the developed method, for the best classification rate, reaches an average sensitivity and specificity of 95% and 97.5%, respectively. An interesting application of this study is the development of an economically viable tool for early identification in seedling certification, in citrus breeding programs, in cultivar protection, or in germplasm core collection.
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Affiliation(s)
- Thiago Massaiti Kuboyama Kubota
- 1 Embrapa Instrumentation, São Carlos, SP, Brazil
- 2 Sao Carlos Institute of Physics, University of Sao Paulo, São Carlos, SP, Brazil
| | | | | | | | - Valdenice M Novelli
- 3 Centro de Citricultura Sylvio Moreira of Instituto Agronômico (CCSM-IAC), Cordeirópolis, SP, Brazil
| | - Marinês Bastianel
- 3 Centro de Citricultura Sylvio Moreira of Instituto Agronômico (CCSM-IAC), Cordeirópolis, SP, Brazil
| | - Cíntia H D Sagawa
- 3 Centro de Citricultura Sylvio Moreira of Instituto Agronômico (CCSM-IAC), Cordeirópolis, SP, Brazil
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Yu M, Yu J, Li H, Wang Y, Yin X, Bo H, Ding H, Zhou Y, Liu Y. Survey and analysis of simple sequence repeats in the Ustilaginoidea virens genome and the development of microsatellite markers. Gene 2016; 585:28-34. [PMID: 26992636 DOI: 10.1016/j.gene.2016.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 11/15/2022]
Abstract
Ustilaginoidea virens is the causal agent of rice false smut, causing quantitative and qualitative losses in rice industry. However, the development and application of simple sequence repeat (SSR) markers for genetic diversity studies in U. virens were limited. This study is the first to perform large-scale development of SSR markers of this pathogen at the genome level, to (1) compare these SSR markers with those of other fungi, (2) analyze the pattern of the SSRs, and (3) obtain more informative genetic markers. U. virens is rich in SSRs, and 13,778 SSRs were identified with a relative abundance of 349.7SSRs/Mb. The most common motifs in the genome or in noncoding regions were mononucleotides, whereas trinucleotides in coding sequences. A total of 6 out of 127 primers were randomly selected to be used to analyze 115 isolates, and these 6 primers showed high polymorphism in U. virens. This study may serve as an important resource for molecular genetic studies in U. virens.
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Affiliation(s)
- Mina Yu
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Junjie Yu
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Huanhuan Li
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Yahui Wang
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Xiaole Yin
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Huiwen Bo
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Life Sciences College of Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Ding
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Life Sciences College of Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Zhou
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Yongfeng Liu
- Institute of Plant protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Science, Nanjing 210014, China.
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20
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Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0141540. [PMID: 26536014 PMCID: PMC4633229 DOI: 10.1371/journal.pone.0141540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/10/2015] [Indexed: 12/12/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
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Affiliation(s)
- Bin Han
- College of Bio-engineering, Shanxi University, Taiyuan, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Zhaohui Tang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Yongkang Ren
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yali Li
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Yanhui Dong
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xinghua Zhao
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
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Biswas MK, Liu Y, Li C, Sheng O, Mayer C, Yi G. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential. PLoS One 2015; 10:e0131312. [PMID: 26121637 PMCID: PMC4488140 DOI: 10.1371/journal.pone.0131312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/01/2015] [Indexed: 01/14/2023] Open
Abstract
The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.
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Affiliation(s)
- Manosh Kumar Biswas
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- The College of Life Science, South China Agricultural University, Guangzhou, China
| | - Yuxuan Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyu Li
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Ou Sheng
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany
| | - Ganjun Yi
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
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22
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Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0141540. [PMID: 26536014 DOI: 10.1371/journal.pone.0141540.t006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/10/2015] [Indexed: 05/21/2023] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
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Affiliation(s)
- Bin Han
- College of Bio-engineering, Shanxi University, Taiyuan, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Zhaohui Tang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yongkang Ren
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yali Li
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yanhui Dong
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xinghua Zhao
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
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