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Tam NT, Nhan DK. Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:358. [PMID: 38785840 PMCID: PMC11117668 DOI: 10.3390/biology13050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.
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Affiliation(s)
- Nguyen Thanh Tam
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
| | - Dang Kieu Nhan
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
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Sathapondecha P, Suksri P, Nuanpirom J, Nakkanong K, Nualsri C, Whankaew S. Development of Gene-Based InDel Markers on Putative Drought Stress-Responsive Genes and Genetic Diversity of Durian (Durio zibethinus). Biochem Genet 2024:10.1007/s10528-023-10638-9. [PMID: 38306004 DOI: 10.1007/s10528-023-10638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024]
Abstract
Insertion-deletion (InDel) markers are co-dominant, relatively abundant and practical for agarose gel genotyping. InDel polymorphism usually affects gene functions. Nucleotide sequences of durian (Durio zibethinus) are available, but InDel makers have not been well established. This study aimed to develop drought-related gene-based InDel markers for durian through bioinformatic analysis of RNA-Seq datasets. The polymorphism of the markers was verified in 24 durian genotypes local to Thailand. Bioinformatic analysis indicated 496 InDel loci having lengths more than 9 bp. To evaluate these InDel markers, 15 InDel loci were selected. Nine markers were successfully amplified a clear polymorphic band pattern on 2% agarose gel. The polymorphic information content (PIC) of these nine markers ranged from 0.1103 to 0.5808. The genetic distance between the 24 genotypes ranged from 0.222 to 0.889. The phylogeny based on the nine InDel loci distinguished the 24 genotypes and divided samples into four groups. This set of gene-based InDel markers on putative drought-responsive genes will be useful for genetic studies.
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Affiliation(s)
- Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Phassorn Suksri
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jiratchaya Nuanpirom
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Korakot Nakkanong
- Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Charassri Nualsri
- Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Sukhuman Whankaew
- Department of Plant Science, Faculty of Technology and Community Development, Thaksin University, Phatthalung Campus, Phatthalung, 93210, Thailand.
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Fan K, Qin Y, Hu X, Xu J, Ye Q, Zhang C, Ding Y, Li G, Chen Y, Liu J, Wang P, Hu Z, Yan X, Xiong H, Liu H, Qin R. Identification of genes associated with fatty acid biosynthesis based on 214 safflower core germplasm. BMC Genomics 2023; 24:763. [PMID: 38082219 PMCID: PMC10712096 DOI: 10.1186/s12864-023-09874-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Safflower (Carthamus tinctorius L.) is an oilseed crop with substantial medicinal and economic value. However, the methods for constructing safflower core germplasm resources are limited, and the molecular mechanisms of lipid biosynthesis in safflower seeds are not well understood. RESULTS In this study, 11 oil-related quantitative traits and 50 pairs of InDel markers were used to assess the diversity of a collection of 605 safflower germplasms. The original safflower germplasm exhibited rich phenotypic diversity, with high variation for most of the phenotypic traits under investigation. Similarly, high genetic diversity was evaluated in the original germplasm, in which the mean Shannon's information index (I), observed heterozygosity (H0), and expected heterozygosity (He) were 0.553, 0.182, and 0.374, respectively. Four subgroups with strong genetic structures were identified and a core germplasm of 214 cultivars was constructed, which is well represented in the original germplasm. Meanwhile, differential expression analysis of the transcriptomes of high and low linoleic acid safflower varieties at two stages of seed development identified a total of 47 genes associated with lipid biosynthesis. High expression of the genes KAS II and SAD enhanced the synthesis and accumulation of oleic acid, while FAD genes like FAD2 (Chr8G0104100), FAD3, FAD7 and FAD8 promoted the consumption of oleic acid conversion. The coordinated regulation of these multiple genes ensures the high accumulation of oleic acid in safflower seed oil. CONCLUSIONS Based on these findings, a core germplasm of 214 cultivars was constructed and 47 candidate genes related to unsaturated fatty acid biosynthesis and lipid accumulation were identified. These results not only provide guidance for further studies to elucidate the molecular basis of oil lipid accumulation in safflower seeds, but also contribute to safflower cultivar improvements.
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Affiliation(s)
- Kangjun Fan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Yonghua Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Xueli Hu
- Industrial Crop Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Qingzhi Ye
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Chengyang Zhang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Yangyang Ding
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Gang Li
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Yan Chen
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Peiqi Wang
- Industrial Crop Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Zunhong Hu
- Industrial Crop Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xingchu Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Hairong Xiong
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China.
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Xu X, Chen B, Zhang J, Lan S, Wu S. Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides. PeerJ 2023; 11:e16056. [PMID: 37744244 PMCID: PMC10512932 DOI: 10.7717/peerj.16056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Background Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.
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Affiliation(s)
- Xinyu Xu
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China
- College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Bihua Chen
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China
| | - Juan Zhang
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, China
| | - Siren Lan
- College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shasha Wu
- College of Landscape and Architecture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Chattopadhyay T, Sangam S, Akhtar S. Rapid genotyping in tomato by VPCR using agarose gel-resolvable InDel markers. 3 Biotech 2023; 13:85. [PMID: 36816752 PMCID: PMC9929007 DOI: 10.1007/s13205-023-03499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Insertion/deletion (InDel) markers are second most abundant polymerase chain reaction (PCR)-based molecular markers having enormous applications in genotyping and molecular breeding in different crops. Although standard polymerase chain reaction (PCR) for DNA amplification generally takes ~ 1.5 to 2 h, small amplicons can be effectively generated using dynamic heating and cooling through PCR with "V"-shaped thermal profile (VPCR) in ~ 15 to 20 min. Here, we evaluated the applicability of a partly modified VPCR method for amplifying InDels of tomato genome. Out of the 31 InDel markers tested in 15 diverse tomato genotypes, 29 markers resulted in sharp amplicons, where 26 markers were found to be polymorphic. Using this method, the individual DNA amplification reactions could be completed within ~ 30 min. The method was effective for primers varying in melting temperature (T m) and GC contents. Furthermore, the need for empirically determining suitable annealing temperature could be bypassed using this generalised thermal profile. Through our results, we advocate the use of this method of DNA amplification in other plants to achieve rapid genotyping using standard molecular biology equipments and procedures. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03499-x.
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Affiliation(s)
- Tirthartha Chattopadhyay
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Surabhi Sangam
- Department of Horticulture (Vegetable and Floriculture), Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
| | - Shirin Akhtar
- Department of Horticulture (Vegetable and Floriculture), Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210 India
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Kim JY, Hwang JE, Eo SH, Kang SG, Moon JC, Kim JA, Park JY, An J, Yeo Y, Yoon J. Development of InDel markers for interspecific hybridization between hill pigeons and feral pigeons based on whole-genome re-sequencing. Sci Rep 2022; 12:22618. [PMID: 36585442 PMCID: PMC9803650 DOI: 10.1038/s41598-022-27147-1] [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: 09/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Interspecific hybridization occurs among birds, and closely related sister taxa tend to hybridize at a high rate. Genomic hybridization markers are useful for understanding the patterns and processes of hybridization and for conserving endangered species in captivity and the wild. In this study, we developed genomic hybridization markers for the F1 progeny of the sister taxa feral pigeons (Columba livia var. domestica) and endangered hill pigeons (Columba rupestris) (family Columbidae). Using whole-genome re-sequencing data, we performed genome-wide analysis for insertion/deletion (InDel) polymorphisms and validated using primers. We conducted polymerase chain reaction (PCR) and agarose gel electrophoresis to identify species-specific InDels. We produced eight F1 hybrids of hill and feral pigeons, and their samples were tested by re-performing analyses and sequencing using 11 species-specific InDel polymorphisms. Eight InDel markers simultaneously amplified two DNA fragments from all F1 hybrids, and there was no abnormality in the sequencing results. The application of genomic tools to detect hybrids can play a crucial role in the assessment of hybridization frequency in the wild. Moreover, systematic captive propagation efforts with hybrids can help control the population decline of hill pigeons.
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Affiliation(s)
- Jin-Yong Kim
- grid.496435.90000 0004 6015 2014Research Center for Endangered Species, National Institute of Ecology, Yeongyang, South Korea
| | - Jung Eun Hwang
- grid.496435.90000 0004 6015 2014Research Center for Endangered Species, National Institute of Ecology, Yeongyang, South Korea
| | - Soo Hyung Eo
- grid.411118.c0000 0004 0647 1065Department of Forest Science, Kongju National University, Yesan, Chungnam, South Korea
| | - Seung-Gu Kang
- grid.496435.90000 0004 6015 2014Research Center for Endangered Species, National Institute of Ecology, Yeongyang, South Korea
| | - Jeong Chan Moon
- grid.496435.90000 0004 6015 2014Research Center for Endangered Species, National Institute of Ecology, Yeongyang, South Korea
| | - Jung A Kim
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, Incheon, South Korea
| | - Jin-Young Park
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, Incheon, South Korea
| | - Junghwa An
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, Incheon, South Korea
| | - Yonggu Yeo
- Conservation and Health Center, Seoul Zoo, Gwacheon, South Korea
| | - Jongmin Yoon
- grid.496435.90000 0004 6015 2014Research Center for Endangered Species, National Institute of Ecology, Yeongyang, South Korea
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Kawasaki E, Wenjing D, Sawada A, Nakajima M, Momose K, Yoshino T, Amano T, Endoh D, Nakajima N, Teraoka H. Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan. Animals (Basel) 2022; 12:ani12172293. [PMID: 36078013 PMCID: PMC9455020 DOI: 10.3390/ani12172293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.
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Affiliation(s)
- Erika Kawasaki
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Dong Wenjing
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Akira Sawada
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Momoko Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | | | | | - Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
- NPO Red-Crowned Crane Conservancy, Kushiro 085-0036, Japan
- Correspondence:
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Li H, Ikram M, Xia Y, Li R, Yuan Q, Zhao W, Siddique KHM, Guo P. Genome-wide identification and development of InDel markers in tobacco ( Nicotiana tabacum L.) using RAD-seq. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1077-1089. [PMID: 35722506 PMCID: PMC9203652 DOI: 10.1007/s12298-022-01187-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 05/03/2023]
Abstract
Insertions and deletions (InDels) can be used as molecular markers in genetic studies and marker-assisted selection breeding. However, genetic improvement in tobacco has been hindered by limited genetic diversity information and relatedness within available germplasm. A Chinese tobacco variety, Yueyan-98, was resequenced using restriction-site associated DNA (RAD-seq) approach to develop InDel markers. In total, 32,884 InDel loci were detected between Yueyan-98 and the K326 reference sequence [18,598 (56.55%) deletions and 14,288 (43.45%) insertions], ranging from 1 to 62 bp in length. Of the 6,733 InDels (> 4 bp) that were suitable for polyacrylamide gel electrophoresis, 150 were randomly selected. These 150 InDels were unevenly distributed on 23 chromosomes, and the highest numbers of InDels were observed on chromosomes Nt05, Nt13, and Nt23. The average density of adjacent InDels was 19.36 Mb. Thirty-seven InDels were located in genic regions. Polymerase chain reaction (PCR)-based markers were developed to validate polymorphism; 113 (79.80%) of the 150 InDel markers showed polymorphism and were further used for genetic diversity analysis of 50 tobacco accessions (13 from China, 1 from Mexico, and 36 from the USA). The average expected heterozygosity (He) and polymorphism information content (PIC) values were 0.28 ± 0.16 and 0.38 ± 0.10, respectively. The average Shannon diversity index (I) was 0.34 ± 0.18, with genetic diversity ranging from 0.13-0.57. The 50 accessions were classified into two groups with a genetic similarity coefficient of 0.68. Principal coordinate analysis (PCoA) and population structure analysis showed similar results and divided the population into two groups unrelated to their geographical origins. AMOVA showed 4% variance among the population and the remaining 96% within the population, suggesting low genetic differentiation between two subpopulations. Furthermore, 10 InDels (19 alleles) were significantly identified for tobacco plant height using GLM+Q model at P < 0.005. Among these, three markers (Nt-I-26, Nt-I-41, and Nt-I-44) were detected in at least two environments, with phenotypic variance explained (PVE) ranging from 14.03 to 32.68%. The polymorphic InDel markers developed can be used for hybrid identification, genetic diversity, genetic linkage map construction, gene mapping, and MAS breeding programs of tobacco. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01187-3.
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Affiliation(s)
- Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Muhammad Ikram
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yanshi Xia
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Ronghua Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Qinghua Yuan
- Guangdong Provincial Engineering & Technology Research Center for Tobacco Breeding and Comprehensive Utilization, Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, 510640 China
| | - Weicai Zhao
- Nanxiong Research Institutes of Guangdong Tobacco Co. Ltd, Nanxiong, 512400 China
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001 Australia
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
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Yang Y, Zhang X, Lei Y, Chang G, Zou Y, Yu S, Wu H, Rong H, Lei Z, Xu C. The effects of H22 tumor on the quality of oocytes and the development of early embryos from host mice: A single-cell RNA sequencing approach. Theriogenology 2022; 179:45-59. [PMID: 34826707 DOI: 10.1016/j.theriogenology.2021.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/30/2021] [Accepted: 11/13/2021] [Indexed: 10/19/2022]
Abstract
The association between cancer and female reproduction remains largely unknown. Here we investigated the quality of oocytes and the developmental potential of zygotes using H22 tumor-bearing mice model. The results showed that the number of oocytes was decreased in tumor-bearing mice compared with the control mice, and accompanied scattered chromosomes was observed. Further study revealed an abnormal epigenetic reprogramming occurred in the zygotes from the H22 tumor-bearing mice, as exemplified by the aberrant 5hmC/5mC modifications in the pronuclei. Finally, single-cell RNA sequencing was performed on the oocytes collected from the H22 tumor-bearing mice. Our data showed that 45 of the 202 differentially expressed genes in tumor-bearing group were closely associated with oocyte quality. Protein interaction analysis indicated that the potential interaction among these 45 genes. Collectively, our study uncovered that the quality of oocytes and early embryonic development were affected by H22 tumor bearing via the altered expression patterns of genes related with reproduction, providing new insights into the reproductive capability of female cancer patients.
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Affiliation(s)
- Yanhong Yang
- The First Affiliated Hospital (School of Clinical Medicine), Guangdong Pharmaceutical University, Nong-Lin-Xia Road 19#, Yue-Xiu District, Guangzhou, 510080, PR China
| | - Xueying Zhang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou, 510006, PR China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, PR China
| | - Yuting Lei
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou, 510006, PR China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, PR China
| | - Yan Zou
- The Reproductive Medical Center of Nanning Second People's Hospital, Nanning, 530031, PR China
| | - Siping Yu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou, 510006, PR China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, PR China
| | - Huijuan Wu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou, 510006, PR China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, PR China
| | - Hedong Rong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou, 510006, PR China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, PR China
| | - Zili Lei
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangzhou, 510006, PR China.
| | - Changlong Xu
- The Reproductive Medical Center of Nanning Second People's Hospital, Nanning, 530031, PR China.
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