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Guo M, Deng L, Gu J, Miao J, Yin J, Li Y, Fang Y, Huang B, Sun Z, Qi F, Dong W, Lu Z, Li S, Hu J, Zhang X, Ren L. Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.). BMC Plant Biol 2024; 24:244. [PMID: 38575936 PMCID: PMC10996145 DOI: 10.1186/s12870-024-04937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND This study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS). RESULTS The nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64-32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis. CONCLUSIONS Overall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.
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Affiliation(s)
- Minjie Guo
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Li Deng
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianzhong Gu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianli Miao
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junhua Yin
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yang Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yuanjin Fang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Bingyan Huang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ziqi Sun
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Feiyan Qi
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhenhua Lu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Shaowei Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junping Hu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Xinyou Zhang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Ren
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China.
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Chen S, Sun M, Xu S, Xue C, Wei S, Zheng P, Gu K, Qiao Z, Liu Z, Zhang M, Wu J. The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp. BMC Plant Biol 2023; 23:430. [PMID: 37710163 PMCID: PMC10503127 DOI: 10.1186/s12870-023-04406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data. DESCRIPTION Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services. CONCLUSIONS The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.
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Affiliation(s)
- Shulin Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Manyi Sun
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaozhuo Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Cheng Xue
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Shuwei Wei
- Shandong Institute of Pomology, Tai'an, 271000, China
| | - Pengfei Zheng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwen Qiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Mingyue Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Jun Wu
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Tian R, Kong Y, Shao Z, Zhang H, Li X, Zhang C. Discovery of genetic loci and causal genes for seed germination via deep re-sequencing in soybean. Mol Breed 2022; 42:45. [PMID: 37313514 PMCID: PMC10248669 DOI: 10.1007/s11032-022-01316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
High seed germination is crucial for mechanical sowing, seedling establishment, growth potential, multiple resistances, and the formation of yield and quality. However, few genetic loci and candidate genes conferring seed germination were explored in soybean at present. In view of this, a natural population containing 199 accessions was assessed for the germination potential (GP) and germination rate (GR) and also was re-sequenced at the average sequencing depth of 18.4 × for each accession. In total, 5,665,469 SNPs were obtained for association analysis, and 470 SNPs in 55 loci on 18 chromosomes were identified to associate with seed germination. Of them, 85 SNPs on chromosomes 1, 10, and 14 were associated with mean value and BLUP value for GP and GR, simultaneously. Moreover, 324 SNPs (68.9% of the total) in four loci were located on chromosome 14 for seed germination, of which 11 SNPs were located in the exons, 30 in introns, 17 in 5'UTR or 3'UTR, and 46 in upstream or downstream. Based on these, 131 candidate genes flanking the associated SNPs were analyzed for gene annotation, SNP mutation, and RNA expression, and three causal genes, Glyma.14G069800 (RNA-binding protein), Glyma.14G071400 (bZIP transcription factor), and Glyma.17G033200 (nucleic acid-binding protein), were screened out and might be responsible for the seed germination. The closely associated SNPs and causal genes provided an important resource and dissecting of genetic basis for seed germination improvement in soybean. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01316-6.
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Affiliation(s)
- Rui Tian
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071000 Hebei Province China
| | - Youbin Kong
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071000 Hebei Province China
| | - Zhenqi Shao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071000 Hebei Province China
| | - Hua Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071000 Hebei Province China
| | - Xihuan Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071000 Hebei Province China
| | - Caiying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Lekai South Street 2596, Baoding City, 071000 Hebei Province China
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Zhou P, Huang H, Lu J, Zhu Z, Xie J, Xia L, Luo S, Zhou K, Chen W, Ding X. The mutated Bacillus amyloliquefaciens strain shows high resistance to Aeromonas hydrophila and Aeromonas veronii in grass carp. Microbiol Res 2021; 250:126801. [PMID: 34139525 DOI: 10.1016/j.micres.2021.126801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
Bacillus amyloliquefaciens X030 (BaX030) has broad-spectrum antibacterial activity against the fish pathogens Aeromonas hydrophila and Aeromonas veronii. To improve its antibacterial effect, BaX030 was subjected to compound mutagenesis of atmospheric and room temperature plasma (ARTP) and nitrosoguanidine (NTG). The results showed that, compared with the original strain, the production of macrolactin A and oxydifficidin in mutated strain N-11 increased to 39 % and 268 %, respectively. The re-sequencing analysis suggested that there were SNPs and InDels in the gene clusters focused on the sucrose utilization pathway, glycolysis pathway and fatty acid synthesis pathway. Scanning electron microscopy revealed that strain N-11 became thin and long. The qRT-PCR results indicated that the expression of immune factors in the liver or kidney tissue of grass carp increased after feeding with N-11. H&E staining and protection experiments also showed that the mortality and surface symptoms of grass carp infected by the two pathogens were significantly reduced. The study identified a probiotic strain with potential application value in aquaculture production and provided a new strategy for the discovery of new strains with higher antibacterial biological activity.
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Affiliation(s)
- Pengji Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Haiyan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Jiaoyang Lu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Zirong Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Junyan Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Sisi Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Kexuan Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Wenhui Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Zhang Z, Qiu M, Du H, Li Q, Yu C, Gan W, Peng H, Xia B, Xiong X, Song X, Yang L, Hu C, Chen J, Yang C, Jiang X. Whole genome re-sequencing identifies unique adaption of single nucleotide polymorphism, insertion/deletion and structure variation related to hypoxia in Tibetan chickens. Gene Expr Patterns 2021; 40:119181. [PMID: 34004346 DOI: 10.1016/j.gep.2021.119181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/25/2021] [Accepted: 04/25/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a biological model to search for genetic diversity of hypoxia adaption. METHODS The whole genome re-sequencing technology was conducted to investigate the genetic diversity. RESULTS In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including HIF1A, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF signaling pathway, MAPK signaling pathway, PPAR signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs. CONCLUSIONS This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands.
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Affiliation(s)
- Zengrong Zhang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China; Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, 610066, China
| | - Mohan Qiu
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Huarui Du
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Qingyun Li
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Chunlin Yu
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Wu Gan
- Shanghai Ying Biotechnology Company, Shanghai, China
| | - Han Peng
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Bo Xia
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Xia Xiong
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Xiaoyan Song
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Li Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Chenming Hu
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Jialei Chen
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China.
| | - Xiaosong Jiang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China; Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, 610066, China.
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Zhao H, Guo T, Lu Z, Liu J, Zhu S, Qiao G, Han M, Yuan C, Wang T, Li F, Zhang Y, Hou F, Yue Y, Yang B. Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep. BMC Genomics 2021; 22:127. [PMID: 33602144 PMCID: PMC7893944 DOI: 10.1186/s12864-021-07399-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. RESULTS A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). CONCLUSION This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.
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Affiliation(s)
- Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Guoyan Qiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Mei Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
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Gibson SJ, Zahra N, Freeman PJ, Howard C, Lancaster O, Veal C, Fontdevila MC, Paredes R, Noguera-Julian M, Slater A, Brookes AJ. Array-based dynamic allele specific hybridization (Array-DASH): Optimization-free microarray processing for multiple simultaneous genomic assays. Anal Biochem 2021; 626:114124. [PMID: 33607059 DOI: 10.1016/j.ab.2021.114124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
We report proof-of-principle experiments regarding a dynamic microarray protocol enabling accurate and semi-quantitative DNA analysis for re-sequencing, fingerprinting and genotyping. Single-stranded target molecules hybridise to surface-bound probes during initial gradual cooling with high-fidelity. Real-time tracking of target denaturation (via fluorescence) during a 'dynamic' gradual heating phase permits 'melt-curve' analysis. The probe most closely matching the target sequence is identified based on the highest melting temperature. We demonstrated a >99% re-sequencing accuracy and a potential detection rate of 1% for SNPs. Experiments employing Hypericum ribosomal ITS regions and HIV genomes illustrated a reliable detection level of 5% plus simultaneous re-sequencing and genotyping. Such performance suggests a range of potential real-world applications involving rapid sequence interrogation, for example, in the Covid-19 pandemic. Guidance is offered towards the development of a commercial platform and dedicated software required to bring this technique into mainstream science.
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Affiliation(s)
- Spencer J Gibson
- Department of Genetics, Adrian Building, University of Leicester, University Road, Leicester, Leicestershire, LE17RH, UK
| | - Nathalie Zahra
- Anglia Ruskin University, Department of Biomedical and Forensic Science, SCI004, East Road, Cambridge, CB1 1PT, UK
| | - Peter J Freeman
- Division of Informatics, Imaging & Data Science, Faculty of Biology, Medicine and Health, The University of Manchester, G.725, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - Caroline Howard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Owen Lancaster
- Department of Genetics, Adrian Building, University of Leicester, University Road, Leicester, Leicestershire, LE17RH, UK
| | - Colin Veal
- Department of Genetics, Adrian Building, University of Leicester, University Road, Leicester, Leicestershire, LE17RH, UK
| | - Maria Casadellà Fontdevila
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Crta. de Canyet s/n, Planta 2a, 08916, Badalona, Catalonia, Spain
| | - Roger Paredes
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Crta. de Canyet s/n, Planta 2a, 08916, Badalona, Catalonia, Spain
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Crta. de Canyet s/n, Planta 2a, 08916, Badalona, Catalonia, Spain
| | - Adrian Slater
- Biomolecular Technology Group, School of Allied Health Sciences, De Montfort University, Hawthorn Building HB1.12, The Gateway, Leicester, Leicestershire, LE19BH, UK
| | - Anthony J Brookes
- Department of Genetics, Adrian Building, University of Leicester, University Road, Leicester, Leicestershire, LE17RH, UK.
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Liu Y, Wang H, Li S, Zhang Y, Cheng X, Xiang W, Wang X. Engineering of primary metabolic pathways for titer improvement of milbemycins in Streptomyces bingchenggensis. Appl Microbiol Biotechnol 2021; 105:1875-1887. [PMID: 33564920 DOI: 10.1007/s00253-021-11164-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022]
Abstract
Milbemycins are used commercially as insect repellents and acaricides; however, their high cost remains a significant challenge to commercial production. Hence, improving the titer of milbemycins for commercial application is an urgent priority. The present study aimed to effectively increase the titer of milbemycins using a combination of genome re-sequencing and metabolic engineering. First, 133 mutation sites were identified by genome re-sequencing in the mutagenized high-yielding strain BC04. Among them, three modifiable candidate genes (sbi_04868 encoding citrate synthase, sbi_06921 and sbi_06922 encoding alpha and beta subunits of acetyl-CoA carboxylase, and sbi_04683 encoding carbon uptake system gluconate transporter) related to primary metabolism were screened and identified. Next, the DNase-deactivated Cpf1-based integrative CRISPRi system was used in S. bingchenggensis to downregulate the transcription level of gene sbi_04868. Then, overexpression of the potential targets sbi_06921-06922 and sbi_04683 further facilitated milbemycin biosynthesis. Finally, those candidate genes were engineered to produce strains with combinatorial downregulation and overexpression, which resulted in the titer of milbemycin A3/A4 increased by 27.6% to 3164.5 mg/L. Our research not only identified three genes in S. bingchenggensis that are closely related to the production of milbemycins, but also offered an efficient engineering strategy to improve the titer of milbemycins using genome re-sequencing. KEY POINTS: • We compared the genomes of two strains with different titers of milbemycins. • We found three genes belonging to primary metabolism influence milbemycin production. • We improved titer of milbemycins by a combinatorial engineering of three targets.
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Affiliation(s)
- Yuqing Liu
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Haiyan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yanyan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xu Cheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Wensheng Xiang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China.
| | - Xiangjing Wang
- School of Life Science, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, China.
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Cheon KS, Won YJ, Jeong YM, Lee YY, Kang DY, Oh J, Oh H, Kim SL, Kim N, Lee E, Yoon IS, Choi I, Baek J, Kim KH, Park HS, Ji H. QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing. Mol Genet Genomics 2020; 295:1129-1140. [PMID: 32458040 PMCID: PMC7391406 DOI: 10.1007/s00438-020-01688-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/11/2020] [Indexed: 11/29/2022]
Abstract
Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions—field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3FD and qPHS-11FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3GH, qPHS-4GH, and qPHS-11GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11GH and qPHS-11FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.
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Affiliation(s)
- Kyeong-Seong Cheon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Yong Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon, 24010, South Korea
| | - Young-Min Jeong
- Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje, 54324, South Korea
| | - Youn-Young Lee
- Seed Industry Promotion Center, Foundation of Agri. Tech. Commercialization & Transfer (FACT), Gimje, 54324, South Korea
| | - Do-Yu Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Jun Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Nyunhee Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Eungyeong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - In Sun Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Inchan Choi
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju, 54874, South Korea.
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Seong HS, Kim NY, Kim DC, Hwang NH, Son DH, Shin JS, Lee JH, Chung WH, Choi JW. Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse. Genes Genomics 2019; 41:621-628. [PMID: 30941726 DOI: 10.1007/s13258-019-00795-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 02/11/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds. OBJECTIVE The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse). RESULTS Using the equine reference genome assembly (EquCab 2.0), more than ~ 6.5 billion sequence reads were successfully mapped, which generated an average of 40.87-fold coverage throughout the genome. Using these data, we detected a total of 12.88 million SNPs, of which 73.7% were found to be novel. All the detected SNPs were deeply annotated to retrieve SNPs in gene regions using the RefSeq and Ensemble gene sets. Approximately 27% of the total SNPs were located within genes, whereas the remaining 73% were found in intergenic regions. Using 129,776 coding SNPs, we retrieved a total of 49,171 nonsynonymous SNPs in 12,351 genes. Furthermore, we identified a total of 10,770 deleterious nonsynonymous SNPs which are predicted to affect protein structure or function. CONCLUSION We showed numerous genomic variants from domestic and wild horse breeds. These results provide a valuable resource for further studies on functions of SNP-containing genes, and can aid in determining the molecular basis underlying variation in economically important traits of horses.
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Affiliation(s)
- Ha-Seung Seong
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Nam-Young Kim
- Subtropical Animal Research Institute, National Institute of Animal Science, RDA, Jeju, 690-150, Republic of Korea
| | - Dae Cheol Kim
- Jeju Special Self-Governing Province Livestock Promotion, Jeju, Republic of Korea
| | - Nam-Hyun Hwang
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Da-Hye Son
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jong Suh Shin
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Joon-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Won-Hyong Chung
- Division of Food Functionality Research, Research Group of Healthcare, Wanju-gun, 55365, Republic of Korea.
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Subbaiyan GK, Masouleh AK, Furtado A, Waters DLE, Henry RJ. Re-sequencing Resources to Improve Starch and Grain Quality in Rice. Methods Mol Biol 2019; 1892:201-40. [PMID: 30397808 DOI: 10.1007/978-1-4939-8914-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.
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Wang H, Lee AR, Park SY, Jin SH, Lee J, Ham TH, Park Y, Zhao WG, Kwon SW. Genome-wide association study reveals candidate genes related to low temperature tolerance in rice ( Oryza sativa) during germination. 3 Biotech 2018; 8:235. [PMID: 29725574 DOI: 10.1007/s13205-018-1252-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/23/2018] [Indexed: 01/05/2023] Open
Abstract
In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.
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Affiliation(s)
- Heng Wang
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Ah-Rim Lee
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - So-Yeon Park
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Sang-Hyeon Jin
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Joohyun Lee
- 2Department of Applied Bioscience, Konkuk University, Seoul, 05029 Republic of Korea
| | - Tae-Ho Ham
- 2Department of Applied Bioscience, Konkuk University, Seoul, 05029 Republic of Korea
- 3Department of Agricultural Science, Korea National Open University, Seoul, 03087 Republic of Korea
| | - Yongjin Park
- 4Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439 Republic of Korea
| | - Wei-Guo Zhao
- 5School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212018 Jiangsu People's Republic of China
| | - Soon-Wook Kwon
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
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Ye S, Yuan X, Lin X, Gao N, Luo Y, Chen Z, Li J, Zhang X, Zhang Z. Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population. J Anim Sci Biotechnol 2018; 9:30. [PMID: 29581880 PMCID: PMC5861640 DOI: 10.1186/s40104-018-0241-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 01/26/2018] [Indexed: 11/24/2022] Open
Abstract
Background Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence (WGS) data. However, sequencing thousands of individuals of interest is expensive. Imputation from SNP panels to WGS data is an attractive and less expensive approach to obtain WGS data. The aims of this study were to investigate the accuracy of imputation and to provide insight into the design and execution of genotype imputation. Results We genotyped 450 chickens with a 600 K SNP array, and sequenced 24 key individuals by whole genome re-sequencing. Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. By increasing the sequencing cost from 24X to 144X, the imputation accuracy increased from 0.525 to 0.698 for Beagle and from 0.654 to 0.823 for FImpute. With fixed sequence depth (12X), increasing the number of sequenced animals from 1 to 24, improved accuracy from 0.421 to 0.897 for FImpute and from 0.396 to 0.777 for Beagle. Using optimally selected key individuals resulted in a higher imputation accuracy compared with using randomly selected individuals as a reference population for re-sequencing. With fixed reference population size (24), imputation accuracy increased from 0.654 to 0.875 for FImpute and from 0.512 to 0.762 for Beagle as the sequencing depth increased from 1X to 12X. With a given total cost of genotyping, accuracy increased with the size of the reference population for FImpute, but the pattern was not valid for Beagle, which showed the highest accuracy at six fold coverage for the scenarios used in this study. Conclusions In conclusion, we comprehensively investigated the impacts of several key factors on genotype imputation. Generally, increasing sequencing cost gave a higher imputation accuracy. But with a fixed sequencing cost, the optimal imputation enhance the performance of WGP and GWAS. An optimal imputation strategy should take size of reference population, imputation algorithms, marker density, and population structure of the target population and methods to select key individuals into consideration comprehensively. This work sheds additional light on how to design and execute genotype imputation for livestock populations. Electronic supplementary material The online version of this article (10.1186/s40104-018-0241-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shaopan Ye
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Xiaolong Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Xiran Lin
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Ning Gao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Yuanyu Luo
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Zanmou Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Xiquan Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong China
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Boonvisut S, Yoshida K, Nakayama K, Watanabe K, Miyashita H, Iwamoto S. Identification of deleterious rare variants in MTTP, PNPLA3, and TM6SF2 in Japanese males and association studies with NAFLD. Lipids Health Dis 2017; 16:183. [PMID: 28950858 PMCID: PMC5615465 DOI: 10.1186/s12944-017-0570-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 09/18/2017] [Indexed: 02/07/2023] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes without excessive alcohol intake. NAFLD is influenced by genetic factors, and the heritability has been estimated at 0.35 to 0.6 by twin studies. We explored rare variants in known NAFLD-associated genes to investigate whether these rare variants are involved in the susceptibility to NAFLD. Methods The target genes for re-sequencing were PNPLA3, TM6SF2, and MTTP. All exons of these three genes were amplified from a discovery panel of 950 Japanese males, and the identified rare variants were further tested for genetic association in 3014 individuals from the Japanese general population and for in vitro functional evaluation. Results Target re-sequencing analysis using next-generation sequencing identified 29 rare variants in 65 Japanese males (6.84%), 12 of which were newly identified base substitutions. A splicing mutation in TM6SF2 that resulted in deletion of 31 amino acids was identified in an NAFLD case. Among eight genotyped rare single-nucleotide polymorphisms (SNPs; minor allele frequency < 0.02), rs143392071 (Tyr220Cys, PNPLA3) significantly increased (odds ratio = 3.52, P = 0.008) and rs756998920 (Val42Ile, MTTP) significantly decreased (odds ratio = 0.03, P = 0.019) the NAFLD risk. Functional assays showed that these two SNPs disrupted protein functions and supported the genetic association. Conclusion Collectively, 1.79% of individuals in our studied population were estimated carriers of rare variants that are potentially associated with NAFLD. Electronic supplementary material The online version of this article (10.1186/s12944-017-0570-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Supichaya Boonvisut
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan.,The Chulabhorn Graduate Institute, 54 Kamphangphet 6 Road, Laksi, Bangkok, 10210, Thailand
| | - Ken Yoshida
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Kazuhiro Nakayama
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Kazuhisa Watanabe
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroshi Miyashita
- Jichi Medical University Health Care Center, Shimotsuke, Tochigi, 329-0498, Japan
| | - Sadahiko Iwamoto
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan.
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Wu Z, Zhang T, Li L, Xu J, Qin X, Zhang T, Cui L, Lou Q, Li J, Chen J. Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing. BMC Plant Biol 2016; 16:182. [PMID: 27553196 PMCID: PMC4995632 DOI: 10.1186/s12870-016-0873-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 08/15/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Parthenocarpy is an important trait for yield and quality in many plants. But due to its complex interactions with genetic and physiological factors, it has not been adequately understood and applied to breeding and production. Finding novel and effective quantitative trait loci (QTLs) is a critical step towards understanding its genetic mechanism. Cucumber (Cucumis sativus L.) is a typical parthenocarpic plant but the QTLs controlling parthenocarpy in cucumber were not mapped on chromosomes, and the linked markers were neither user-friendly nor confirmed by previous studies. Hence, we conducted a two-season QTL study of parthenocarpy based on the cucumber genome with 145 F2:3 families derived from a cross between EC1 (a parthenocarpic inbred line) and 8419 s-1 (a non-parthenocarpic inbred line) in order to map novel QTLs. Whole genome re-sequencing was also performed both to develop effective linked markers and to predict candidate genes. RESULTS A genetic linkage map, employing 133 Simple Sequence Repeats (SSR) markers and nine Insertion/Deletion (InDel) markers spanning 808.1 cM on seven chromosomes, was constructed from an F2 population. Seven novel QTLs were identified on chromosomes 1, 2, 3, 5 and 7. Parthenocarpy 2.1 (Parth2.1), a QTL on chromosome 2, was a major-effect QTL with a logarithm of odds (LOD) score of 9.0 and phenotypic variance explained (PVE) of 17.0 % in the spring season and with a LOD score of 6.2 and PVE of 10.2 % in the fall season. We confirmed this QTL using a residual heterozygous line97-5 (RHL97-5). Effectiveness of linked markers of the Parth2.1 was validated in F3:4 population and in 21 inbred lines. Within this region, there were 57 genes with nonsynonymous SNPs/InDels in the coding sequence. Based on further combined analysis with transcriptome data between two parents, CsARF19, CsWD40, CsEIN1, CsPPR, CsHEXO3, CsMDL, CsDJC77 and CsSMAX1 were predicted as potential candidate genes controlling parthenocarpy. CONCLUSIONS A major-effect QTL Parth2.1 and six minor-effect QTLs mainly contribute to the genetic architecture of parthenocarpy in cucumber. SSR16226 and Indel-T-39 can be used in marker-assisted selection (MAS) of cucumber breeding. Whole genome re-sequencing enhances the efficiency of polymorphic marker development and prediction of candidate genes.
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Affiliation(s)
- Zhe Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
- College of Horticulture, Shanxi Agricultural University, Shanxi, 030801 China
| | - Ting Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lei Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jian Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tinglin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Li Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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Gohil KN, Neurgaonkar PS, Paranjpe A, Dastager SG, Dharne MS. Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions. Genom Data 2016; 8:72-6. [PMID: 27222803 PMCID: PMC4856823 DOI: 10.1016/j.gdata.2016.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 12/21/2022]
Abstract
Advances in de novo sequencing technologies allow us to track deeper insights into microbial genomes for restructuring events during the course of their evolution inside and outside the host. Bacterial species belonging to Ochrobactrum genus are being reported as emerging, and opportunistic pathogens in this technology driven era probably due to insertion and deletion of genes. The Ochrobactrumintermedium M86 was isolated in 2005 from a case of non-ulcer dyspeptic human stomach followed by its first draft genome sequence in 2009. Here we report re-sequencing of O. intermedium M86 laboratory adapted strain in terms of gain and loss of genes. We also attempted for finer scale genome sequence with 10 times more genome coverage than earlier one followed by comparative evaluation on Ion PGM and Illumina MiSeq. Despite their similarities at genomic level, lab-adapted strain mainly lacked genes encoding for transposase protein, insertion elements family, phage tail-proteins that were not detected in original strain on both chromosomes. Interestingly, a 5 kb indel was detected in chromosome 2 that was absent in original strain mapped with phage integrase gene of Rhizobium spp. and may be acquired and integrated through horizontal gene transfer indicating the gene loss and gene gain phenomenon in this genus. Majority of indel fragments did not match with known genes indicating more bioinformatic dissection of this fragment. Additionally we report genes related to antibiotic resistance, heavy metal tolerance in earlier and re-sequenced strain. Though SNPs detected, there did not span urease and flagellar genes. We also conclude that third generation sequencing technologies might be useful for understanding genomic architecture and re-arrangement of genes in the genome due to their ability of larger coverage that can be used to trace evolutionary aspects in microbial system.
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Affiliation(s)
- Kushal N Gohil
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Priya S Neurgaonkar
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Aditi Paranjpe
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Syed G Dastager
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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Li S, Xie K, Li W, Zou T, Ren Y, Wang S, Deng Q, Zheng A, Zhu J, Liu H, Wang L, Ai P, Gao F, Huang B, Cao X, Li P. Re-sequencing and genetic variation identification of a rice line with ideal plant architecture. Rice (N Y) 2012; 5:18. [PMID: 27234240 PMCID: PMC5520836 DOI: 10.1186/1939-8433-5-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/30/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND The ideal plant architecture (IPA) includes several important characteristics such as low tiller numbers, few or no unproductive tillers, more grains per panicle, and thick and sturdy stems. We have developed an indica restorer line 7302R that displays the IPA phenotype in terms of tiller number, grain number, and stem strength. However, its mechanism had to be clarified. FINDINGS We performed re-sequencing and genome-wide variation analysis of 7302R using the Solexa sequencing technology. With the genomic sequence of the indica cultivar 9311 as reference, 307 627 SNPs, 57 372 InDels, and 3 096 SVs were identified in the 7302R genome. The 7302R-specific variations were investigated via the synteny analysis of all the SNPs of 7302R with those of the previous sequenced none-IPA-type lines IR24, MH63, and SH527. Moreover, we found 178 168 7302R-specific SNPs across the whole genome and 30 239 SNPs in the predicted mRNA regions, among which 8 517 were Non-syn CDS. In addition, 263 large-effect SNPs that were expected to affect the integrity of encoded proteins were identified from the 7302R-specific SNPs. SNPs of several important previously cloned rice genes were also identified by aligning the 7302R sequence with other sequence lines. CONCLUSIONS Our results provided several candidates account for the IPA phenotype of 7302R. These results therefore lay the groundwork for long-term efforts to uncover important genes and alleles for rice plant architecture construction, also offer useful data resources for future genetic and genomic studies in rice.
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Affiliation(s)
- Shuangcheng Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014 Ya’an, Sichuan China
| | - Kailong Xie
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Wenbo Li
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Ting Zou
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Yun Ren
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014 Ya’an, Sichuan China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014 Ya’an, Sichuan China
| | - Aiping Zheng
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lingxia Wang
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peng Ai
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Fengyan Gao
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Bin Huang
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Xuemei Cao
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130 China
- Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014 Ya’an, Sichuan China
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