• 中文核心期刊
  • CSCD来源期刊
  • 中国科技核心期刊
  • CA、CABI、ZR收录期刊

Message Board

Respected readers, authors and reviewers, you can add comments to this page on any questions about the contribution, review,        editing and publication of this journal. We will give you an answer as soon as possible. Thank you for your support!

Name
E-mail
Phone
Title
Content
Verification Code
Volume 39 Issue 6
Jun.  2024
Turn off MathJax
Article Contents
ZHANG Y M, XIAO H, LAN X L, et al. Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing [J]. Fujian Journal of Agricultural Sciences,2024,39(6):652−661 doi: 10.19303/j.issn.1008-0384.2024.06.004
Citation: ZHANG Y M, XIAO H, LAN X L, et al. Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing [J]. Fujian Journal of Agricultural Sciences,2024,39(6):652−661 doi: 10.19303/j.issn.1008-0384.2024.06.004

Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing

doi: 10.19303/j.issn.1008-0384.2024.06.004
  • Received Date: 2024-05-17
  • Accepted Date: 2024-07-24
  • Rev Recd Date: 2024-06-11
  • Available Online: 2024-08-15
  • Publish Date: 2024-06-28
  •   Objective  Genetic variations in the southern high-protein soybeans were revealed by re-sequencing the whole genome.  Method   High-throughput sequencing was conducted on the whole genome of the southern high-protein soybean Fudou 234 to detect genetic variations.  Result  In the 64757037 clean reads, the sequencing depth was 17× with genome coverage of 98.08% (1×) and 96.25% (5×). There were 1478393 single nucleotide polymorphisms (SNPs) and 356739 small insertion-deletions (Small InDels) identified. Among them, 14323 non-synonymous SNP mutations and 4186Small InDel mutated genes were found in the coding sequence (CDS). Analysis by COG (Clusters of orthologous groups of proteins) revealed that signal transduction mechanisms, transcription, carbohydrate translocation and metabolism and KEGG(Kyoto encyclopedia of genes and genomes) analyses revealed that the pathways of carbon metabolism, starch and sucrose metabolism, amino acid biosynthesis, phytohormone signalling, and endoplasmic reticulum protein processing were associated with genetic variation in Fudou 234. In addition, by studying the candidate genes in two major segments of soybean kernel protein quantitative trait locus (QTL), 10 SNP and 7 Small InDel type variations were discovered in 65 genes.  Conclusion  The genetic variations in the southern high-protein soybeans deviated from the regular varieties were unveiled to provide new venue for breeding and developing molecular markers in studying soybeans.
  • loading
  • [1]
    CAO P, ZHAO Y, WU F J, et al. Multi-omics techniques for soybean molecular breeding [J]. International Journal of Molecular Sciences, 2022, 23(9): 4994. doi: 10.3390/ijms23094994
    [2]
    XU X Y, BAI G H. Whole-genome resequencing: Changing the paradigms of SNP detection, molecular mapping and gene discovery [J]. Molecular Breeding, 2015, 35(1): 33. doi: 10.1007/s11032-015-0240-6
    [3]
    HUANG X H, FENG Q, QIAN Q, et al. High-throughput genotyping by whole-genome resequencing [J]. Genome Research, 2009, 19(6): 1068−1076. doi: 10.1101/gr.089516.108
    [4]
    PETEREIT J, MARSH J I, BAYER P E, et al. Genetic and genomic resources for soybean breeding research [J]. Plants, 2022, 11(9): 1181. doi: 10.3390/plants11091181
    [5]
    YANG C M, YAN J, JIANG S Q, et al. Resequencing 250 soybean accessions: New insights into genes associated with agronomic traits and genetic networks[J]. Genomics, Proteomics & Bioinformatics, 2022, 20(1): 29-41.
    [6]
    LIU N, NIU Y C, ZHANG G W, et al. Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean [J]. Horticulture Research, 2022, 9: uhab052. doi: 10.1093/hr/uhab052
    [7]
    LEE K J, KIM D S, KIM J B, et al. Identification of candidate genes for an early-maturing soybean mutant by genome resequencing analysis [J]. Molecular Genetics and Genomics, 2016, 291(4): 1561−1571. doi: 10.1007/s00438-016-1183-2
    [8]
    MALDONADO DOS SANTOS J V, VALLIYODAN B, JOSHI T, et al. Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing [J]. BMC Genomics, 2016, 17: 110. doi: 10.1186/s12864-016-2431-x
    [9]
    JIANG H, JIA H Y, HAO X S, et al. Mapping Locus RSC11K and predicting candidate gene resistant to Soybean mosaic virus strain SC11 through linkage analysis combined with genome resequencing of the parents in soybean [J]. Genomics, 2022, 114(4): 110387. doi: 10.1016/j.ygeno.2022.110387
    [10]
    YUAN Y, YANG Y Q, SHEN Y C, et al. Mapping and functional analysis of candidate genes involved in resistance to soybean (Glycine max) mosaic virus strain SC3 [J]. Plant Breeding, 2020, 139(3): 618−625. doi: 10.1111/pbr.12799
    [11]
    林国强, 张轼, 滕振勇, 等. 高蛋白大豆福豆234的选育及高产农艺措施数学模型 [J]. 福建农业学报, 2005, 20(2):69−73. doi: 10.3969/j.issn.1008-0384.2005.02.002

    LIN G Q, ZHANG S, TENG Z Y, et al. Breeding and mathematical model of agronomic measures for high yield and protein content soybean variety Fudou 234 [J]. Fujian Journal of Agricultural Sciences, 2005, 20(2): 69−73. (in Chinese) doi: 10.3969/j.issn.1008-0384.2005.02.002
    [12]
    ABOUL-MAATY N A F, ORABY H A S. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method [J]. Bulletin of the National Research Centre, 2019, 43(1): 25. doi: 10.1186/s42269-019-0066-1
    [13]
    张彦威, 李伟, 张礼凤, 等. 基于重测序的大豆新品种齐黄34的全基因组变异挖掘 [J]. 中国油料作物学报, 2016, 38(2):150−158. doi: 10.7505/j.issn.1007-9084.2016.02.003

    ZHANG Y W, LI W, ZHANG L F, et al. Genome-wide variations of soybean cultivar Qihuang 34 by whole genome re-sequencing [J]. Chinese Journal of Oil Crop Sciences, 2016, 38(2): 150−158. (in Chinese) doi: 10.7505/j.issn.1007-9084.2016.02.003
    [14]
    郭丹丹, 袁凤杰, 郁晓敏. 基于重测序的籽粒型和鲜食型大豆的全基因组变异分析 [J]. 分子植物育种, 2019, 17(22):7306−7312.

    GUO D D, YUAN F J, YU X M. Genome-wide variation analysis of grain and vegetable soybeans based on re-sequencing [J]. Molecular Plant Breeding, 2019, 17(22): 7306−7312. (in Chinese)
    [15]
    LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform [J]. Bioinformatics, 2009, 25(14): 1754−1760. doi: 10.1093/bioinformatics/btp324
    [16]
    LI H, HANDSAKER B, WYSOKER A, et al. The Sequence Alignment/Map format and SAMtools [J]. Bioinformatics, 2009, 25(16): 2078−2079. doi: 10.1093/bioinformatics/btp352
    [17]
    MCKENNA A, HANNA M, BANKS E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [J]. Genome Research, 2010, 20(9): 1297−1303. doi: 10.1101/gr.107524.110
    [18]
    沈丽丽, 曹斌斌, 杨光耀, 等. 毛竹及其2种竿型变异类型的全基因组重测序分析 [J]. 基因组学与应用生物学, 2023, 42(6):581−592.

    SHEN L L, CAO B B, YANG G Y, et al. Whole genome resequencing analysis of moso bamboo(Phyllostachys edulis)and its two culm variants [J]. Genomics and Applied Biology, 2023, 42(6): 581−592. (in Chinese)
    [19]
    CINGOLANI P, PLATTS A, WANG L L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 [J]. Fly, 2012, 6(2): 80−92. doi: 10.4161/fly.19695
    [20]
    魏荷, 王金社, 卢为国. 大豆籽粒蛋白质含量分子遗传研究进展 [J]. 中国油料作物学报, 2015, 37(3):394−410. doi: 10.7505/j.issn.1007-9084.2015.03.021

    WEI H, WANG J S, LU W G. Molecular genetic advances in soybean seed protein [J]. Chinese Journal of Oil Crop Sciences, 2015, 37(3): 394−410. (in Chinese) doi: 10.7505/j.issn.1007-9084.2015.03.021
    [21]
    BANDILLO N, JARQUIN D, SONG Q J, et al. A population structure and genome-wide association analysis on the USDA soybean germplasm collection[J]. The Plant Genome, 2015, 8(3): eplantgenome2015.04. 0024.
    [22]
    PATIL G, MIAN R, VUONG T, et al. Molecular mapping and genomics of soybean seed protein: A review and perspective for the future [J]. Theoretical and Applied Genetics, 2017, 130(10): 1975−1991. doi: 10.1007/s00122-017-2955-8
    [23]
    VAN K, MCHALE L K. Meta-analyses of QTLs associated with protein and oil contents and compositions in soybean[Glycine max (L.) Merr. ]seed [J]. International Journal of Molecular Sciences, 2017, 18(6): 1180. doi: 10.3390/ijms18061180
    [24]
    LAM H M, XU X, LIU X, et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection [J]. Nature Genetics, 2010, 42: 1053−1059. doi: 10.1038/ng.715
    [25]
    SCHMUTZ J, CANNON S B, SCHLUETER J, et al. Genome sequence of the palaeopolyploid soybean [J]. Nature, 2010, 463: 178−183. doi: 10.1038/nature08670
    [26]
    郭茜茜. 大豆子粒蛋白质积累与碳代谢关系的研究[D]. 哈尔滨: 东北农业大学, 2010:16-41.

    GUO Q Q. Study on the relationship between protein accumulation and carbon metabolism in soybean seeds[D]. Harbin: Northeast Agricultural University, 2010:16-41. (in Chinese)
    [27]
    PATIL G, VUONG T D, KALE S, et al. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping [J]. Plant Biotechnology Journal, 2018, 16(11): 1939−1953. doi: 10.1111/pbi.12929
    [28]
    王嘉, 曾召琼, 梁建秋, 等. 基于全基因组重测序的大豆分子标记开发及籽粒蛋白质含量QTL定位 [J]. 中国农业科学, 2019, 52(16):2743−2757. doi: 10.3864/j.issn.0578-1752.2019.16.001

    WANG J, ZENG Z Q, LIANG J Q, et al. Development new molecular markers for quantitative trait locus (QTL) analysis of the seed protein content based on whole genome re-sequencing in soybean [J]. Scientia Agricultura Sinica, 2019, 52(16): 2743−2757. (in Chinese) doi: 10.3864/j.issn.0578-1752.2019.16.001
    [29]
    FLIEGE C E, WARD R A, VOGEL P, et al. Fine mapping and cloning of the major seed protein quantitative trait loci on soybean chromosome 20 [J]. The Plant Journal: for Cell and Molecular Biology, 2022, 110(1): 114−128. doi: 10.1111/tpj.15658
    [30]
    MA Q J, SUN M H, LU J, et al. Transcription factor AREB2 is involved in soluble sugar accumulation by activating sugar transporter and amylase genes [J]. Plant Physiology, 2017, 174(4): 2348−2362. doi: 10.1104/pp.17.00502
    [31]
    张计育, 王刚, 王涛, 等. SWEET蛋白在植物生长发育中的功能作用研究进展[J]. 植物资源与环境学报, 2023, 32(5): 1-15.

    ZHANG J Y, WANG G, WANG T, et al. Research progress on functional roles of SWEET proteins in plant growth and development[J]. Journal of Plant Resources and Environment, 2023, 32(5): 1-15. (in Chinese) Development[J]. Journal of Plant Resources and Environment, 2023, 32(5): 1-15. (in Chinese)
    [32]
    CHEN L Q, QU X Q, HOU B H, et al. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport [J]. Science, 2012, 335(6065): 207−211. doi: 10.1126/science.1213351
    [33]
    TAKAHASHI F, SATO-NARA K, KOBAYASHI K, et al. Sugar-induced adventitious roots in Arabidopsis seedlings [J]. Journal of Plant Research, 2003, 116(2): 83−91. doi: 10.1007/s10265-002-0074-2
    [34]
    WANG S D, YOKOSHO K, GUO R Z, et al. The soybean sugar transporter GmSWEET15 mediates sucrose export from endosperm to early embryo [J]. Plant Physiology, 2019, 180(4): 2133−2141. doi: 10.1104/pp.19.00641
    [35]
    柯博洋, 李文龙, 张彩英. 大豆SWEET基因在荚粒发育过程中与逆境胁迫下的表达 [J]. 中国农业科技导报, 2023, 25(8):33−52.

    KE B Y, LI W L, ZHANG C Y. Expressions of SWEET genes during pod and seed developments and under different stress conditions in soybean [J]. Journal of Agricultural Science and Technology, 2023, 25(8): 33−52. (in Chinese)
    [36]
    PATIL G, VALLIYODAN B, DESHMUKH R, et al. Soybean (Glycine max) SWEET gene family: Insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis [J]. BMC Genomics, 2015, 16(1): 520. doi: 10.1186/s12864-015-1730-y
    [37]
    RANOCHA P, DENANCÉ N, VANHOLME R, et al. Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers [J]. The Plant Journal: for Cell and Molecular Biology, 2010, 63(3): 469−483. doi: 10.1111/j.1365-313X.2010.04256.x
    [38]
    PAL L, SANDHU S K, BHATIA D, et al. Genome-wide association study for candidate genes controlling seed yield and its components in rapeseed (Brassica napus subsp. napus) [J]. Physiology and Molecular Biology of Plants, 2021, 27(9): 1933−1951. doi: 10.1007/s12298-021-01060-9
    [39]
    LIU C, ZENG L B, ZHU S Y, et al. Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud) [J]. DNA Research: an International Journal for Rapid Publication of Reports on Genes and Genomes, 2018, 25(2): 173−181. doi: 10.1093/dnares/dsx047
    [40]
    刘顺湖, 周瑞宝, 盖钧镒. 大豆蛋白质有关性状遗传的分离分析 [J]. 作物学报, 2009, 35(11):1958−1966. doi: 10.3724/SP.J.1006.2009.01958

    LIU S H, ZHOU R B, GAI J Y. Segregation analysis for inheritance of protein related traits in soybean[Glycine max (L. ) merr. [J]. Acta Agronomica Sinica, 2009, 35(11): 1958−1966. (in Chinese) doi: 10.3724/SP.J.1006.2009.01958
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(6)  / Tables(1)

    Article Metrics

    Article views (154) PDF downloads(54) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return