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Home > Archive>Volume 24, Issue 6, 2023 >1744-1754. DOI:10.13430/j.cnki.jpgr.20230419003
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Bioinformatics and Gene Diversity Analysis of the DMP Genes in Soybean
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Affiliation:

1.School of Agronomy，Anhui Agricultural University，Hefei 230036;2.Institute of Crop Sciences， Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Soybean Biology in Beijing，Ministry of Ariculture and Rural Affairs， Beijing 100081;3.College of Life Sciences， Northeast Forestry University， Harbin 150040， Heilongjiang;4.College of Agriculture， Northeast Agricultural University， Harbin 150030， Heilongjiang

Fund Project:

Foundation project： The Innovation Project of Chinese Academy of Agricultural Sciences

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    Abstract:

    Double haploid techniques have been widely used to accelerate plant breeding， and in recent years， maize （Zea mays L.） lines containing mutations in the membrane protein （DMP） of the functionally unknown domain DUF679 have been used as haploidy-induced lines. In this study， soybean DMP genes with more than 60% homology with maize DMP gene were searched and bioinformatic analysis was performed. The molecular mechanism and biodiversity of GmDMP gene in soybean were investigated by using 2214 resequencing databases. The analysis results show that： GmDMP1 （Glyma.18G097400） and GmDMP2 （Glyma.18G098300） have high evolutionary affinity with maize DMP gene. The full length of genes is 645 bp， the homology rate of amino acid sequence is over 95%， and the number of encoded amino acids is completely consistent with the isoelectric point. The phosphorylation distribution differs at only one site. Both GmDMP1 and GmDMP2 genes have the same domain DUF679， which is more likely to locate in the ER， and both are transmembrane non-secreting hydrophilic proteins. There were 3 and 1 non-synonymous mutations of GmDMP1 and GmDMP2 genes in 2214 germplasm resources， respectively， consisting of 3 and 2 haplotypes. GmDMP1H3 has been strongly selected during domestication， and the mutation site of the GmDMP1H1 and GmDMP1H2 haplotypes is located in the DUF679 domain. It is possible to obtain a haploid inducible line by mutating two DMP genes in soybean， thus shortening the breeding life of soybean.

    Reference
    [1] Chaudhary J, Patil G B, Sonah H, Deshmukh R K, Vuong T D, Valliyodan B, Nguyen H T. Expanding omics resources for improvement of soybean seed composition traits. Frontiers in Plant Science, 2015, 6: 1021
    [2] Clemente T E, Cahoon E B. Soybean oil: Genetic approaches for modification of functionality and total content. Plant Physiology, 2009, 151(3):1030-1040
    [3] Chen L, Yang H, Fang Y, Guo W, Chen H, Zhang X, Dai W, Chen S, Hao Q, Yuan S, Zhang C, Huang Y, Shan Z, Yang Z, Qiu D, Liu X, Tran L P, Zhou X, Cao D. Overexpression of GmMYB14 improves high-density yield and drought tolerance of soybean through regulating plant architecture mediated by the brassinosteroid pathway. Plant Biotechnology Journal, 2021, 19(4): 702-716
    [4] Liu S, Zhang M, Feng F, Tian Z. Toward a "green revolution" for soybean. Molecular Plant, 2020, 13(5): 688-697
    [5] Ainsworth E A, Yendrek C R, Skoneczka J A, Long S P. Accelerating yield potential in soybean: Potential targets for biotechnological improvement. Plant Cell Environment, 2012, 35(1): 38-52
    [6] Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. Plant Biotechnology Journal, 2022, 20(2): 256-282
    [7] Chaikam V, Molenaar W, Melchinger A E, Boddupalli P M. Doubled haploid technology for line development in maize: Technical advances and prospects. Theoretical and Applied Genetics, 2019, 132(12): 3227-3243
    [8] Gajecka M, Marzec M, Chmielewska B, Jelonek J, Zbieszczyk J, Szarejko I. Changes in plastid biogenesis leading to the formation of albino regenerants in barley microspore culture. BMC Plant Biology, 2021, 21(1): 22
    [9] Jacquier N M A, Gilles L M, Pyott D E, Martinant J P, Rogowsky P M, Widiez T. Puzzling out plant reproduction by haploid induction for innovations in plant breeding. Nature Plants, 2020, 6(6): 610-619
    [10] Coe E H. A line of maize with high haploid frequency. Americam Naturalist, 1959, 93(873): 381-382
    [11] Kelliher T, Starr D, Richbourg L, Chintamanani S, Delzer B, Nuccio M L, Green J, Chen Z, McCuiston J, Wang W, Liebler T, Bullock P, Martin B. MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction. Nature, 2017, 542(7639): 105-109
    [12] Liu C, Li X, Meng D, Zhong Y, Chen C, Dong X, Xu X, Chen B, Li W, Li L, Tian X, Zhao H, Song W, Luo H, Zhang Q, Lai J, Jin W, Yan J, Chen S. A 4 bp insertion at ZmPLA1 encoding a putative phospholipase a generates haploid induction in maize. Molecular Plant, 2017, 10(3): 520-522
    [13] Zhong Y, Liu C, Qi X, Jiao Y, Wang D, Wang Y, Liu Z, Chen C, Chen B, Tian X, Li J, Chen M, Dong X, Xu X, Li L, Li W, Liu W, Jin W, Lai J, Chen S. Mutation of ZmDMP enhances haploid induction in maize. Nature Plants, 2019, 5(6): 575-580
    [14] Liu G, Lin Q, Jin S, Gao C. The CRISPR-Cas toolbox and gene editing technologies. Molecular Cell, 2022, 82(2): 333-347
    [15] Zhong Y, Chen B, Li M, Wang D, Jiao Y, Qi X, Wang M, Liu Z, Chen C, Wang Y, Chen M, Li J, Xiao Z, Cheng D, Liu W, Boutilier K, Liu C, Chen S. A DMP-triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis. Nature Plants, 2020, 6(5): 466-472
    [16] Zhong Y, Chen B, Wang D, Zhu X, Li M, Zhang J, Chen M, Wang M, Riksen T, Liu J, Qi X, Wang Y, Cheng D, Liu Z, Li J, Chen C, Jiao Y, Liu W, Huang S, Liu C, Boutilier K, Chen S. In vivo maternal haploid induction in tomato. Plant Biotechnology Journal, 2022, 20(2): 250-252
    [17] Li Y, Li D, Xiao Q, Wang H, Wen J, Tu J, Shen J, Fu T, Yi B. An in planta haploid induction system in Brassica napus. Jourmal of Integrative Plant Biology, 2022, 64(6): 1140-1144
    [18] Wang N, Xia X, Jiang T, Li L, Zhang P, Niu L, Cheng H, Wang K, Lin H. In planta haploid induction by genome editing of DMP in the model legume Medicago truncatula. Plant Biotechnology Journal, 2022, 20(1): 22-24
    [19] Li Y H, Qin C, Wang L, Jiao C Z, Hong H L, Tian Y, Li Y F, Xing G N, Wang J, Gu Y Z, Gao X P, Li D L, Li H Y, Liu Z X, Jing X, Feng B B, Zhao T, Guan R X, Guo Y, Liu J, Yan Z, Zhang L J, Ge T L, Li X K, Wang X B, Qiu H M, Zhang W H, Luan X Y, Han Y P, Han D Z, Chang R Z, Guo Y L, Reif J C, Jackson S A, Liu B,Tian S L, Qiu L J. Genome-wide signatures of the geographic expansion and breeding of soybean. Science China Life Sciences, 2023, 66(2): 350-365
    [20] Turner-Hissong S D, Mabry M E, Beissinger T M, Ross-Ibarra J, Pires J C. Evolutionary insights into plant breeding. Current Opinion in Plant Biology, 2020, 54: 93-100
    [21] Nagamine A, Ezura H. Genome editing for improving crop nutrition. Frontiers in Genome Editing, 2022, 4: 850104
    [22] Lin X, Liu B, Weller J L, Abe J, Kong F. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. Journal of Integrative Plant Biology, 2021, 63(6): 981-994
    [23] Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. Plant Biotechnology Journal, 2022, 20(2): 256-282
    [24] Chaudhary M, Mukherjee T K, Singh R, Gupta M, Goyal S, Singhal P, Kumar R, Bhusal N, Sharma P. CRISPR/Cas technology for improving nutritional values in the agricultural sector: An update. Molecular Biology Reports, 2022, 49(7): 7101-7110
    [25] Weyen J. Applications of doubled haploids in plant breeding and applied research. Methods in Molecular Biology, 2021, 2287: 23-39
    [26] Kelliher T, Starr D, Su X, Tang G, Chen Z, Carter J, Wittich P E, Dong S, Green J, Burch E, McCuiston J, Gu W, Sun Y, Strebe T, Roberts J, Bate N J, Que Q. One-step genome editing of elite crop germplasm during haploid induction. Nature Biotechnology, 2019, 37(3): 287-292
    [27] Ferrie A M R, Bhowmik P, Rajagopalan N, Kagale S. CRISPR/Cas9-mediated targeted mutagenesis in wheat doubled haploids. Methods in Molecular Biology, 2020, 2072: 183-198
    [28] Cistué L, Echávarri B. Barley isolated microspore culture. Methods in Molecular Biology, 2021, 2287: 187-197
    [29] Kuniyoshi D, Masuda I, Kanaoka Y, Shimazaki-Kishi Y, Okamoto Y, Yasui H, Yamamoto T, Nagaki K, Hoshino Y, Koide Y, Takamure I, Kishima Y. Diploid male gametes circumvent hybrid sterility between asian and african rice species. Frontiers in Plant Science, 2020, 11: 579305
    [30] Burk L G, Gerstel D U, Wernsman E A. Maternal haploids of nicotiana tabacum l from seed. Science, 1979, 206(4418): 585
    [31] Kasha K J, Kao K N. High frequency haploid production in barley (Hordeum vulgare L.). Nature, 1970, 225(5235): 874-876
    [32] Satpathy P, de la Fuente S A, Ott V, Müller A, Büchner H, Daghma D E S, Kumlehn J. Generation of doubled haploid barley by interspecific pollination with hordeum bulbosum. Methods in Molecular Biology, 2021, 2287: 215-226
    [33] Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-omics techniques for soybean molecular breeding. International Journal of Molecular Sciences,2022, 23(9): 4994
    [34] Thudi M, Palakurthi R, Schnable J C, Chitikineni A, Dreisigacker S, Mace E, Srivastava R K, Satyavathi C T, Odeny D, Tiwari V K, Lam H M, Hong Y B, Singh V K, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson S A, Close T J, Shubo W, Varshney R K. Genomic resources in plant breeding for sustainable agriculture. Journal of Plant Physiology, 2021, 257: 153351
    [35] Varshney R K, Bohra A, Roorkiwal M, Barmukh R, Cowling W A, Chitikineni A, Lam H M, Hickey L T, Croser J S, Bayer P E, Edwards D, Crossa J, Weckwerth W, Millar H, Kumar A, Bevan M W, Siddique K H M. Fast-forward breeding for a food-secure world. Trends in Genetics, 2021, 37(12): 1124-1136
    [36] Zhang H, Goettel W, Song Q, Jiang H, Hu Z, Wang M L, An Y C. Selection of GmSWEET39 for oil and protein improvement in soybean. PLoS Genetics, 2020, 16(11): e1009114
    [37] Qi Z, Song J, Zhang K, Liu S, Tian X, Wang Y, Fang Y, Li X, Wang J, Yang C, Jiang S, Sun X, Tian Z, Li W, Ning H. Identification of QTNs controlling 100-seed weight in soybean using multilocus genome-wide association studies. Frontiers in Genetics, 2020, 11: 689
    [38] Duan Z, Zhang M, Zhang Z, Liang S, Fan L, Yang X, Yuan Y, Pan Y, Zhou G, Liu S, Tian Z. Natural allelic variation of GmST05 controlling seed size and quality in soybean. Plant Biotechnology Journal, 2022, 20(9): 1807-1818
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History
  • Received:April 19,2023
  • Revised:May 13,2023
  • Online: October 31,2023
  • Published: October 31,2023
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