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| Gene mapping of a novel glossy mutant in Brassica napus L. based on whole genome resequencing technology |
Yancheng WEN( ),Junping HE,Dongfang CAI,Shufen ZHANG,Jiacheng ZHU,Jianping WANG,Jinhua CAO,Lei ZHAO,Dongguo WANG,Yizi LIU |
| Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China |
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Abstract Epicuticular wax in the rape is one of the protective barriers in stress environments. We previously reported one glossy mutant DL22B077-1 in Brassica napus L. controlled by a pair of dominant genes. In order to further understand its genetic mechanism, the glossy genes in the F2 population were mapped by whole genome resequencing technology and bulk segregated analysis (BSA) in this study. A total of 1 0661.75 Mb of clean bases were obtained, with an average Q30 of 92.99%, an average mapping ratio of 97.73%, an average sequencing depth of 24×, and an average coverage ratio of 82.06%, which indicated that the sequencing quality was high. In addition, the correlations between the glossy characters and markers of single nucleotide polymorphism (SNP) and insertion-deletion (In-Del) in genomic domains were analyzed. In the SNP marker, seven associated regions and 1 509 genes on five chromosomes were obtained. In the In-Del marker, 15 associated regions and 2 633 genes on 11 chromosomes were obtained. The final association results were the intersection of two kinds of markers, which was the 1.79 Mb associated region from 8.60 Mb to 10.39 Mb on chromosome C8, and there were a total of 130 candidate genes in this region. A total of 119 genes in the 130 candidate genes were annotated, which participated in the construction of cellular components and were involved in molecular functions and biological processes. In B. napus, DL22B077-1 was the first glossy mutant whose glossy genes were located on chromosome C8, so it was a novel glossy mutant. The above results lay a theoretical foundation for breeding rape varieties with high and stable yields and improving resistance cultivation techniques.
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Received: 19 December 2022
Published: 29 August 2023
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Corresponding Authors:
Yancheng WEN
E-mail: ychwen65@163.com
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Cite this article:
Yancheng WEN,Junping HE,Dongfang CAI,Shufen ZHANG,Jiacheng ZHU,Jianping WANG,Jinhua CAO,Lei ZHAO,Dongguo WANG,Yizi LIU. Gene mapping of a novel glossy mutant in Brassica napus L. based on whole genome resequencing technology. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(4): 497-506.
URL:
https://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2022.12.191 OR https://www.zjujournals.com/agr/Y2023/V49/I4/497
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基于全基因组重测序技术的甘蓝型油菜光叶突变体基因定位
表皮蜡质是油菜适应逆境的保护措施之一。本课题组前期报道了一个由1对显性基因控制的甘蓝型油菜（Brassica napus L.）光叶突变体DL22B077-1。为了进一步了解其遗传机制，本研究利用全基因组重测序技术和分离群体分析法（bulk segregated analysis, BSA）通过F2群体进行基因定位，获得的有效碱基数达10 661.75 Mb，其中，Q30均值为92.99%，平均作图率为97.73%，平均测序深度为24×，平均覆盖率为82.06%，测序质量较高；此外，分析了单核苷酸多态性（single nucleotide polymorphism, SNP）标记和插入-缺失（insertion-deletion, In-Del）标记与光叶性状的相关性。通过SNP标记，在5条染色体上得到7个相关区域和1 509个相关基因。通过In-Del标记，在11条染色体上得到15个相关区域和2 633个相关基因。SNP标记和In-Del标记关联分析结果的交集部分为C8染色体上8.60～10.39 Mb区域，总长度为1.79 Mb，共计130个候选基因，其中119个基因得到注释，它们参与了细胞成分的构建，确保了分子功能和生物过程的顺利进行。DL22B077-1是第一个将蜡质基因定位到C8染色体上的甘蓝型油菜光叶突变体，据此判断其为新的光叶突变体。上述结果为选育高产稳产油菜品种、改良油菜抗逆栽培技术奠定了理论基础。
关键词：
甘蓝型油菜,
光叶突变体,
全基因组重测序,
基因定位
|
|
| [1] |
ABE A, KOSUGI S, YOSHIDA K, et al. Genome sequencing reveals agronomical important loci in rice using MutMap[J]. Nature Biotechnology, 2012, 30(2): 174-178. DOI: 10.1038/nbt.2095
doi: 10.1038/nbt.2095
|
|
|
| [2] |
HANNOUFA A, MCNEVIN J, LEMIEUX B. Epicuticular waxes of eceriferum mutants of Arabidopsis thaliana [J]. Phyto-chemistry, 1993, 33(4): 851-855. DOI: 10.1016/0031-9422(93)85289-4
doi: 10.1016/0031-9422(93)85289-4
|
|
|
| [3] |
WANG T Y, XING J W, LIU X Y, et al. GCN5 contributes to stem cuticular wax biosynthesis by histone acetylation of CER3 in Arabidopsis [J]. Journal of Experimental Botany, 2018, 69(12): 2911-2922. DOI: 10.1093/jxb/ery077
doi: 10.1093/jxb/ery077
|
|
|
| [4] |
LU P, QIN J X, WANG G X, et al. Comparative fine mapping of the Wax 1 (W1) locus in hexaploid wheat[J]. Theoretical and Applied Genetics, 2015, 128(8): 1595-1603. DOI: 10.1007/s00122-015-2534-9
doi: 10.1007/s00122-015-2534-9
|
|
|
| [5] |
丰锦.水稻OsWTF1和OsWTF2基因的蜡质合成及耐逆相关功能分析[D].湖南,长沙:湖南农业大学,2021.
FENG J. Functional analysis of OsWTF1 and OsWTF2 genes in wax synthesis and abiotic stress tolerance[D]. Changsha, Hunan: Hunan Agricultural University, 2021. (in Chinese with English abstract)
|
|
|
| [6] |
胡阳,宋莉萍,汪爱华,等.普通白菜薹茎亮绿性状遗传规律研究及基因定位[J].中国蔬菜,2021(8):37-45. DOI:10.19928/j.cnki.1000-6346.2021.0036
HU Y, SONG L P, WANG A H, et al. Genetic research and gene mapping of the stalk glossy trait in pakchoi[J]. China Vegetables, 2021(8): 37-45. (in Chinese with English abstract)
doi: 10.19928/j.cnki.1000-6346.2021.0036
|
|
|
| [7] |
李景涛.结球甘蓝无蜡粉亮绿性状遗传分析及分子标记研究[D].北京:中国农业科学院,2012.
LI J T. Genetic analysis and molecular marker on glossy waxless character in cabbage[D]. Beijing: Chinese Academy of Agricultural Sciences, 2012. (in Chinese with English abstract)
|
|
|
| [8] |
唐俊.结球甘蓝亮绿性状遗传与基因的精细定位[D].北京:中国农业科学院,2015.
TANG J. Inheritance and fine mapping of the glossy gene in cabbage[D]. Beijing: Chinese Academy of Agricultural Sciences, 2015. (in Chinese with English abstract)
|
|
|
| [9] |
石利朝,曾爱松,李家仪,等.牛心甘蓝蜡粉缺失突变体410M特征的研究[J].南京农业大学学报,2018,41(1):57-63. DOI:10.7685/jnau.201705001
SHI L C, ZENG A S, LI J Y, et al. Studies on characteristics of a heart-shaped glossy cabbage mutant 410M[J]. Journal of Nanjing Agricultural University, 2018, 41(1): 57-63. (in Chinese with English abstract)
doi: 10.7685/jnau.201705001
|
|
|
| [10] |
MO J G, LI W Q, YU Q, et al. Inheritance of the waxless character of Brassica napus Nilla glossy[J]. Canadian Journal of Plant Science, 1995, 75(4): 893-894. DOI: 10.4141/cjps95-148
doi: 10.4141/cjps95-148
|
|
|
| [11] |
刘忠松,官春云,陈社员,等.甘蓝型油菜显性无蜡粉基因的染色体组定位[J].湖南农业大学学报,2000,26(3):182-184. DOI:10.13331/j.cnki.jhau.2000.03.008
LIU Z S, GUAN C Y, CHEN S Y, et al. Genomic location of the dominant gene for waxlessness in rapeseed (Brassica napus L.)[J]. Journal of Hunan Agricultural University, 2000, 26(3): 182-184. ( in Chinese with English abstract)
doi: 10.13331/j.cnki.jhau.2000.03.008
|
|
|
| [12] |
PU Y Y, GAO J, GUO Y L, et al. A novel dominant glossy mutation causes suppression of wax biosynthesis pathway and deficiency of cuticular wax in Brassica napus [J]. BMC Plant Biology, 2013, 13: 215. DOI: 10.1186/1471-2229-13-215
doi: 10.1186/1471-2229-13-215
|
|
|
| [13] |
MO J G, LI W Q, WANG J H. Inheritance and agronomic performance of waxless character in Brassica napus L.[J]. Plant Breeding, 1992, 108: 256-259. DOI: 10.1111/j.1439-0523.1992.tb00127.x
doi: 10.1111/j.1439-0523.1992.tb00127.x
|
|
|
| [14] |
王婧,刘泓利,宋超,等.甘蓝型油菜叶表皮蜡质组分及结构与菌核病抗性关系[J].植物生理学报,2012,48(10):958-964. DOI:10.13592/j.cnki.ppj.2012.10.001
WANG J, LIU H L, SONG C, et al. Relationship between Brassica napus epicuticular wax composition and structure and resistance to Sclerotinia sclerotiorum [J]. Plant Physiology Journal, 2012, 48(10): 958-964. (in Chinese with English abstract)
doi: 10.13592/j.cnki.ppj.2012.10.001
|
|
|
| [15] |
刘杰.甘蓝型油菜光叶基因的克隆和功能分析[D].湖北,武汉:华中农业大学,2020.
LIU J. Map-based cloning and functional analysis of the glossy gene in Brassica napus [D]. Wuhan, Hubei: Huazhong Agricultural University, 2020. (in Chinese with English abstract)
|
|
|
| [16] |
文雁成,何俊平,蔡东芳,等.甘蓝型油菜表皮蜡粉遗传规律及其抗逆效应研究[J].中国油料作物学报,2022,44(6):1190-1198. DOI:10.19802/j.issn.1007-9084.2021265
WEN Y C, HE J P, CAI D F, et al. Genetic rule of cuticular wax in Brassica napus L. and their roles in stress resistance[J]. Chinese Journal of Oilseed Crops Sciences, 2022, 44(6): 1190-1198. (in Chinese with English abstract)
doi: 10.19802/j.issn.1007-9084.2021265
|
|
|
| [17] |
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: 25. DOI: 10.1186/s42269-019-0066-1
doi: 10.1186/s42269-019-0066-1
|
|
|
| [18] |
CHALHOUB B, DENOEUD F, LIU S Y, et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J]. Science, 2014, 345(6199): 950-953. DOI: 10.1126/science.1253435
doi: 10.1126/science.1253435
|
|
|
| [19] |
HILL J T, DEMAREST B L, BISGROVE B W, et al. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq[J]. Genome Research, 2013, 23(4): 687-697. DOI: 10.1101/gr.146936.112
doi: 10.1101/gr.146936.112
|
|
|
| [20] |
FEKIH R, TAKAGI H, TAMIRU M, et al. MutMap+: mapping and mutant identification without crossing in rice[J]. PLoS ONE, 2013, 8(7): e68529. DOI: 10.1371/journal.pone.0068529
doi: 10.1371/journal.pone.0068529
|
|
|
| [21] |
AARTS M G, KEIJZER C J, STIEKEMA W J, et al. Molecular characterization of the CER1 gene of Arabidopsis involved in epicuticular wax biosynthesis and pollen fertility[J]. Plant Cell, 1995, 7(12): 2115-2127. DOI: 10.1105/tpc.7.12.2115
doi: 10.1105/tpc.7.12.2115
|
|
|
| [22] |
TASSONE E E, LIPKA A E, TOMASI P L, et al. Chemical variation for leaf cuticular waxes and their levels revealed in a diverse panel of Brassica napus L.[J]. Industrial Crops and Products, 2015, 79: 77-83. DOI: 10.1016/j.indcrop.2015.10.047
doi: 10.1016/j.indcrop.2015.10.047
|
|
|
| [23] |
WANG C J, LI Y X, XIE F, et al. Cloning of the Brcer1 gene involved in cuticular wax production in a glossy mutant of non-heading Chinese cabbage (Brassica rapa L. var. communis)[J]. Molecular Breeding, 2017, 37(11): 142. DOI: 10.1007/s11032-017-0745-2
doi: 10.1007/s11032-017-0745-2
|
|
|
| [24] |
WANG C J, LI H L, LI Y X, et al. Genetic characterization and fine mapping BrCER4 in involved cuticular wax formation in purple cai-tai (Brassica rapa L. var. purpurea)[J]. Molecular Breeding, 2019, 39(1): 12. DOI: 10.1007/s11032-018-0919-6
doi: 10.1007/s11032-018-0919-6
|
|
|
| [25] |
张曦,王秋实,邹春蕾,等.大白菜花茎蜡粉基因的遗传分析与初步定位[J].分子植物育种,2013,11(6):804-808. DOI:10.3969/mpb.011.000804
ZHANG X, WANG Q S, ZOU C L, et al. Genetic analysis and preliminary mapping of wax gene on stem in Chinese cabbage[J]. Molecular Plant Breeding, 2013, 11(6): 804-808. (in Chinese with English abstract)
doi: 10.3969/mpb.011.000804
|
|
|
| [26] |
LIU D M, TANG J, LIU Z Z, et al. Cgl2 plays an essential role in cuticular wax biosynthesis in cabbage (Brassica oleracea L. var. capitata)[J]. BMC Plant Biology, 2017, 17: 223. DOI: 10.1186/s12870-017-1162-8
doi: 10.1186/s12870-017-1162-8
|
|
|
| [27] |
LIU D M, TANG J, LIU Z Z, et al. Fine mapping of BoGL1, a gene controlling the glossy green trait in cabbage (Brassica oleracea L. var. capitata)[J]. Molecular Breeding, 2017, 37(5): 69. DOI: 10.1007/s11032-017-0674-0
doi: 10.1007/s11032-017-0674-0
|
|
|
| [28] |
祝利霞.甘蓝型油菜黄化和光叶突变体的基因定位及克隆[D].湖北,武汉:华中农业大学,2014.
ZHU L X. Mapping and cloning the genes in chloroplyll-deficient and glossy mutants in Brassica napus L.[D]. Wuhan, Hubei: Huazhong Agricultural University, 2014. (in Chinese with English abstract)
|
|
|
| [29] |
孙红,苏同兵,于拴仓,等.白菜叶片表皮蜡粉成分及合成相关基因表达分析[J].中国蔬菜,2017(7):42-48. DOI:10.19928/j.cnki.1000-6346.2017.07.009
SUN H, SU T B, YU S C, et al. Analysis of leaf cuticular wax composition of Brassica rapa L. and related gene expression[J]. China Vegetables, 2017(7): 42-48. (in Chinese with English abstract)
doi: 10.19928/j.cnki.1000-6346.2017.07.009
|
|
|
| [30] |
刘泽洲.结球甘蓝蜡质缺失基因cgl-1的精细定位与分析[D].北京:中国农业大学,2017. DOI:10.3389/fpls.2017.00239
LIU Z Z. Fine-mapping and analysis of cgl-1, a gene conferring glossy trait in cabbage (Brassica oleracea L. var. capitata)[D]. Beijing: China Agricultural University, 2017. (in Chinese with English abstract)
doi: 10.3389/fpls.2017.00239
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