一个控制油菜半矮杆性状的主效新位点BnaSD.C3的精细定位及候选基因分析

doi:10.1016/j.jia.2023.02.017

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (10): 2981-2992.DOI: 10.1016/j.jia.2023.02.017

一个控制油菜半矮杆性状的主效新位点BnaSD.C3的精细定位及候选基因分析

收稿日期:2022-10-09 接受日期:2023-01-12 出版日期:2023-10-20 发布日期:2023-02-15

BnaSD.C3 is a novel major quantitative trait locus affecting semi-dwarf architecture in Brassica napus L.

WANG Xiao-dong^{1, 2}^*, CAI Ying²^*, PANG Cheng-ke^{1, 2}, ZHAO Xiao-zhen¹, SHI Rui¹, LIU Hong-fang², CHEN Feng¹, ZHANG Wei¹, FU San-xiong¹, HU Mao-long¹, HUA Wei², ZHENG Ming^2#, ZHANG Jie-fu^1#

¹ Provincial Key Laboratory of Agrobiology/Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing 210014, P.R.China
²Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, P.R.China

Received:2022-10-09 Accepted:2023-01-12 Online:2023-10-20 Published:2023-02-15
About author:WANG Xiao-dong, E-mail: xdwang120@163.com; CAI Ying, E-mail: caiying19960317@126.com; #Correspondence ZHANG Jie-fu, Tel: +86-25-84390657, E-mail: jiefu_z@163.com; ZHENG Ming, E-mail: zhengming@caas.cn * These authors contributed equally to this study.
Supported by:
The work was supported by the National Natural Science Foundation of China (32172065 and 32172095), the earmarked Fund for China Agriculture Research System (CARS-12), the Central Public-interest Scientific Institution Basal Research Fund, China (Y2022QC21) and the Jiangsu Collaborative Innovation Center for Modern Crop Production, China.

摘要/Abstract

摘要：

株高是影响甘蓝型油菜产量、收获指数和抗倒伏性的关键株型特征，然而，油菜株高的遗传调控机制仍不清楚。本研究利用EMS诱变获得了一个半矮杆突变体df34，遗传分析结果表明，df34的半矮杆性状由一对半显性基因控制。利用BSA-Seq方法将目的基因定位到C3染色体上，命名为BnaSD.C3。随后，利用图位克隆的方法，将BnaSD.C3精细定位到“Darmor-bzh”基因组的297.35 kb区间内。然而，在“Darmor-bzh”基因组上的这一区间内，没有潜在的调控株高性状的候选基因。结合基因组重测序、转录组测序、植物激素分析、结构变异分析和基因功能注释等信息，在“ZS11”参考基因组上，发现BnaC03G0466900ZS和BnaC03G0478900ZS为BnaSD.C3的重要候选基因。本研究为甘蓝型油菜矮化及株型育种提供了新的基因资源，为解析甘蓝型油菜株高的遗传调控机制提供了新的见解。

Abstract:

Plant height is a key plant architectural trait that affects the seed yield, harvest index and lodging resistance in Brassica napus L., although the genetic mechanisms affecting plant height remain unclear. Here, a semi-dwarf mutant, df34, was obtained by ethyl methanesulphonate-induced mutagenesis. Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene, which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing, and this gene was named BnaSD.C3. Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the “Darmor-bzh” genome, but there was no potential candidate gene for the semi-dwarf trait underlying this interval. Furthermore, the interval was aligned to the Zhongshuang 11 reference genome. Finally, combining structural variation analysis, transcriptome sequencing, phytohormone analyses and gene annotation information, BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34. This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in B. napus

Key words: Brassica napus L. , fine mapping , phytohormone analysis , plant height , transcriptome analysis

WANG Xiao-dong, CAI Ying, PANG Cheng-ke, ZHAO Xiao-zhen, SHI Rui, LIU Hong-fang, CHEN Feng, ZHANG Wei, FU San-xiong, HU Mao-long, HUA Wei, ZHENG Ming, ZHANG Jie-fu. 一个控制油菜半矮杆性状的主效新位点BnaSD.C3的精细定位及候选基因分析[J]. Journal of Integrative Agriculture, 2023, 22(10): 2981-2992.

WANG Xiao-dong, CAI Ying, PANG Cheng-ke, ZHAO Xiao-zhen, SHI Rui, LIU Hong-fang, CHEN Feng, ZHANG Wei, FU San-xiong, HU Mao-long, HUA Wei, ZHENG Ming, ZHANG Jie-fu. BnaSD.C3 is a novel major quantitative trait locus affecting semi-dwarf architecture in Brassica napus L.[J]. Journal of Integrative Agriculture, 2023, 22(10): 2981-2992.

参考文献

Barkan A, Small I. 2014. Pentatricopeptide repeat proteins in plants. Annual Review of Plant Biology, 65, 415–442.

Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.

Canino G, Bocian E, Barbezier N, Echeverría M, Forner J, Binder S, Marchfelder A. 2009. Arabidopsis encodes four tRNase Z enzymes. Plant Physiology, 150, 1494–1502.

Cao X W, Liu B, Zhang Y M. 2013. SEA: A software package of segregation analysis of quantitative traits in plants. Journal of Nanjing Agricultural University, 36, 1–6. (in Chinese)

Chalhoub B, Denoeud F, Liu S Y, Parkin I A P, Tang H B, Wang X Y, Chiquet J, Belcram H, Tong C B, Samans B, Correa M, Silva C D, Just J, Falentin C, Koh C S, Clainche I L, Bernard M, Bento P, Noel B, Labadie K, et al. 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 345, 950–953.

Fan S H, Zhang L, Tang M, Cai Y, Liu J L, Liu H F, Liu J, Terzaghi W, Wang H Z, Hua W, Zheng M. 2021. CRISPR/Cas9-targeted mutagenesis of the BnaA03.BP gene confers semi-dwarf and compact architecture to rapeseed (Brassica napus L.). Plant Biotechnology Journal, 19, 2383–2385.

Foisset N, Delourme R, Barret P, Renard M. 1995. Molecular tagging of the dwarf BREIZH (Bzh) gene in Brassica napus. Theoretical and Applied Genetics, 91, 756–761.

Fu L, Yan D, Gao L F, Liu P, Zhao G Y, Jia J Z, Ren Z L. 2022. TaIAA15 genes regulate plant architecture in wheat. Journal of Integrative Agriculture, 21, 1243–1252.

Fu T D, Zhou Y M. 2013. Progress and future development of hybrid rapeseed in China. Engineering Sciences, 11, 13–18.

Haïli N, Arnal N, Quadrado M, Amiar S, Tcherkez G, Dahan J, Briozzo P, des Francs-Small C C, Vrielynck N, Mireau H. 2013. The pentatricopeptide repeat MTSF1 protein stabilizes the nad4 mRNA in Arabidopsis mitochondria. Nucleic Acids Research, 41, 6650–6663.

He Y J, Wu D M, Wei D Y, Fu Y, Cui Y X, Dong H L, Tan C D, Qian W. 2017. GWAS, QTL mapping and gene expression analyses in Brassica napus reveal genetic control of branching morphogenesis. Scientific Reports, 7, 1–9.

Huang J, Kim C M, Xuan Y H, Liu J, Kim T H, Kim B K, Han C D. 2013. Formin homology 1 (OsFH1) regulates root-hair elongation in rice (Oryza sativa). Planta, 237, 1227–1239.

Jiang L, Liu X, Xiong G S, Liu H H, Chen F L, Wang L, Meng X B, Liu G F, Yu H, Yuan Y D, Yi W, Zhao L H, Ma H L, He Y Z, Wu Z S, Melcher K, Qian Q, Xu H E, Wang Y H, Li J Y. 2013. DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature, 504, 401–405.

Kim D, Paggi J M, Park C, Bennett C, Salzberg S L. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37, 907–915.

Koprivova A, des Francs-Small C C, Calder G, Mugford S T, Tanz S, Lee B R, Zechmann B, Small I, Kopriva S. 2010. Identification of a pentatricopeptide repeat protein implicated in splicing of intron 1 of mitochondrial nad7 transcripts. Journal of Biological Chemistry, 285, 32192–32199.

Korasick D A, Westfall C S, Lee S G, Nanao M H, Dumas R, Hagen G, Guilfoyle T J, Jez J M, Strader L C. 2014. Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression. Proceedings of the National Academy of Sciences of the United States of America, 111, 5427–5432.

Lee K, Han J H, Park Y, des Francs-Small C C, Small I, Kang H. 2017. The mitochondrial pentatricopeptide repeat protein PPR19 is involved in the stabilization of NADH dehydrogenase 1 transcripts and is crucial for mitochondrial function and Arabidopsis thaliana development. New Phytologist, 215, 202–216.

Lee K, Kang H. 2020. Roles of organellar RNA-binding proteins in plant growth, development, and abiotic stress responses. International Journal of Molecular Sciences, 21, 4548.

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079.

Li H T, Li J J, Song J R, Zhao B, Guo C C, Wang B, Zhang Q H, Wang J, King G J, Liu K D. 2019. An auxin signaling gene BnaA3.IAA7 contributes to improved plant architecture and yield heterosis in rapeseed. New Phytologist, 222, 837–851.

Li X, Xiang F J, Zhang W, Yan J D, Li X M, Zhong M, Yang P, Chen C Y, Liu X M, Mao D H, Zhao X Y. 2021. Characterization and fine mapping of a new dwarf mutant in Brassica napus. BMC Plant Biology, 21, 117.

Liu C, Wang J L, Huang T D, Wang F, Yuan F, Cheng X M, Zhang Y, Shi S W, Wu J S, Liu K D. 2010. A missense mutation in the VHYNP motif of a DELLA protein causes a semi-dwarf mutant phenotype in Brassica napus. Theoretical and Applied Genetics, 121, 249–258.

Liu S Y, Raman H, Xiang Y, Zhao C J, Huang J Y, Zhang Y Y. 2022. De novo design of future rapeseed crops: challenges and opportunities. The Crop Journal, 10, 587–596.

Liu Z, Dong F M, Wang X, Wang T, Su R, Hong D F, Yang G S. 2017. A pentatricopeptide repeat protein restores nap cytoplasmic male sterility in Brassica napus. Journal of Experimental Botany, 68, 4115–4123.

Liu Z, Yang Z H, Wang X, Li K, An H, Liu J, Yang G S, Fu T D, Yi B, Hong D F. 2016. A mitochondria-targeted PPR protein restores pol cytoplasmic male sterility by reducing orf224 transcript levels in oilseed rape. Molecular Plant, 9, 1082–1084.

Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.

Luo X, Ma C Z, Yue Y, Hu K N, Li Y Y, Duan Z Q, Wu M, Tu J X, Shen J X, Yi B, Fu T D. 2015. Unravelling the complex trait of harvest index in rapeseed (Brassica napus L.) with association mapping. BMC Genomics, 16, 1–10.

Lyu J Y, Guo Y, Du C L, Yu H B, Guo L J, Liu L, Zhao H X, Wang X F, Hu S W. 2022. BnERF114.A1, a rapeseed gene encoding APETALA2/ETHYLENE RESPONSE FACTOR, regulates plant architecture through auxin accumulation in the apex in Arabidopsis. International Journal of Molecular Sciences, 23, 2210.

Peng J, Richards D E, Hartley N M, Murphy G P, Devos K M, Flintham J E, Beales J, Fish L J, Worland A J, Pelica F, Sudhakar D, Christou P, Snape J W, Gale M D, Harberd N P. 1999. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature, 400, 256–261.

Rausell A, Kanhonou R, Yenush L, Serrano R, Ros R. 2003. The translation initiation factor eIF1A is an important determinant in the tolerance to NaCl stress in yeast and plants. The Plant Journal, 34, 257–267.

Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush G S, Kitano H, Matsuoka M. 2002. A mutant gibberellin-synthesis gene in rice. Nature, 416, 701–702.

Shen Y S, Yang Y, Xu E S, Ge X H, Xiang Y, Li Z Y. 2018. Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed (Brassica napus L.). Theoretical and Applied Genetics, 131, 67–78.

Song J M, Guan Z L, Hu J L, Guo C C, Yang Z Q, Wang S, Liu D X, Wang B, Lu S P, Zhou R, Xie W Z, Cheng Y F, Zhang Y T, Liu K D, Yang Q Y, Chen L L, Guo L. 2020. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6, 34–45.

Sriboon S, Li H T, Guo C C, Senkhamwong T, Dai C, Liu K D. 2020. Knock-out of TERMINAL FLOWER 1 genes altered flowering time and plant architecture in Brassica napus. BMC Genetics, 21, 52.

Stevens R, Grelon M, Vezon D, Oh J, Meyer P, Perennes C, Domenichini S, Bergounioux C. 2004. A CDC45 homolog in Arabidopsis is essential for meiosis, as shown by RNA interference-induced gene silencing. The Plant Cell, 16, 99–113.

Sun F M, Fan G Y, Hu Q, Zhou Y M, Guan M, Tong C B, Li J N, Du D Z, Qi C K, Jiang L C, Liu W Q, Huang A M, Chen W B, Yu J Y, Mei D S, Meng J L, Zeng P, Shi J Q, Liu K D, Wang X, et al. 2017. The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype. The Plant Journal, 92, 452–468.

Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano L M, Kamoun S, Terauchi R. 2013. QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. The Plant Journal, 74, 174–183.

Tanaka N, Uraguchi S, Kajikawa M, Saito A, Ohmori Y, Fujiwara T. 2018. A rice PHD-finger protein OsTITANIA, is a growth regulator that functions through elevating expression of transporter genes for multiple metals. The Plant Journal, 96, 997–1006.

Wang H, Cheng H T, Wang W X, Liu J, Hao M Y, Mei D S, Zhou R J, Fu L, Hu Q. 2016. Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq. Scientific Reports, 6, 1–10.

Wang K, Li M, Hakonarson H. 2010. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38, e164.

Wang X D, Chen L, Wang A N, Wang H, Tian J H, Zhao X P, Chao H B, Zhao Y J, Zhao W G, Xiang J, Gan J P, Li M T. 2016. Quantitative trait loci analysis and genome-wide comparison for silique related traits in Brassica napus. BMC Plant Biology, 16, 71.

Wang X D, Wang H, Long Y, Liu L Z, Zhao Y J, Tian J H, Zhao W G, Li B J, Chen L, Chao H B, Li M T. 2015. Dynamic and comparative QTL analysis for plant height in different developmental stages of Brassica napus L. Theoretical and Applied Genetics, 128, 1175–1192.

Wang X D, Zheng M, Liu H F, Zhang L, Chen F, Zhang W, Fan S H, Peng M M, Hu M L, Wang H Z, Zhang J F, Hua W. 2020. Fine-mapping and transcriptome analysis of a candidate gene controlling plant height in Brassica napus L. Biotechnology for Biofuels, 13, 42.

Wang Y H, Li J Y. 2008. Molecular basis of plant architecture. Annual Review of Plant Biology, 59, 253–279.

Xie C, Mao X Z, Huang J J, Ding Y, Wu J M, Dong S, Kong L, Gao G, Li C Y, Wei L P. 2011. KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 39, W316–W322.

Xie X Z, Wu N H. 2002. Introns in higher plant genes. Chinese Science Bulletin, 47, 1409–1415.

Yang M, He J B, Wan S B, Li W Y, Chen W J, Wang Y M, Jiang X M, Cheng P F, Chu P, Shen W, Guan R Z. 2021. Fine mapping of the BnaC04.BIL1 gene controlling plant height in Brassica napus L. BMC Plant Biology, 21, 359.

Ye S H, Yan L, Ma X W, Chen Y P, Wu L M, Ma T T, Zhao L, Yi B, Ma C Z, Tu J X, Shen J X, Fu T D, Wen J. 2022. Combined BSA-Seq based mapping and RNA-Seq profiling reveal candidate genes associated with plant architecture in Brassica napus. International Journal of Molecular Sciences, 23, 2472.

Yokoyama Y, Kobayashi S, Kidou S. 2019. PHD type zinc finger protein PFP represses flowering by modulating FLC expression in Arabidopsis thaliana. Plant Growth Regulation, 88, 49–59.

Young M D, Wakefield M J, Smyth G K, Oshlack A. 2010. Gene ontology analysis for RNA-seq: Accounting for selection bias. Genome Biology, 11, R14.

Zhang B, Zhao N, Liu Y Y, Jia L, Fu Y, He X X, Liu K F, Xu Z J, Bao B L. 2019. Novel molecular markers for high-throughput sex characterization of cynoglossus semilaevis. Aquaculture, 513, 734331.

Zhao B, Li H T, Li J J, Wang B, Dai C, Wang J, Liu K D. 2017. Brassica napus DS-3, encoding a DELLA protein, negatively regulates stem elongation through gibberellin signaling pathway. Theoretical and Applied Genetics, 130, 727–741.

Zhao B, Wang B, Li Z H, Guo T, Zhao J W, Guan Z L, Liu K D. 2019. Identification and characterization of a new dwarf locus DS-4 encoding an Aux/IAA7 protein in Brassica napus. Theoretical and Applied Genetics, 132, 1435–1449.

Zheng M, Terzaghi W, Wang H Z, Hua W. 2022. Integrated strategies for increasing rapeseed yield. Trends in Plant Science, 27, 742–745.

Zheng M, Zhang L, Tang M, Liu J L, Liu H F, Yang H L, Fan S H, Terzaghi W, Wang H Z, Hua W. 2020. Knockout of two BnaMAX1 homologs by CRISPR/Cas9-targeted mutagenesis improves plant architecture and increases yield in rapeseed (Brassica napus L.). Plant Biotechnology Journal, 18, 644–654.

Zhou J X, Su X M, Zheng S Y, Wu C J, Su Y N, Jiang Z, Li L, Chen S, He X J. 2022. The Arabidopsis NuA4 histone acetyltransferase complex is required for chlorophyll biosynthesis and photosynthesis. Journal of Integrative Plant Biology, 64, 901–914.

一个控制油菜半矮杆性状的主效新位点BnaSD.C3的精细定位及候选基因分析

BnaSD.C3 is a novel major quantitative trait locus affecting semi-dwarf architecture in Brassica napus L.

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics