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.
|