Boutilier K, Offringa R, Sharma V K, Kieft H, Ouellet T, Zhang L, Hattori J, Liu C M, Van Lammeren A A, Miki B L, Custers J B, Van Lookeren Campagne M M. 2002. Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. The Plant Cell, 14, 1737–1749.

Breyer D, Kopertekh L, Reheul D. 2014. Alternatives to antibiotic resistance marker genes for in vitro selection of genetically modified plants-scientific developments, current use, operational access and biosafety considerations. Critical Reviews in Plant Sciences, 33, 286–330.

Chen J, Tomes S, Gleave A P, Hall W, Luo Z, Xu J, Yao J L. 2022. Significant improvement of apple (Malus domestica Borkh.) transgenic plant production by pre-transformation with a Baby boom transcription factor. Horticulture Research, 9, uhab014.

Dai S H, Zheng P, Marmey P, Zhang S P, Tian W Z, Chen S Y, Beachy R N, Fauquet C. 2001. Comparative analysis of transgenic rice plants obtained by Agrobacterium-mediated transformation and particle bombardment. Molecular Breeding, 7, 25–33.

Das D K, Rahman A. 2010. Expression of a bacterial chitinase (ChiB) gene enhances antifungal potential in transgenic Litchi chinensis Sonn. (cv. Bedana). Current Trends in Biotechnology and Pharmacy, 4, 820–833.

Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. 2010. MYB transcription factors in Arabidopsis. Trends in Plant Science, 15, 573–581.

Florez S L, Erwin R L, Maximova S N, Guiltinan M J, Curtis W R. 2015. Enhanced somatic embryogenesis in Theobroma cacao using the homologous BABY BOOM transcription factor. BMC Plant Biology, 15, 121–133.

Gambino G, Gribaudo I. 2012. Genetic transformation of fruit trees: Current status and remaining challenges. Transgenic Research, 21, 1163–1181.

Gelvin S B. 2003. Agrobacterium-mediated plant transformation: The biology behind the “Gene-Jockeying” tool. Microbiology and Molecular Biology Reviews, 67, 16–37.

Hu B, Lai B, Wang D, Li J Q, Chen L H, Qin Y Q, Wang H C, Qin Y H, Hu G B, Zhao J T. 2018. Three LcABFs are involved in the regulation of chlorophyll degradation and anthocyanin biosynthesis during fruit ripening in Litchi chinensis. Plant and Cell Physiology, 60, 448–461.

Hu B, Zhao J T, Lai B, Qin Y H, Wang H C, Hu G B. 2016. LcGST4 is an anthocyanin-related glutathione S-transferase gene in Litchi chinensis Sonn. Plant Cell Reports, 35, 831–843.

Hu G B, Feng J T, Xiang X, Wang J B, Salojärvi J, Liu C M, Wu Z X, Zhang J S, Liang X M, Jiang Z D, Liu W, Ou L X, Li J W, Fan G Y, Mai Y X, Chen C J, Zhang X T, Zheng J K, Zhang Y Q, Peng H X, et al. 2022. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nature Genetics, 54, 73–83.

Jauhar P P, Peterson T S. 2001. Hybrids between durum wheat and Thinopyrum junceiforme: Prospects for breeding for scab resistance. Euphytica, 118, 127–136.

Jones H D. 2005. Wheat transformation: Current technology and applications to grain development and composition. Journal of Cereal Science, 41, 137–147.

Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Research, 32, 277–280.

Kavitah G, Taghipour F, Huyop F. 2010. Investigation of factors in optimizing Agrobacterium-mediated gene transfer in Citrullus lanatus cv. round dragon. Journal of Biological Sciences, 10, 3.

Khanna H, Becker D, Kleidon J, Dale J. 2004. Centrifugation assisted Agrobacterium tumefaciens-mediated transformation (CAAT) of embryogenic cell suspensions of banana (Musa spp. Cavendish AAA and Lady finger AAB). Molecular Breeding, 14, 239–252.

Kim C Y, Ahn Y O, Kim S H, Kim Y H, Lee H S, Catanach A S, Jacobs J M, Conner A J, Kwak S S. 2010. The sweet potato IbMYB1 gene as a potential visible marker for sweet potato intragenic vector system. Physiologia Plantarum, 139, 229–240.

Kim D, Langmead B, Salzberg S L. 2015. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.

Kortstee A J, Khan S A, Helderman C, Trindade L M, Wu Y, Visser R G, Brendolise C, Allan A, Schouten H J, Jacobsen E. 2011. Anthocyanin production as a potential visual selection marker during plant transformation. Transgenic Research, 20, 1253–1264.

Lai B, Li X J, Hu B, Qin Y H, Huang X M, Wang H C, Hu G B. 2014. LcMYB1 is a key determinant of differential anthocyanin accumulation among genotypes, tissues, developmental phases and ABA and light stimuli in Litchi chinensis. PLoS ONE, 9, e86293.

Li S N, Wang W Y, Gao J L, Yin K Q, Wang R, Wang C C, Petersen M, Mundy J, Qiu J L. 2016. MYB75 phosphorylation by MPK4 is required for light-induced anthocyanin accumulation in Arabidopsis. The Plant Cell, 28, 2866–2883.

Liu J Y, Osbourn A, Ma P D. 2015. MYB transcription factors as regulators of phenylpropanoid metabolism in plants. Molecular Plant, 8, 689–708.

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.

Lowe K, Wu E, Wang N, Hoerster G, Hastings C, Cho M J, Scelonge C, Lenderts B, Chamberlin M, Cushatt J, Wang L, Ryan L, Khan T, Chow-Yiu J, Hua W, Yu M, Banh J, Bao Z, Brink K, Igo E, et al. 2016. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. The Plant Cell, 28, 1998–2015.

Ma A N, Wang D, Lu H L, Wang H C, Qin Y H, Hu G B, Zhao J T. 2021. LcCOP1 and LcHY5 control the suppression and induction of anthocyanin accumulation in bagging and debagging litchi fruit pericarp. Scientia Horticulturae, 287, 110281.

Mao X Z, Cai T, Olyarchuk J G, Wei L P. 2005. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics, 19, 3787–3793.

Maren N A, Duan H, Da K, Yencho G C, Ranney T G, Liu W. 2022. Genotype-independent plant transformation. Horticulture Research, 9, uhac047.

Matveeva T V, Lutova L A. 2014. Horizontal gene transfer from Agrobacterium to plants. Frontiers in Plant Science, 5, 326–337.

McFarland F L, Collier R, Walter N, Martinell B, Kaeppler S M, Kaeppler H F. 2023. A key to totipotency: Wuschel-like homeobox 2a unlocks embryogenic culture response in maize (Zea mays L.). Plant Biotechnology Journal, 21, 1860–1872.

Mir H, Cholin S S, Perveen N. 2018. Biotechnological advances in litchi (Llitchi chinensis sonn.): Present scenario and future prospects in crop improvement - A review. Acta Horticulturae, 1211, 123–134.

Ouakfaoui S E, Schnell J, Abdeen A, Colville A, Labbé H, Han S, Baum B, Laberge S, Miki B. 2010. Control of somatic embryogenesis and embryo development by AP2 transcription factors. Plant Molecular Biology, 74, 313–326.

Ou Y S, Zheng X, Wang R Z. 1985. Tumorigenesis and T-DNA transfer by Agrobacterium tumorigenicum in litchi. Journal of Genetics and Genomics, 1, 44–47.

Park S C, Kim Y H, Kim S H, Jeong Y J, Kim C Y, Lee J S, Bae J Y, Ahn M J, Jeong J C, Lee H S, Kwak S S. 2015. Overexpression of the IbMYB1 gene in an orange-fleshed sweet potato cultivar produces a dual-pigmented transgenic sweet potato with improved antioxidant activity. Physiologia Plant, 153, 525–537.

Paul J Y, Khanna H, Kleidon J, Hoang P, Geijskes J, Daniells J, Zaplin E, Rosenberg Y, James A, Mlalazi B, Deo P, Arinaitwe G, Namanya P, Becker D, Tindamanyire J, Tushemereirwe W, Harding R, Dale J. 2016. Golden bananas in the field: Elevated fruit pro-vitamin A from the expression of a single banana transgene. Plant Biotechnology Journal, 15, 520–532.

Peng Y, Yuan Y, Chang W, Zheng L, Ma W, Ren H, Liu P, Zhu L, Su J, Ma F, Li M, Ma B. 2023. Transcriptional repression of MdMa1 by MdMYB21 in Ma locus decreases malic acid content in apple fruit. Plant Journal, 115, 1231–1242.

Pierroz G. 2023. Making babies: How auxin regulates somatic embryogenesis in Arabidopsis tissue culture. Plant Journal, 113, 5–6.

Puchooa D. 2004. Expression of green fluorescent protein gene in litchi (Litchi chinensis Sonn.) tissues. Journal of Applied Horticulture, 6, 535–537.

Qin Y Q, Wang D, Fu J X, Zhang Z K, Qin Y H, Hu G B, Zhao J T. 2021. Agrobacterium rhizogenes-mediated hairy root transformation as an efficient system for gene function analysis in Litchi chinensis. Plant Methods, 17, 103–112.

Rai M K, Shekhawat N S. 2014. Recent advances in genetic engineering for improvement of fruit crops. Plant Cell Tissue & Organ Culture, 116, 1–15.

Rai M K, Shekhawat N S. 2015. Genomic resources in fruit plants: An assessment of current status. Critical Reviews in Biotechnology, 35, 438–447.

Scorza R, Morgens P H, Cordts J M, Mante S, Callahan A M. 1990. Agrobacterium-mediated transformation of peach (Prunus persica L. batsch) leaf segments, immature embryos, and long-term embryogenic callus. Vitro Cellular & Developmental Biology, 26, 829–834.

Su Y H, Liu Y B, Bai B, Zhang X S. 2015. Establishment of embryonic shoot-root axis is involved in auxin and cytokinin response during Arabidopsis somatic embryogenesis. Frontiers in Plant Science, 5, 792–801.

Tanaka Y, Sasaki N, Ohmiya A. 2008. Biosynthesis of plant pigments: Anthocyanins, betalains and carotenoids. The Plant Journal, 54, 733–749.

Tang L P, Zhang X S, Su Y H. 2020. Regulation of cell reprogramming by auxin during somatic embryogenesis. aBIOTECH, 1, 185–193.

Tvorogova V E, Fedorova Y A, Potsenkovskaya E A, Kudriashov A A, Efremova E P, Kvitkovskaya V A, Wolabu T W, Zhang F, Tadege M, Lutova L A. 2019. The WUSCHEL-related homeobox transcription factor MtWOX9-1 stimulates somatic embryogenesis in Medicago truncatula. Plant Cell Tissue & Organ Culture, 138, 517–527.

Wang D, Chen L, Yang Y B, Abbas F, Qin Y Q, Lu H L, Lai B, Wu Z C, Hu B, Qin Y H, Wang H C, Zhao J T, Hu G B. 2023. Integrated metabolome and transcriptome analysis reveals the cause of anthocyanin biosynthesis deficiency in litchi aril. Physiologia Plantarum, 175, e13860.

Wang Y, Pijut P M. 2014. Improvement of Agrobacterium-mediated transformation and rooting of black cherry. In Vitro Cellular and Development Biology, 50, 307–316.

Wei Y Z, Hu F C, Hu G B, Li X J, Huang X M, Wang H C. 2011. Differential expression of anthocyanin biosynthetic genes in relation to anthocyanin accumulation in the pericarp of Litchi chinensis Sonn. PLoS ONE, 6, e19455.

Wójcik A M, Wójcikowska B, Gaj M D. 2020. Current perspectives on the auxin-mediated genetic network that controls the induction of somatic embryogenesis in plants. International Journal of Molecular Sciences, 21, 1333–1352.

Xie X B, Li S, Zhang R F, Zhao J, Chen Y C, Zhao Q, Yao Y X, You C X, Zhang X S, Hao Y J. 2012. The bHLH transcription factor MdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples. Plant, Cell & Environment, 35, 1884–1897.

Xu W J, Dubos C, Lepiniec L. 2015. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Science, 20, 176–185.

Yao J L, Cohen D, Atkinson R, Richardson K, Morris B. 1995. Regeneration of transgenic plants from the commercial apple cultivar Royal Gala. Plant Cell Report, 14, 407–412.

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, 14–26.

Zhang B, Yang H J, Qu D, Zhu Z Z, Yang Y Z, Zhao Z Y. 2022. The MdBBX22-miR858-MdMYB9/11/12 module regulates proanthocyanidin biosynthesis in apple peel. Plant Biotechnology Journal, 20, 1683–1700.

Zhao R, Qi S, Cui Y, Gao Y, Jiang S, Zhao J, Zhang J, Kong L. 2022. Transcriptomic and physiological analysis identifies a gene network module highly associated with brassinosteroid regulation in hybrid sweetgum tissues differing in the capability of somatic embryogenesis. Horticulture Research, 9, uhab047.

Zheng L, Liao L, Duan C, Ma W, Peng Y, Yuan Y, Han Y, Ma F, Li M, Ma B. 2023. Allelic variation of MdMYB123 controls malic acid content by regulating MdMa1 and MdMa11 expression in apple. Plant Physiology, 192, 1877–1891.

Ziemienowicz A. 2014. Agrobacterium-mediated plant transformation: Factors, applications and recent advances. Biocatalysis and Agricultural Biotechnology, 4, 95–102.