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Ed.)"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1111\/nph.14284","article-title":"Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots","volume":"214","author":"Wei","year":"2017","journal-title":"New Phytol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1111\/pbi.13033","article-title":"Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death","volume":"17","author":"Guo","year":"2019","journal-title":"Plant Biotechnol. 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