Transcriptomic analysis of contrasting inbred lines and F2 segregant of Chinese cabbage provides valuable information on leaf morphology
Leaf morphology influences plant growth and productivity and is controlled by genetic and environmental cues. The various morphotypes of Brassica rapa provide an excellent resource for genetic and molecular studies of morphological traits.
This study aimed to identify genes regulating leaf morphology using segregating B. rapa p F2 population.
Phenotyping and transcriptomic analyses were performed on an F2 population derived from a cross between Rapid cycling B. rapa (RCBr) and B. rapa ssp. penkinensis, inbred line Kenshin. Analyses focused on four target traits: lamina (leaf) length (LL), lamina width (LW), petiole length (PL), and leaf margin (LM).
All four traits were controlled by multiple QTLs, and expression of 466 and 602 genes showed positive and negative correlation with leaf phenotypes, respectively. From this microarray analysis, large numbers of genes were putatively identified as leaf morphology-related genes. The Gene Ontology (GO) category containing the highest number of differentially expressed genes (DEGs) was “phytohormones”. The sets of genes enriched in the four leaf phenotypes did not overlap, indicating that each phenotype was regulated by a different set of genes. The expression of BrAS2, BrAN3, BrCYCB1;2, BrCYCB2;1,4, BrCYCB3;1, CrCYCBD3;2, BrULT1, and BrANT seemed to be related to leaf size traits (LL and LW), whereas BrCUC1, BrCUC2, and BrCUC3 expression for LM trait.
An analysis integrating the results of the current study with previously published data revealed that Kenshin alleles largely determined LL and LW but LM resulted from RCBr alleles. Genes identified in this study could be used to develop molecular markers for use in Brassica breeding projects and for the dissection of gene function.
KeywordsBr135K microarray DEGs Leaf phenotype Leaf size Brassica rapa Kenshin Rapid cycling Brassica rapa.
This work was supported by a grant from the Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry, and Fisheries (Grant 213007-05-2-SB620), Republic of Korea.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest, financial or otherwise.
Human and animal rights
No animals/humans were used for studies that are base of this research.
- Albinsky D, Kusano M, Higuchi M, Hayashi N, Kobayashi M, Fukushima A, Mori M, Ichikawa T, Matsui K, Kuroda H, Horii Y, Tsumoto Y, Sakakibara H, Hirochika H, Matsui M, Saito K (2010) Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism. Mol Plant 3:125–142CrossRefGoogle Scholar
- Ashburner M. Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefGoogle Scholar
- Bonnema G, Carpio DPD, Zhao JJ (2011) Diversity analysis and molecular taxonomy of Brassica vegetable crops. In: Kole C, Sadowski J (eds) Genetics, genomics and breeding of crop plants. Science Publishers, pp 81–124Google Scholar
- Cavalier DM, Lerouxel O, Neumetzler L, Yamauchi K, Reinecke A, Freshour G, Zabotina OA, Hahn MG, Burgert I, Pauly M, Raikhel NV, Keegstra K (2008) Disrupting two Arabidopsis thaliana xylosyltransferase genes results in plants deficient in xyloglucan, a major primary cell wall component. Plant Cell 20:1519–1537CrossRefGoogle Scholar
- Choi SR, Yu X, Dhandapani V, Li X, Wang Z, Lee SY, Oh SH, Pang W, Ramchiary N, Hong CP, Park S, Piao Z, Kim H, Lim YP (2017) Integrated analysis of leaf morphological and color traits in different populations of Chinese cabbage (Brassica rapa ssp. pekinensis). Theor Appl Genet 130:1617–1634CrossRefGoogle Scholar
- Goldman IL (1999) Teaching recurrent selection in the classroom with Wisconsin fast plants. Hort Technol 9:579–584Google Scholar
- Iwakawa H, Iwasaki M, Kojima S, Ueno Y, Soma T, Tanaka H, Semiarti E, Machida Y, Machida C (2007) Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves. Plant J 51:173–184CrossRefGoogle Scholar
- Kim GT, Cho KH (2006) Recent advances in the genetic regulation of the shape of simple leaves. Physiol Plant 126:494–502Google Scholar
- Li X, Ramchiary N, Dhandapani V, Choi SR, Hur Y, Nou IS, Yoon MK, Lim YP (2013) Quantitative trait loci mapping in Brassica rapa revealed the structural and functional conservation of genetic loci governing morphological and yield component traits in the A, B, and C subgenomes of Brassica species. DNA Res 20:1–16CrossRefGoogle Scholar
- Li X, Wang W, Wang Z, Li K, Lim YP, Piao Z (2015) Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa. Front Plant Sci 6:432Google Scholar
- Plackett AR, Powers SJ, Fernandez-Garcia N, Urbanova T, Takebayashi Y, Seo M, Jikumaru Y, Benlloch R, Nilsson O, Ruiz-Rivero O, Phillips AL, Wilson ZA, Thomas SG, Hedden P (2012) Analysis of the developmental roles of the Arabidopsis gibberellin 20-oxidases demonstrates that GA20ox1, -2, and -3 are the dominant paralogs. Plant Cell 24:941–960CrossRefGoogle Scholar
- Rédei GP, Hirono Y (1964) Linkage studies. Arabidopsis Inf Serv 1:9–10Google Scholar
- Semiarti E, Ueno Y, Tsukaya H, Iwakawa H, Machida C, Machida Y (2001) The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves. Development 128:1771–1783Google Scholar