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The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation.
aBIOTECH. 2022 Sep; 3(3):178-196.A

Abstract

Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy "flowers" through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia "Chiang Mai Pink" and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a residual signal of whole-genome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among C. alismatifolia cultivars. In addition, we identified the key genes that produce different colored bracts in C. alismatifolia, such as F3'5'H, DFR, ANS and several transcription factors for anthocyanin synthesis, as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C. alismatifolia and related species. It is also important to understand the variation in the evolution of the Zingiberaceae family.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-022-00081-6.

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Authors+Show Affiliations

Liao X
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China.
Ye Y
Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China.
Zhang X
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China.
Peng D
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China.
Hou M
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China.
Fu G
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China.
Tan J
Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China.
Zhao J
Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650504 China.
Jiang R
Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest Crops, Guangxi Forestry Research Institute, Nanning, 530002 China.
Xu Y
Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China.
Liu J
Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China.
Yang J
Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA.
Liu W
Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607 USA.
Tembrock LR
Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523 USA.
Zhu G
Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China.
Wu Z
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China. Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200 China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

36304840

Citation

Liao, Xuezhu, et al. "The Genomic and Bulked Segregant Analysis of Curcuma Alismatifolia Revealed Its Diverse Bract Pigmentation." ABIOTECH, vol. 3, no. 3, 2022, pp. 178-196.
Liao X, Ye Y, Zhang X, et al. The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation. aBIOTECH. 2022;3(3):178-196.
Liao, X., Ye, Y., Zhang, X., Peng, D., Hou, M., Fu, G., Tan, J., Zhao, J., Jiang, R., Xu, Y., Liu, J., Yang, J., Liu, W., Tembrock, L. R., Zhu, G., & Wu, Z. (2022). The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation. ABIOTECH, 3(3), 178-196. https://doi.org/10.1007/s42994-022-00081-6
Liao X, et al. The Genomic and Bulked Segregant Analysis of Curcuma Alismatifolia Revealed Its Diverse Bract Pigmentation. aBIOTECH. 2022;3(3):178-196. PubMed PMID: 36304840.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation. AU - Liao,Xuezhu, AU - Ye,Yuanjun, AU - Zhang,Xiaoni, AU - Peng,Dan, AU - Hou,Mengmeng, AU - Fu,Gaofei, AU - Tan,Jianjun, AU - Zhao,Jianli, AU - Jiang,Rihong, AU - Xu,Yechun, AU - Liu,Jinmei, AU - Yang,Jinliang, AU - Liu,Wusheng, AU - Tembrock,Luke R, AU - Zhu,Genfa, AU - Wu,Zhiqiang, Y1 - 2022/10/06/ PY - 2022/07/08/received PY - 2022/09/05/accepted PY - 2022/10/28/entrez PY - 2022/10/29/pubmed PY - 2022/10/29/medline KW - Anthocyanin synthesis KW - Floriculture KW - Genome evolution KW - Siam tulip KW - Zingiberaceae SP - 178 EP - 196 JF - aBIOTECH JO - aBIOTECH VL - 3 IS - 3 N2 - : Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy "flowers" through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia "Chiang Mai Pink" and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a residual signal of whole-genome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among C. alismatifolia cultivars. In addition, we identified the key genes that produce different colored bracts in C. alismatifolia, such as F3'5'H, DFR, ANS and several transcription factors for anthocyanin synthesis, as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C. alismatifolia and related species. It is also important to understand the variation in the evolution of the Zingiberaceae family. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-022-00081-6. SN - 2662-1738 UR - https://www.unboundmedicine.com/medline/citation/36304840/The_genomic_and_bulked_segregant_analysis_of_Curcuma_alismatifolia_revealed_its_diverse_bract_pigmentation_ DB - PRIME DP - Unbound Medicine ER -