The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

Author:

Liao Xuezhu,Ye Yuanjun,Zhang Xiaoni,Peng Dan,Hou Mengmeng,Fu Gaofei,Tan Jianjun,Zhao Jianli,Jiang Rihong,Xu Yechun,Liu Jinmei,Yang Jinliang,Liu Wusheng,Tembrock Luke R.,Zhu Genfa,Wu ZhiqiangORCID

Abstract

AbstractCompared 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.

Funder

The Chinese Academy of Agricultural Sciences Elite Youth Program and Kunpeng Institute of Modern Agriculture at Foshan

The opening project of Laboratory of Ecology and Evolutionary Biology from Yunnan University

The project of Shenzhen Zhongnonghuadu Ecological Technology Co., Ltd.

the USDA National Institute of Food and Agriculture Hatch project

Publisher

Springer Science and Business Media LLC

Subject

Plant Science,Genetics,Agronomy and Crop Science,Biochemistry, Genetics and Molecular Biology (miscellaneous),Molecular Biology,Biotechnology

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