Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd

Pei Xu; Ying Wang; Fengshuo Sun; Rongling Wu; Huilong Du; Yuhong Wang; Libo Jiang; Xiaohua Wu; Xinyi Wu; Liming Yang; Nailin Xing; Yaowen Hu; Baogen Wang; Yunping Huang; Ye Tao; Qiang Gao; Chengzhi Liang; Yanwei Li; Zhongfu Lu; Guojing Li

doi:10.1111/tpj.15358

Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd

Plant J. 2021 Aug;107(3):956-968. doi: 10.1111/tpj.15358. Epub 2021 Jul 5.

Authors

Pei Xu^{1

2}, Ying Wang¹, Fengshuo Sun³, Rongling Wu^{3

4}, Huilong Du⁵, Yuhong Wang⁶, Libo Jiang³, Xiaohua Wu¹, Xinyi Wu¹, Liming Yang⁷, Nailin Xing⁶, Yaowen Hu¹, Baogen Wang¹, Yunping Huang⁶, Ye Tao⁸, Qiang Gao⁵, Chengzhi Liang⁵, Yanwei Li¹, Zhongfu Lu¹, Guojing Li^{1

2}

Affiliations

¹ Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
² State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
³ Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
⁴ Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, USA.
⁵ Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
⁶ Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China.
⁷ College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
⁸ Biozeron Biotechnology Co., Ltd, Shanghai, China.

PMID: 34043857
DOI: 10.1111/tpj.15358

Abstract

The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

Keywords: bottle gourd; fruit shape; functional mapping; genome; geometric morphometrics; long-read sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cucurbitaceae / genetics*
Cucurbitaceae / physiology*
Fruit / anatomy & histology*
Fruit / genetics*
Gene Expression Regulation, Plant / physiology*
Genome, Plant / physiology*
Quantitative Trait Loci
Synteny