Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits

Xiaofeng Cai; Xuepeng Sun; Chenxi Xu; Honghe Sun; Xiaoli Wang; Chenhui Ge; Zhonghua Zhang; Quanxi Wang; Zhangjun Fei; Chen Jiao; Quanhua Wang

doi:10.1038/s41467-021-27432-z

Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits

Nat Commun. 2021 Dec 13;12(1):7246. doi: 10.1038/s41467-021-27432-z.

Authors

Xiaofeng Cai^#^{1

2}, Xuepeng Sun^#^{3

4}, Chenxi Xu^#¹, Honghe Sun^{3

5}, Xiaoli Wang¹, Chenhui Ge¹, Zhonghua Zhang⁶, Quanxi Wang⁷, Zhangjun Fei^{8

9}, Chen Jiao^#^{10

11}, Quanhua Wang¹²

Affiliations

¹ Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China.
² Qinghai Key Laboratory of Vegetable Genetics and Physiology, Qinghai University, 810016, Xining, China.
³ Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
⁴ College of Agriculture and Food Science, Zhejiang A&F University, 311300, Hangzhou, China.
⁵ Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
⁶ Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, 266109, Qingdao, China.
⁷ College of Life Science and Technology, Harbin Normal University, 150025, Harbin, China. wangqx@shnu.edu.cn.
⁸ Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. zf25@cornell.edu.
⁹ USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, 18, USA. zf25@cornell.edu.
¹⁰ Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. biochenjiao@zju.edu.cn.
¹¹ Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China. biochenjiao@zju.edu.cn.
¹² Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China. wangquanhua@shnu.edu.cn.

^# Contributed equally.

Abstract

Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.

Publication types

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

MeSH terms

Chenopodiaceae / genetics
Chromosomes, Plant / genetics
Domestication*
Genetic Variation
Genome, Plant / genetics*
Genomics
Karyotype
Phenotype
Phylogeny
Plant Breeding
Spinacia oleracea / genetics*
Vegetables / genetics*