A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

Feiyang Ji; Qingguo Ma; Wenting Zhang; Jie Liu; Yu Feng; Peng Zhao; Xiaobo Song; Jiaxin Chen; Junpei Zhang; Xin Wei; Ye Zhou; Yingying Chang; Pu Zhang; Xuehui Huang; Jie Qiu; Dong Pei

doi:10.1186/s13059-021-02517-6

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

Genome Biol. 2021 Oct 27;22(1):300. doi: 10.1186/s13059-021-02517-6.

Authors

Feiyang Ji¹, Qingguo Ma¹, Wenting Zhang², Jie Liu², Yu Feng³, Peng Zhao⁴, Xiaobo Song¹, Jiaxin Chen², Junpei Zhang¹, Xin Wei², Ye Zhou¹, Yingying Chang⁵, Pu Zhang¹, Xuehui Huang², Jie Qiu⁶, Dong Pei⁷

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
² Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
³ Systematic & Evolutionary Botany and Biodiversity group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
⁴ Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
⁵ Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan Province, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs of Colleges and Universities in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.
⁶ Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China. [email protected].
⁷ State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China. [email protected].

Abstract

Background: Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored.

Results: We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively.

Conclusions: The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

Keywords: Adaptation; GWAS; Improvement; Juglans regia; Walnut.

Publication types

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

MeSH terms

Crop Production
Environment
Evolution, Molecular
Genetic Variation
Genome, Plant*
Juglans / genetics*
Mutation