Haplotype Analysis of Chloroplast Genomes for Jujube Breeding

Guanglong Hu; Yang Wu; Chaojun Guo; Dongye Lu; Ningguang Dong; Bo Chen; Yanjie Qiao; Yuping Zhang; Qinghua Pan

doi:10.3389/fpls.2022.841767

Haplotype Analysis of Chloroplast Genomes for Jujube Breeding

Front Plant Sci. 2022 Mar 10:13:841767. doi: 10.3389/fpls.2022.841767. eCollection 2022.

Authors

Guanglong Hu¹, Yang Wu¹, Chaojun Guo¹, Dongye Lu¹, Ningguang Dong¹, Bo Chen¹, Yanjie Qiao¹, Yuping Zhang¹, Qinghua Pan¹

Affiliation

¹ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.

Abstract

Jujube (family Rhamnaceae) is an important economic fruit tree in China. In this study, we reported 26 chloroplast (cp) sequences of jujube using Illumina paired-end sequencing. The sequence length of cp genome was 161, 367-161, 849 bp, which was composed of a large single-copy region (89053-89437 bp) and a small single-copy region (19356-19362 bp) separated by a pair of reverse repeat regions (26478-26533 bp). Each cp genome encodes the same 130 genes, including 112 unique genes, being quite conserved in genome structure and gene sequence. A total of 118 single base substitutions (SNPs) and 130 InDels were detected in 65 jujube accessions. Phylogenetic and haplotype network construction methods were used to analyze the origin and evolution of jujube and its sour-tasting relatives. We detected 32 effective haplotypes, consisting of 20 unique jujube haplotypes and 9 unique sour-jujube haplotypes. Compared with sour-jujube, jujube showed greater haplotype diversity at the chloroplast DNA level. To cultivate crisp and sweet fruit varieties featuring strong resistance, by combining the characteristics of sour-jujube and cultivated jujube, three hybrid combinations were suggested for reciprocal crosses: "Dongzao" × "Jingzao39," "Dongzao" × "Jingzao60," "Dongzao" × "Jingzao28." This study provides the basis for jujube species' identification and breeding, and lays the foundation for future research.

Keywords: Ziziphus jujuba; breeding strategy; chloroplast genome; evolutionary relationship; genomic structure; phylogenetic analysis.

Grants and funding

This work was financially supported by the Special Fund for the Construction of Scientific and Technological Innovation Capability (Grant Nos. KJCX20220101 and KJCX20210114), the Key Research and Design Program of Hebei Province (Grant No. 20326807D), and the Presidential Foundation of Institute of Forestry and Pomology (Grant Nos. LGYJJ202000 and LGYJJ202002).