Haplotype Analysis of Chloroplast Genomes for Jujube Breeding

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.

Genomic divergence and demographic history of Quercus aliena populations

“…Chloroplast genomes are less commonly used at the intraspecies level owing to less polymorphism in practice [ 19 , 26 , 27 ]. However, with the advent of NGS sequencing methods, whole chloroplast genomes have been sequenced and used in population studies, such as of the medicinal plants Arnebia euchroma and Arnebia guttata [ 28 ], the endangered species Ulmus laevis [ 29 ] and Bretschneidera sinensis [ 30 ], the fruit tree Ziziphus jujuba [ 31 ], and the ornamental plants Aquilegia ecalcarata [ 15 ] and Lagerstroemia indica [ 32 ]. These findings suggest that chloroplast genome sequences contain many SNPs and indels suitable for genetic diversity and phylogeography studies.…”

The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq

“…It is particularly important to keep track of genetic inheritance patterns of haplotypes in crop breeding pedigrees to support new genomic combinations with desired traits ( Varshney et al, 2021 ). In jujube breeding, chloroplast genome haplotypes were previously used as a guide for the next breeding plan in order to produce fruits with highly desirable traits ( Hu et al, 2022 ). For a well-studied crop plant such as E. guineensis , only certain pedigrees are chosen because they carry the desired traits for commercial seed production.…”

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

“…The phylogeny of the species in Lagerstroemia was well resolved based on the whole plastome sequences from this paper and from previous studies [ 30 , 32 , 46 ], revealing the maternal donor of crape myrtle cultivars. Only a few studies have assessed the intraspecific variation of the whole plastomes and nrDNA sequences [ 18 , 20 , 21 , 47 , 48 ]. The plastid genome markers have less use in analyzing the genetic diversity of cultivars, owing to their limited polymorphic sites.…”