Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube

Abstract

Summary The Chinese jujube (Ziziphus jujuba Mill.), a member of the Rhamnaceae family, is an important perennial fruit tree crop of substantial economic, ecological and nutritional value, and is also used as a traditional herbal medicine. Here, we report the resequencing of 493 jujube accessions, including 202 wild and 291 cultivated accessions at >16× depth. Our population genomic analyses revealed that the Shanxi–Shaanxi area of China was jujube's primary domestication centre and that jujube was then disseminated into East China before finally extending into South China. Divergence events analysis indicated that Ziziphus acidojujuba and Ziziphus jujuba diverged around 2.7 Mya, suggesting the interesting possibility that a long pre‐domestication period may have occurred prior to human intervention. Using the large genetic polymorphism data set, we identified a 15‐bp tandem insertion in the promoter of the jujube ortholog of the POLLEN DEFECTIVE IN GUIDANCE 1 (POD1) gene, which was strongly associated with seed‐setting rate. Integrating genome‐wide association study (GWAS), transcriptome data, expression analysis and transgenic validation in tomato, we identified a DA3/UBIQUITIN‐SPECIFIC PROTEASE 14 (UBP14) ortholog, which negatively regulate fruit weight in jujube. We also identified candidate genes, which have likely influenced the selection of fruit sweetness and crispness texture traits among fresh and dry jujubes. Our study not only illuminates the genetic basis of jujube evolution and domestication and provides a deep and rich genomic resource to facilitate both crop improvement and hypothesis‐driven basic research, but also identifies multiple agriculturally important genes for this unique perennial tree fruit species.

Domestication of Crop Metabolomes: Desired and Unintended Consequences

“…In recent years transcriptomics has been used to study the effect of domestication on a wide range of species including the major cereals rice [47,48], maize [49,50], wheat (Triticum aestivum) [51], and barley [52], as well as cotton (Gossypium hirsutum) [53], tomato [54,55], eggplant (Solanum melongena) [56,57], peppers [58], sunflower (Helianthus annuus) [59], common bean (Phaseolus vulgaris) [60], curcubita [61], and a range of more other crops including chickpea (Cicer arietinum) [62], lupin (Lupinus albus) [63], pistachio (Pistacia vera) [64], spinach (Spinacia oleracea) [65], lettuce (Lactuca sativa) [66], and jujube (Ziziphus jujube) [67]. A common theme that emerges from these studies is that domestication is associated with a large reduction in allelic diversity, with estimates suggesting that our current crops contain on average only 6% of the allelic diversity present in wild species gene pools [68].…”

Morphological and Biochemical Diversity in Fruits of Unsprayed Rosa canina and Rosa dumalis Ecotypes Found in Different Agroecological Conditions

“…Our results on fruit-flesh ratio was comparable with the above studies. Wild edible fruits had greater gene diversity and they also had unique gene combinations [40][41][42]. It is well understanding that wild species increase crop genetic diversity [39,43].…”

Re-Sequencing and Transcriptomic Analysis Reveal Differences in Nitrite Reductase in Jujube Fruit (Ziziphus Jujube)

“…[10]. Cultivated jujube trees and wild jujube showed different characteristics, such as tree vs. shrub habit, sparsely thorned vs. heavily thorned, and large vs. small fruits, respectively, through arti cial selection for important agronomic characters [8,11,12]. Most cultivated jujube varieties produce relatively fewer seeds due to self-incompatibility or cross-incompatibility.…”