![]() ![]() ![]() ![]() These results will improve our understanding of the lychee genome, accelerating genetic improvement of lychee and its relatives in Sapindaceae. We also investigated expression patterns of allelic genes and potential regulatory mechanisms involved in timing of flowering and fruit maturation. To address these questions and provide a genome-enabled breeding platform, we generated a high-quality reference genome of the highly heterozygous cultivar ‘Feizixiao’ (2 n = 2× = 30) and resequenced 72 wild or cultivated accessions to explore the structure and evolution of the lychee genome as well as its origin and domestication history. However, the exact center(s) of origin and the history of lychee domestication remains unknown. Lychee originated in broad, yet isolated and distant, regions of southern China, where numerous wild lychees exist in the Hainan and Yunnan rainforests, and hilly areas of western Guangdong and eastern Guangxi. The extreme perishability of lychee fruit renders it impossible to sustain a fresh, year-round supply. About 80% of fruits are produced within a short period from early June to mid-July. EEMCs are rare and of little production value, while cultivars with better fruit quality always belong to the LMC group. Lychee cultivars are classified into three groups based on the fruit maturation period: extremely early maturing cultivars (EEMC), early-to-intermediate-maturing cultivars (EMC) and late-maturing cultivars (LMC) 2, 3. Over 400 lychee cultivars are preserved at the National Lychee Germplasm Resources in Guangzhou, China. This long cultivation history has facilitated the generation of diverse lychee germplasm. The oldest lychee tree, ‘Songxiang’, from Fujian, China, is over 1,250 years old, and is still fruiting today. Lychee trees have the longest productive lifespans among tropical and subtropical fruit trees. In the ancient Tang Dynasty, roughly 1,300–1,100 years ago, the Emperor set up a courier service with fast horse relays to transport fresh lychee from southern China to the imperial court because of the prodigious flavor of this spoilable fruit. The earliest record of lychee cultivation traces back to the second century bc. Lychee has been cultivated in southern China for millennia. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. Lychee is an exotic tropical fruit with a distinct flavor. Nature Genetics volume 54, pages 73–83 ( 2022) Cite this article ![]() Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars ![]()
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