Colle Marivi, Leisner Courtney P, Wai Ching Man, Ou Shujun, Bird Kevin A, Wang Jie, Wisecaver Jennifer H, Yocca Alan E, Alger Elizabeth I, Tang Haibao, Xiong Zhiyong, Callow Pete, Ben-Zvi Gil, Brodt Avital, Baruch Kobi, Swale Thomas, Shiue Lily, Song Guo-Qing, Childs Kevin L, Schilmiller Anthony, Vorsa Nicholi, Buell C Robin, VanBuren Robert, Jiang Ning, Edger Patrick P
Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.
MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.
Gigascience. 2019 Mar 1;8(3). doi: 10.1093/gigascience/giz012.
Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size.
Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development.
These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.
高丛蓝莓（Vaccinium corymbosum）长期以来因其独特的风味和具有促进健康作用的植物营养素成分而被食用。然而，由于缺乏足够的基因组资源以及对编码关键性状的潜在遗传学了解有限，蓝莓果实品质改良的育种工作受到了极大阻碍。高丛蓝莓的基因组组装尤其具有挑战性，很大程度上是由于其多倍体性质和基因组大小。
在此，我们展示了栽培品种“德雷珀”的染色体水平和单倍型定相基因组组装，该品种在由71个栽培品种和13个野生越橘物种组成的多样性群体中具有最高的抗氧化水平。我们利用这个基因组，结合在果实发育过程中测量的基因表达和代谢物数据，来鉴定参与重要植物营养素生物合成以及与优良果实品质相关的其他代谢物的候选基因。全基因组分析表明，多倍体和串联基因重复都改变了参与关键植物营养素生物合成的各种途径。此外，基因表达分析表明存在一个时空特异性优势表达的亚基因组，包括在果实发育期间。
这些发现和参考基因组将成为指导未来高丛蓝莓重要农艺性状基因组辅助育种的宝贵资源。
