State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
Genome Biol. 2021 Oct 27;22(1):300. doi: 10.1186/s13059-021-02517-6.
Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored.
We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively.
The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.
普通核桃（Juglans regia L.）由于其健康益处和宜人的口感，是世界上四大最受欢迎的坚果之一。尽管具有经济重要性，但对其适应和农艺性状的进化历史和遗传控制仍在很大程度上未被探索。
我们基于 815 个核桃样本的全基因组重测序，报告了一个全面的核桃基因组变异图谱。进化分析表明，中国的 J. regia 与 J. sigillata 分化，在两个物种分裂后发生了广泛的杂交。与一年生作物不同，中国普通核桃在改良过程中，遗传多样性和杂合有害突变持续增加。选择扫描分析确定了 902 个在改良普通核桃中与亲本组群相比独特选择的基因。鉴定出 5 个主要效应位点参与了核桃对温度、降水和海拔的适应。全基因组关联研究揭示了 27 个与 18 个重要农艺性状相关的基因组位点，其中 JrFAD2 和 JrANR 分别是控制油酸含量和坚果内果皮颜色的潜在主要效应候选基因。
本研究产生并探索了迄今为止最大的核桃基因组资源，揭示了它们的进化历史，并破解了这种经济上至关重要的作物树木的农艺性状和环境适应的遗传密码。
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