Yang Junwei, Liu Yun, Liang Bin, Yang Qinqin, Li Xuecheng, Chen Jiacai, Li Hongwei, Lyu Yaqing, Lin Tao
State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Hortic Res. 2023 Jul 8;10(8):uhad142. doi: 10.1093/hr/uhad142. eCollection 2023 Aug.
The long and intricate domestication history of the tomato () includes selection sweeps that have not been fully explored, and these sweeps show significant evolutionary trajectories of domestication traits. Using three distinct selection strategies, we represented comprehensive selected sweeps from 53 (PIM) and 166 (BIG) accessions, which are defined as pseudo-domestication in this study. We identified 390 potential selection sweeps, some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process. During tomato pseudo-domestication, we discovered a minor-effect allele of the gene related to fruit weight (FW), as well as the major haplotypes of / (), /, and / () in cultivars. Furthermore, 18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies. By examining population differentiation, we identified the causative variation underlying the divergence of fruit flavonoids across the large-fruited tomatoes and validated (), a gene that may affect flavonoid content by modulating the expression profile. Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.
番茄漫长而复杂的驯化历史包括尚未得到充分探索的选择清除，这些选择清除显示出驯化性状的显著进化轨迹。我们采用三种不同的选择策略，展示了来自53份秘鲁番茄（PIM）和166份大果番茄（BIG）种质的全面选择清除情况，在本研究中这些被定义为伪驯化。我们鉴定出390个潜在的选择清除区域，其中一些对果实相关性状有显著影响，并且对伪驯化过程至关重要。在番茄伪驯化过程中，我们发现了一个与果实重量（FW）相关的基因的微效等位基因，以及栽培品种中SlARF4/SlARF5（ARF4/ARF5）、SlARF6/SlARF8（ARF6/ARF8）和SlARF2/ SlARF7（ARF2/ARF7）的主要单倍型。此外，在全基因组关联研究中发现18个位点与FW以及六个果实相关农艺性状显著相关。通过研究群体分化，我们确定了大果番茄果实类黄酮差异的因果变异，并验证了SlMYB12基因，该基因可能通过调节CHS表达谱来影响类黄酮含量。我们的结果为果实性状的遗传基础提供了新的研究途径，并为番茄基因组辅助育种提供了优良的基因组资源。
