Li Xiongwei, Wang Jiabo, Su Mingshen, Zhang Minghao, Hu Yang, Du Jihong, Zhou Huijuan, Yang Xiaofeng, Zhang Xianan, Jia Huijuan, Gao Zhongshan, Ye Zhengwen
Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University, Ministry of Education), Chengdu, Sichuan 610041, China.
Hortic Res. 2023 May 31;10(7):uhad117. doi: 10.1093/hr/uhad117. eCollection 2023 Jul.
'Chinese Cling' is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and -3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the 'Shanghai Shuimi' landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.
“中华粘核”因其风味宜人，是桃育种史上的重要创始品种。全基因组关联研究（GWAS）与基因组选择相结合是果树育种中很有前景的工具，因为从杂交到品种发布之间存在相当长的时间间隔。在本研究中，对来自上海种质资源的242个桃子进行了基因分型，共检测到145456个单核苷酸多态性（SNP）。记录了果肉颜色、果实形状、果面茸毛、花型、花粉不育性、可溶性固形物含量这六个农艺性状，以及14种关键挥发性气味化合物（VOC），用于多性状GWAS分析。除了已报道的候选基因外，还鉴定出六个与这些性状相关的新基因。39个显著的SNP与八种VOC相关。通过RNA测序对VOC的推定候选基因进行了验证，包括在生物合成途径中发现的与芳樟醇、可溶性固形物含量和乙酸-3-己烯酯相关的三个基因。与单性状模型值0.1017相比，多性状基因组预测将γ-癸内酯的预测能力提高到了0.7415。设计了一个PTS1-SSR标记来预测芳樟醇含量，并确认了有利基因型187/187，主要存在于“上海水蜜”地方品种中。总体而言，我们的研究结果将有助于确定具有理想表型的桃品种，并显示多性状基因组预测在提高高度相关遗传性状准确性方面的潜力。该诊断标记对于育种者弥合数量性状位点与标记辅助选择之间的差距以培育强香型品种具有重要价值。
