Integration of genomics, transcriptomics and metabolomics identifies candidate loci underlying fruit weight in loquat

生物 数量性状位点 种质资源 人口 转录组 枇杷属 基因组学 粳稻 代谢组学 候选基因 功能基因组学 遗传学 基因组 生物技术 植物 基因 生物信息学 基因表达 人口学 社会学
作者
Ze Peng,Chongbin Zhao,Shuqing Liu,Yihan Guo,Huji Xu,Guibing Hu,Zongli Liu,Xiuping Chen,Junwei Chen,Shunquan Lin,Weixu Su,Xianghui Yang
出处
期刊:Horticulture research [Nature Portfolio]
卷期号:9 被引量:9
标识
DOI:10.1093/hr/uhac037
摘要

Abstract Fruit weight is an integral part of fruit quality and directly influences the commodity value and economic return of fruit crops. Despite the importance of fruit weight, its underlying molecular mechanisms remain understudied, especially for perennial fruit tree crops such as cultivated loquat (Eriobotrya japonica Lindl.). Auxin is known to regulate fruit development, but its role and metabolism during the development of loquat fruit remain obscure. In this study, we used a multi-omics approach, integrating whole-genome resequencing-based quantitative trait locus (QTL) mapping with an F1 population, population genomics analysis using germplasm accessions, transcriptome analysis, and metabolic profiling to identify genomic regions potentially associated with fruit weight in loquat. We identified three major loci associated with fruit weight, supported by both QTL mapping and comparative genomic analysis between small- and large-fruited loquat cultivars. Comparison between two genotypes with contrasting fruit weight performance by transcriptomic and metabolic profiling revealed an important role for auxin in the regulation of fruit development, especially at the fruit enlargement stage. The multi-omics approach identified homologs of ETHYLENE INSENSITIVE 4 (EjEIN4) and TORNADO 1 (EjTRN1) as promising candidates for the control of fruit weight. Three single nucleotide polymorphism (SNP) markers were also closely associated with fruit weight. Results from this study provide insights into the genetic and metabolic controls of fruit weight in loquat from multiple perspectives. The candidate genomic regions, genes, and sequence variants will facilitate our understanding of the molecular basis of fruit weight and lay a foundation for future breeding and manipulation of fruit weight in loquat.
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