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Article|07 Feb 2022|OPEN
Integration of genomics, transcriptomics and metabolomics identifies candidate loci underlying fruit weight in loquat
Ze Peng1 ,† , Chongbin Zhao1 ,† , Shuqing Li1 , Yihan Guo1 , Hongxia Xu3 , Guibing Hu1 , Zongli Liu1 , Xiuping Chen2 , Junwei Chen3 , Shunquan Lin1 , Wenbing Su1,2 , , Xianghui Yang,1 ,
1State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China
2Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
3Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
*Corresponding author. E-mail: suwenbing13@163.com,gzyxh@scau.edu.cn
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhac037 (2022)
doi: https://doi.org/10.1093/hr/uhac037
Views: 191

Received: 03 Nov 2021
Accepted: 30 Jan 2022
Published online: 07 Feb 2022

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.