Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis

Binbin Du; Jindong Wu; Meng Wang; Jia Wu; Chaoyue Sun; Xingen Zhang; Xifeng Ren; Qifei Wang

doi:10.3389/fpls.2023.1319889

Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis

Front Plant Sci. 2024 Jan 11:14:1319889. doi: 10.3389/fpls.2023.1319889. eCollection 2023.

Authors

Binbin Du¹, Jindong Wu¹, Meng Wang², Jia Wu¹, Chaoyue Sun¹, Xingen Zhang¹, Xifeng Ren³, Qifei Wang⁴

Affiliations

¹ College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, China.
² Xingtai Agriculture and Rural Bureau, Xingtai, Hebei, China.
³ Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
⁴ Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.

Abstract

Improving barley grain quality is a major goal in barley breeding. In this study, a total of 35 papers focusing on quantitative trait loci (QTLs) mapping for barley quality traits published since 2000 were collected. Among the 454 QTLs identified in these studies, 349 of them were mapped onto high-density consensus maps, which were used for QTL meta-analysis. Through QTL meta-analysis, the initial QTLs were integrated into 41 meta-QTLs (MQTLs) with an average confidence interval (CI) of 1. 66 cM, which is 88.9% narrower than that of the initial QTLs. Among the 41 identified MQTLs, 25 were subsequently validated in publications using genome-wide association study (GWAS). From these 25 validated MQTLs, ten breeder's MQTLs were selected. Synteny analysis comparing barley and wheat MQTLs revealed orthologous relationships between eight breeder's MQTLs and 45 wheat MQTLs. Additionally, 17 barley homologs associated with rice quality traits were identified within the regions of the breeder's MQTLs through comparative analysis. The findings of this study provide valuable insights for molecular marker-assisted breeding and the identification of candidate genes related to quality traits in barley.

Keywords: MQTL; QTL meta-analysis; barley; candidate gene; quality traits.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This project was supported by the National Natural Science Foundation of China (Grant No. 32001493) and the fund for High-level Talents Research Initiation Funding Project (Grant No. WGKQ2022029).