Pinpointing MQTLs and candidate genes related to early maturity in upland cotton through the integration of meta‑analysis, RNA-seq, and VIGS approaches

Early maturity is one of the primary traits associated with fiber yield, fiber quality and mechanized harvesting in China’s cotton agriculture. Mapping QTLs and mining candidate genes associated with maturity in cotton are critical for molecular improvement efforts that aim to increase early maturity traits in cotton. Integrating a large collection of cotton QTLs is an effective approach for revealing meta-QTLs (MQTLs) to identify candidate genes influencing early maturity in upland cotton. In this research, 1096 original QTLs linked to nine early maturity related traits were identified from 37 independent studies. Additionally, 772 initial QTLs were projected onto a consensus map containing 5051 markers, and 84 MQTLs were identified for traits related to early maturity. Among the MQTLs, 37 regions were verified via SNP loci reported in genome-wide association studies (GWAS) on early maturity traits in cotton. Finally, 118 candidate genes were successfully annotated in five major MQTL regions. Two candidate genes ( GhMYOB7 and GhNSRB ) linked to early maturity were identified via RNA-seq and qRT PCR experiments. Furthermore, virus-induced gene silencing (VIGS) revealed that GhMYOB7 and GhNSRB are crucial genes that control early flowering in cotton. The results of this study lay a foundation for exploring the genetic mechanisms underlying early maturity traits in upland cotton and provide a theoretical basis for the development of early maturity cotton cultivars. • MQTLs for traits related to early maturity were identified in upland cotton. • Out of 37 MQTLs that were verified by GWAS, five major MQTLs were detected. • Two key genes ( GhMYOB7 and GhNSRB ) associated with flowering time were identified.