QTL and candidate gene identification of the node of the first fruiting branch (NFFB) by QTL-seq in upland cotton (Gossypium hirsutum L.)

Jingjing Zhang,Meng Zhang,Xiaoqian Cheng,Shuxun Yu,Hengling Wei,Aimin Wu,Xiaoyun Jia,Hantao Wang,Xiaohao Guo,Shuaishuai Cheng

doi:10.1186/s12864-021-08164-2

Abstract

BackgroundThe node of the first fruiting branch (NFFB) is an important precocious trait in cotton. Many studies have been conducted on the localization of quantitative trait loci (QTLs) and genes related to fiber quality and yield, but there has been little attention to traits related to early maturity, especially the NFFB, in cotton.ResultsTo identify the QTL associated with the NFFB in cotton, a BC4F2 population comprising 278 individual plants was constructed. The parents and two DNA bulks for high and low NFFB were whole genome sequenced, and 243.8 Gb of clean nucleotide data were generated. A total of 449,302 polymorphic SNPs and 135,353 Indels between two bulks were identified for QTL-seq. Seventeen QTLs were detected and localized on 11 chromosomes in the cotton genome, among which two QTLs (qNFFB-Dt2–1 and qNFFB-Dt3–3) were located in hotspots. Two candidate genes (GhAPL and GhHDA5) related to the NFFB were identified using quantitative real-time PCR (qRT-PCR) and virus-induced gene silencing (VIGS) experiments in this study. Both genes exhibited higher expression levels in the early-maturing cotton material RIL182 during flower bud differentiation, and the silencing of GhAPL and GhHDA5 delayed the flowering time and increased the NFFB compared to those of VA plants in cotton.ConclusionsOur study preliminarily found that GhAPL and GhHDA5 are related to the early maturity in cotton. The findings provide a basis for the further functional verification of candidate genes related to the NFFB and contribute to the study of early maturity in cotton.

Highlights

The node of the first fruiting branch (NFFB) is an important precocious trait in cotton
The pCLCrVA::GhPDS-silenced plants had an obvious leaves whitening phenotype, which suggested that the virusinduced gene silencing (VIGS) assay was successful (Additional file 9: Fig. S5). quantitative real-time PCR (qRT-PCR) was performed to evaluate the effects of gene silencing, and the results showed that the expression levels of GhAPL and GhHDA5 in positive plants were downregulated by approximately 41 and 36%, respectively, compared to the levels in control plants (Fig. 7b)
Two major Quantitative trait loci (QTLs) for the NFFB were detected by QTL-seq and colocalization, and two candidate genes related to early maturity were obtained using qRT-PCR and VIGS assays

Summary

Introduction

The node of the first fruiting branch (NFFB) is an important precocious trait in cotton. Many studies have been conducted on the localization of quantitative trait loci (QTLs) and genes related to fiber quality and yield, but there has been little attention to traits related to early maturity, especially the NFFB, in cotton. Maturity is a very complex agronomic trait that involves budding date, growth period, flowering time, NFFB, and the height of the NFFB [3]. These quantitative traits related to early maturity are regulated by both quantitative trait loci and the environment, which are reflected in different genetic models [4, 5]. In order to improve the land competition between grain and cotton, cotton breeding for early maturity has attracted increasing attention

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Discussion

Conclusion