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. 2023 Apr 5;23(1):179.
doi: 10.1186/s12870-023-04147-5.

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

Hao Niu  1 , Meng Kuang  1 , Longyu Huang  1 , Haihong Shang  2   3 , Youlu Yuan  4 , Qun Ge  5
Affiliations

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

Hao Niu et al. BMC Plant Biol. .

Abstract

Background: Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield.

Results: Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation.

Conclusions: A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.

Keywords: Boll weight; Candidate gene; Lint percentage; Quantitative trait locus (QTL); Upland cotton (Gossypium hirsutum L.).

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Fig. 1
Fig. 1
The histograms of the LP and BW in P-EZ60 (EZ60) and P-CCRI60 (CCRI60) in Anyang and Weixian in 2020 and 2021
Fig. 2
Fig. 2
Manhattan-plots of LP and BW using the genetic model 3VmrMLM. X-axes are cotton chromosomes. Y-axes on the left side report -log10 P-values of the main-effect QTNs, which were obtained from single-marker genome-wide scans for all the markers in the first step of 3VmrMLM; Y-axes on the right side report LOD scores, which were obtained from likelihood ratio tests for significant and suggested QTNs, with a threshold of LOD = 3.0 (dashed line) in the second step of 3VmrMLM. These LOD scores are indicated by points with straight lines
Fig. 3
Fig. 3
A physical map of QTLs for LP and BW from the two RIL populations. The green letters are QTLs for LP, and the red letters are QTLs for BW. The scale on the left is in Mb
Fig. 4
Fig. 4
A histogram of candidate genes enriched in different KEGG pathways for LP. The x-axis indicates the number of candidate genes. The y-axis represents biological processes. The details are listed in Table S9
Fig. 5
Fig. 5
A histogram of candidate genes enriched in different KEGG pathways for BW. The x-axis indicates the number of candidate genes. The y-axis represents biological processes. The details are listed in Table S10
Fig. 6
Fig. 6
Gene expression profiles of the candidate genes of LP and BW QTLs during fiber development in EZ60 and ZR014121. Each column represents one sample, and rows represent candidate genes. The expression levels of the candidate genes (FPKM) were log2-normalized (i.e., log2(FPKM + 0.01)) and presented in different colours on the scale bar. ZR indicates cotton line ZR014121; DPA indicates days post-anthesis. 0 DPA represents the ovule development stage. 5, 10, 15, 20, and 25 DPA represent the fiber development stages. Detailed information on gene expression is shown in Table S11
Fig. 7
Fig. 7
Protein–protein interaction of the candidate genes of the QTLs for LP and BW. Network nodes represent proteins with splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus. Colored nodes: query proteins and first shell of interactors; white nodes: second shell of interactors; Empty nodes: unknown proteins. 3D structure filled nodes: some 3D structures are known or predicted. Edges represent protein–protein associations. Associations are meant to be specific and meaningful (i.e., proteins jointly contribute to a shared function); this does not necessarily mean that they physically bind to each other. Known Interactions, blue: from curated databases; purple: experimentally determined. Predicted Interactions, green: gene neighborhood, red: gene fusions; indigo: gene co-occurrence; Others, yellow: textmining, black: co-expression, light purple: protein homology
Fig. 8
Fig. 8
Major gene coexpression network of the candidate genes of the QTLs for LP and BW. Lines indicate co-expression of two linked genes. Network nodes represent genes. The size of the circle shows the betweenness centrality points of the gene. The size of the circle indicates that the gene plays an important role in co-expression. In this graph, genes with higher betweenness centrality points are marked in green and placed in the outer circle, and genes with smaller BC values are marked in red and placed in the inner circle. The three genes in the outer ring, Gh_D03G1056, Gh_D03G1064, and Gh_D03G1134 were candidate genes for LP, and Gh_A02G0111 was a candidate gene for BW
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