QTL Verification and Candidate Gene Screening of Fiber Quality and Lint Percentage in the Secondary Segregating Population of Gossypium hirsutum

Abstract

Fiber quality traits, especially fiber strength, length, and micronaire (FS, FL, and FM), have been recognized as critical fiber attributes in the textile industry, while the lint percentage (LP) was an important indicator to evaluate the cotton lint yield. So far, the genetic mechanism behind the formation of these traits is still unclear. Quantitative trait loci (QTL) identification and candidate gene validation provide an effective methodology to uncover the genetic and molecular basis of FL, FS, FM, and LP. A previous study identified three important QTL/QTL cluster loci, harboring at least one of the above traits on chromosomes A01, A07, and D12 via a recombinant inbred line (RIL) population derived from a cross of Lumianyan28 (L28) × Xinluzao24 (X24). A secondary segregating population (F₂) was developed from a cross between L28 and an RIL, RIL40 (L28 × RIL40). Based on the population, genetic linkage maps of the previous QTL cluster intervals on A01 (6.70-10.15 Mb), A07 (85.48-93.43 Mb), and D12 (0.40-1.43 Mb) were constructed, which span 12.25, 15.90, and 5.56 cM, with 2, 14, and 4 simple sequence repeat (SSR) and insertion/deletion (Indel) markers, respectively. QTLs of FL, FS, FM, and LP on these three intervals were verified by composite interval mapping (CIM) using WinQTL Cartographer 2.5 software via phenotyping of F₂ and its derived F_2:3 populations. The results validated the previous primary QTL identification of FL, FS, FM, and LP. Analysis of the RNA-seq data of the developing fibers of L28 and RIL40 at 10, 20, and 30 days post anthesis (DPA) identified seven differentially expressed genes (DEGs) as potential candidate genes. qRT-PCR verified that five of them were consistent with the RNA-seq result. These genes may be involved in regulating fiber development, leading to the formation of FL, FS, FM, and LP. This study provides an experimental foundation for further exploration of these functional genes to dissect the genetic mechanism of cotton fiber development.

Keywords: Gossypium hirsutum; QTL; fiber quality; lint percentage; secondary segregating population.

Figure 1

The phenotypic distribution of fiber quality traits and lint percentage of F₂ and F_2:3 populations. Dotted diamond bar presents phenotype distribution of F₂ population; Trellis presents phenotype distribution of F_2:3 population. The curve on the graph represents the fitted normal distribution of the population. The red and blue arrows indicate the positions of L28 and RIL40 in the distribution, respectively. FL, fiber length; FS, fiber strength; FM, fiber mocronaire; LP, lint percentage.

Figure 2

QTLs of fiber quality traits and LP on genetic linkage maps. (a) QTLs of fiber quality traits (FL, FS, and FM) and LP on A01, A07, and D12 in primary linkage analysis of RIL population; (b,c) QTLs of fiber quality traits (FL, FS, and FM) and LP on the physical maps, and on the linkage maps of secondary segregating population; (d) differentially expressed genes (DEGs) in developing fibers between L28 and RIL40 in the target QTL intervals.

Figure 3

Expression clustering of the dynamically expressed genes in the QTL intervals on chromosomes A01 (6.70–10.15 Mb), A07 (85.48–93.43 Mb), and D12 (0.40–1.43 Mb) in TM-1 gene expression database. Each cluster presents a similar gene expression profiling. The red zigzag line in the figure presents the fitted expression trend of each gene cluster. The yellow lines represent the gene expression profiles are more proximal to the fitted expression trend, while the green lines less proximal to the fitted expression trend.

Figure 4

qRT-PCR analysis of candidate genes during fiber development of L28 and RIL40. *, ** and *** indicate the difference between L28 and RIL40 reaching a significant level at p < 0.05, p < 0.01 and p < 0.001 in t-test, respectively.