Abstract
BackgroundMicronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the genetic architecture of micronaire at the genomic level is unclear. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments.ResultsGWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism (SNP) array. A total of 11 quantitative trait loci (QTLs) for micronaire were detected on 10 chromosomes. These 11 QTLs included 27 identified genes with specific expression patterns. A novel QTL, qFM-A12–1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene. GhFLA9 was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis. The expression level of GhFLA9 was significantly higher in the low micronaire line (Msco-12) than that in the high micronaire line (Chuangyou-9).ConclusionsThis study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.
Highlights
Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber
Phenotypic variation of fiber micronaire (FM) Significant variation in FM was observed in 83 upland cotton accessions; FM varied from 2.73 to 6.50, with an average of 4.65 (Table 1 and Fig. S1)
The H2 value of FM obtained in the present study was relatively high (86.27%) and very similar to the H2 values (76.37%~94.00%) obtained in previous studies (Ma et al 2020; Sun et al 2010). These results indicated that the FM trait is mainly influenced by the genotype and is suitable for genome-wide association study (GWAS)
Summary
Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments. Fiber development mainly includes four stages: initial development, elongation, secondary wall thickening, and maturity (Pang et al 2010). Thickening of the secondary wall of the cotton fiber is a complex physiological process that mainly involves the synthesis and deposition of cellulose, usually starts 16∼19 days after flowering and is jointly regulated by the expression of many genes (Yan 2010). The analysis and identification of the candidate genes that regulate FM at the QTL mapping level have important theoretical value for molecular breeding of cotton quality and identification of genetic mechanisms of cotton fiber development
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