Genetic variation of dynamic fiber elongation and developmental quantitative trait locus mapping of fiber length in upland cotton (Gossypium hirsutum L.)

Abstract

BackgroundIn upland cotton (Gossypium hirsutum L.), genotypes with the same mature fiber length (FL) might possess different genes and exhibit differential expression of genes related to fiber elongation at different fiber developmental stages. However, there is a lack of information on the genetic variation influencing fiber length and its quantitative trait loci (QTLs) during the fiber elongation stage. In this study, a subset of upland cotton accessions was selected based on a previous GWAS conducted in China and grown in multiple environments to determine the dynamic fiber length at 10, 15, 20, and 25 days post-anthesis (DPA) and maturity. The germplasm lines were genotyped with the Cotton 63 K Illumina single-nucleotide polymorphism (SNP) array for GWAS.ResultsA total of 25, 38, 57, 89 and 88 SNPs showed significant correlations with fiber length at 10, 15, 20 and 25 DPA and maturity, respectively. In addition, 60 more promising SNPs were detected in at least two tests and two FL developmental time points, and 20 SNPs were located within the confidence intervals of QTLs identified in previous studies. The fastest fiber-length growth rates were obtained at 10 to 15 DPA in 69 upland cotton lines and at 15 to 20 DPA in 14 upland cotton accessions, and 10 SNPs showed significant correlations with the fiber-length growth rate. A combined transcriptome and qRT-PCR analysis revealed that two genes (D10G1008 and D13G2037) showed differential expression between two long-fiber genotypes and two short-fiber genotypes.ConclusionsThis study provides important new insights into the genetic basis of the time-dependent fiber-length trait and reveals candidate SNPs and genes for improving fiber length in upland cotton.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5309-2) contains supplementary material, which is available to authorized users.

Identification of Candidate Genes Controlling Fiber Quality Traits in Upland Cotton through Integration of Meta-QTL, Significant SNP and Transcriptomic Data

“…Collection of QTLs and SNPs associated with ber quality traits A total of 12 QTL mapping studies for cotton ber quality traits were used in this study, in which the mapping population size ranged from 107 to 503 lines (Table 1) (Ali et al 2018;Diouf et al 2018;Huang et al 2017;Jia et al 2018;Keerio et al 2018;Li et al 2016a;Liu et al 2018b;Ma et al 2018a;Tan et al 2018;Wang et al 2015;Zou et al 2018), and the number of SNP markers ranged from 168 to 19,191 (Table 1). As a result, a total of 884 initial QTLs related to cotton ber quality traits were collected, which were unevenly distributed on each chromosome, and ranged from 12 to 57 (Fig.…”

“…The articles providing QTL intervals and anking markers were selected for QTL collection. Finally, 884 QTLs with respect to FE, FL, FS, MIC, FU, spinning consistency index (SCI), short ber (SF), ber re ectance (FR) and ber yellowness (FY) traits were identi ed from the web of science (Ali et al 2018;Diouf et al 2018;Huang et al 2017;Jia et al 2018;Keerio et al 2018;Li et al 2016a;Liu et al 2018b;Ma et al 2018a;Tan et al 2018;Wang et al 2015;Zou et al 2018). QTL numbers, traits, population type and size, and number of markers are listed in Table 1.…”

“…A peroxidase gene (GhPRXR1) required for oil content in upland cotton was identi ed by the combination of genome-wide association and transcriptome analysis (Ma et al 2019). Two candidate genes for ber elongation and developmental were identi ed by the combination of genome-wide association and transcriptome analysis (Ma et al 2018a).…”

“…In this study, 884 QTLs associated with cotton ber traits from 12 studies (Ali et al 2018;Diouf et al 2018;Huang et al 2017;Jia et al 2018;Keerio et al 2018;Li et al 2016a;Liu et al 2018b;Ma et al 2018a;Tan et al 2018;Wang et al 2015;Zou et al 2018) were used for meta-QTL analysis based on upland cotton reference genome TM-1 (Zhang et al 2015a), and 74 meta-QTLs were identi ed. Combined with 8589 signi cant SNP loci associated to cotton ber quality traits collected from 15 previous publications (Chandnani et al 2018;Fang et al 2017;Gapare et al 2017;Handi et al 2017;Huang et al 2017;Islam et al 2016;Li et al 2017b;Liu et al 2018b;Ma et al 2018a;Ma et al 2018b;Su et al 2016;Su et al 2018;Sun et al 2017;Wen et al 2018), 297 candidate genes associated with cotton ber quality traits were identi ed. Twenty genes showed high expression speci cally in the developing bers, some of which are associated with the ber development.…”

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

“…Cotton (Gossypium spp. ), an important economic crop, is widely used mainly to provide natural bers for the textile industry [1]. Heterosis utilization is an important way to improve the productivity and quality of cotton ber [2].…”