Genome-Scale Analysis of the WRI-Like Family in Gossypium and Functional Characterization of GhWRI1a Controlling Triacylglycerol Content

Cotton (Gossypium spp.) is the most important natural fiber crop and the source of cottonseed oil, a basic by-product after ginning. AtWRI1 and its orthologs in several other crop species have been previously used to increase triacylglycerols in seeds and vegetative tissues. In the present study, we identified 22, 17, 9, and 11 WRI-like genes in G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, respectively. This gene family was divided into four subgroups, and a more WRI2-like subfamily was identified compared with dicotyledonous Arabidopsis. An analysis of chromosomal distributions revealed that the 22 GhWRI genes were distributed on eight At and eight Dt subgenome chromosomes. Moreover, GhWRI1a was highly expressed in ovules 20–35 days after anthesis and was selected for further functional analysis. Ectopic expression of GhWRI1a rescued the seed phenotype of a wri1-7 mutant and increased the oil content of Arabidopsis seeds. Our comprehensive genome-wide analysis of the cotton WRI-like gene family lays a solid foundation for further studies

A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

Abstract Background Small auxin-up RNA (SAUR) gene family is the largest family of early auxin response genes in higher plants, which have been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in cotton (Gossypium spp.). Results In the study, we identified 145, 97, 214, and 176 SAUR homologous genes in the sequenced genomes of G. raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. A phylogenetic analysis revealed that the SAUR genes can be classified into 10 groups. A further analysis of chromosomal locations and gene duplications showed that tandem duplication and segmental duplication events contributed to the expansion of the SAUR gene family in cotton. An exon-intron organization and motif analysis revealed the conservation of SAUR-specific domains, and the auxin responsive elements existed in most of the upstream sequences. The expression levels of 16 GhSAUR genes in response to an exogenous application of IAA were determined by a quantitative RT-PCR analysis. The genome-wide RNA-seq data and qRT-PCR analysis of selected SAUR genes in developing fibers revealed their differential expressions. The physical mapping showed that 20 SAUR genes were co-localized with fiber length quantitative trait locus (QTL) hotspots. Single nucleotide polymorphisms (SNPs) were detected for 12 of these 20 genes between G. hirsutum and G. barbadense, but no SNPs were identified between two backcross inbred lines with differing fiber lengths derived from a cross between the two cultivated tetraploids. Conclusions This study provides an important piece of genomic information for the SAUR genes in cotton and lays a solid foundation for elucidating the functions of SAUR genes in auxin signaling pathways to regulate cotton growth

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

Abstract Background In 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. Results A 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. Conclusions This 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

Additional file 7: Figure S1. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

Phylogenetic relationships, gene structure and motif compositions of the Gossypium arboreum SAUR genes. (A) The phylogenetic tree was constructed using MEGA 6.0 with the Neighbour-Joining (NJ) method with 1000 bootstrap replicates. (B) Exon/intron structures of SAUR genes from G. arboreum. The introns, CDS are represented by black lines, green and blue boxes respectively. The scale bar represents 0.5 kb. (C) Protein motif. Each motif is represented in the colored box. (PDF 2081 kb

Additional file 2: Table S2. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

SAUR gene family in Gossypium arboreum. (XLS 47 kb

Additional file 3: Table S3. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

SAUR gene family in Gossypium hirsutum. (XLSX 28 kb

Additional file 5: Table S5. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

The number of SAUR genes from 12 species classified into groups I - X. (XLSX 9 kb

Additional file 1: Table S1. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

Primers used for qRT-PCR analysis. (XLSX 9 kb

Additional file 12: Figure S5. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

Sequence alignment of the predicted SAUR genes between four sequenced Gossypium species. The red boxes indicate sequence variations of G. hirsutum (TM-1) and G. barbadense (3-79 and Xinhai 21). Gh1 indicate TM-1 sequenced by Zhang et al. (2015). Gb1 and Gb2 indicate 3-79 and Xinhai21 sequenced by Yuan et al. (2015) and Liu et al. (2015), respectively. Gr and Ga indicate two diploid genomes sequenced by Paterson et al. (2013) and Li et al. (2014), respectively. (PDF 335 kb

Additional file 8: Figure S2. of A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton

Phylogenetic relationships, gene structure and motif compositions of the Gossypium hirsutum SAUR genes. (A) The phylogenetic tree was constructed using MEGA 6.0 with the Neighbour-Joining (NJ) method with 1000 bootstrap replicates. (B) Exon/intron structures of SAUR genes from G. hirsutum. The introns, CDS are represented by black lines, green and blue boxes respectively. The scale bar represents 0.5 kb. (C) Protein motif. Each motif is represented in the colored box. (PDF 509 kb