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Key message Background-independent (BI) and stably expressed (SE) quantitative trait loci (QTLs) were identified using two sets of introgression lines across multiple environments. Genetic background more greatly affected fiber quality traits than environmental factors. Sixty-one SE-QTLs, including two BI-QTLs, were novel and 48 SE-QTLs, including seven BI-QTLs, were previously reported. Abstract Cotton fiber quality traits are controlled by QTLs and are susceptible to environmental influence. Fiber quality improvement is an essential goal in cotton breeding but is hindered by limited knowledge of the genetic basis of fiber quality traits. In this study, two sets of introgression lines of Gossypium hirsutum × G. barbadense were used to dissect the QTL stability of three fiber quality traits (fiber length, strength and micronaire) across environments using 551 simple sequence repeat markers selected from our high-density genetic map. A total of 76 and 120 QTLs were detected in the CCRI36 and CCRI45 backgrounds, respectively. Nine BI-QTLs were found, and 78 (41.71%) of the detected QTLs were reported previously. Thirty-nine and 79 QTLs were SE-QTLs in at least two environments in the CCRI36 and CCRI45 backgrounds, respectively. Forty-eight SE-QTLs, including seven BI-QTLs, were confirmed in previous reports, and 61 SE-QTLs, including two BI-QTLs, were considered novel. These results indicate that genetic background more strongly impacts on fiber quality traits than environmental factors. Twenty-three clusters with BI- and/or SE-QTLs were identified, 19 of which harbored favorable alleles from G. barbadense for two or three fiber quality traits. This study is the first report using two sets of introgression lines to identify fiber quality QTLs across environments in cotton, providing insights into the effect of genetic backgrounds and environments on the QTL expression of fiber quality and important information for the genetic basis underlying fiber quality traits toward QTL cloning and molecular breeding.

Background Plant height (PH) and fruit branch number (FBN) are important traits for improving yield and mechanical harvesting of cotton. In order to identify genes of PH and FBN in cotton germplasms to develop superior cultivars, quantitative trait loci (QTLs) for these traits were detected based on the phenotypic evaluation data in nine environments across four locations and 4 years and a previously reported genetic linkage map of an recombinant inbred line (RIL) population of upland cotton. Results In total, 53 QTLs of PH and FBN, were identified on 21 chromosomes of the cotton genome except chromosomes c02, c09-c11, and c22. For PH, 27 QTLs explaining 3.81%–8.54% proportions of phenotypic variance were identified on 18 chromosomes except c02, c08-c12, c15, and c22. For FBN, 26 QTLs explaining 3.23%–11.00% proportions of phenotypic variance were identified on 16 chromosomes except c02-c03, c06, c09-c11, c17, c22-c23, and c25. Eight QTLs were simultaneously identified in at least two environments. Three QTL clusters containing seven QTLs were identified on three chromosomes (c01, c18 and c21). Eleven QTLs were the same as previously reported ones, while the rest were newly identified. Conclusions The QTLs and QTL clusters identified in the current study will be helpful to further understand the genetic mechanism of PH and FBN development of cotton and will enhance the development of excellent cultivars for mechanical managements in cotton production.

Callose deposition occurs during plant growth and development, as well as when plants are under biotic and abiotic stress. Callose synthase is a key enzyme for the synthesis of callose. In this study, 27, 28, 16, and 15 callose synthase family members were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum using the sequence of Arabidopsis callose synthase. The CalSs were divided into five groups by phylogenetic, gene structure, and conservative motif analysis. The conserved motifs and gene structures of CalSs in each group were highly similar. Based on the analysis of cis-acting elements, it is inferred that GhCalSs were regulated by abiotic stress. WGD/Segmental duplication promoted the amplification of the CalS gene in cotton, and purification selection had an important function in the CalS family. The transcriptome data and qRT-PCR under cold, heat, salt, and PEG treatments showed that GhCalSs were involved in abiotic stress. The expression patterns of GhCalSs were different in various tissues. We predicted that GhCalS4, which was highly expressed in fibers, had an important effect on fiber elongation. Hence, these results help us understand the role of GhCalSs in fiber development and stress response.

Verticillium wilt is the second serious vascular wilt caused by the phytopathogenic fungus Verticillium dahliae Kleb. It has distributed worldwide, causing serious yield losses and fiber quality reduction in cotton production. The pathogen has developed different mechanisms like the production of cell wall degrading enzymes, activation of virulence genes and protein effectors to succeed in its infection. Cotton plant has also evolved multiple mechanisms in response to the fungus infection, including a strong production of lignin and callose deposition to strengthen the cell wall, burst of reactive oxygen species, accumulation of defene hormones, expression of defense-related genes, and target-directed strategies like cross-kingdom RNAi for specific virulent gene silencing. This review summarizes the recent progress made over the past two decades in understanding the interactions between cotton plant and the pathogen Verticillium dahliae during the infection process. The review also discusses the achievements in the control practices of cotton verticillium wilt in recent years, including cultivation practices, biological control, and molecular breeding strategies. These studies reveal that effective management strategies are needed to control the disease, while cultural practices and biological control approaches show promising results in the future. Furthermore, the biological control approaches developed in recent years, including antagonistic fungi, endophytic bacteria, and host induced gene silencing strategies provide efficient choices for integrated disease management.

Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.

Summary Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty‐seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA‐Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu‐chr13‐2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.

Chromosome segment substitution lines (CSSLs) are ideal materials for identifying genetic effects. In this study, CSSL MBI7561 with excellent fiber quality that was selected from BC4F3:5 of CCRI45 (Gossypium hirsutum) × Hai1 (Gossypium barbadense) was used to construct 3 secondary segregating populations with 2 generations (BC5F2 and BC5F2:3). Eighty-one polymorphic markers related to 33 chromosome introgressive segments on 18 chromosomes were finally screened using 2292 SSR markers which covered the whole tetraploid cotton genome. A total of 129 quantitative trait loci (QTL) associated with fiber quality (103) and yield-related traits (26) were detected on 17 chromosomes, explaining 0.85-30.35% of the phenotypic variation; 39 were stable (30.2%), 53 were common (41.1%), 76 were new (58.9%), and 86 had favorable effects on the related traits. More QTL were distributed in the Dt subgenome than in the At subgenome. Twenty-five stable QTL clusters (with stable or common QTL) were detected on 22 chromosome introgressed segments. Finally, the 6 important chromosome introgressed segments (Seg-A02-1, Seg-A06-1, Seg-A07-2, Seg-A07-3, Seg-D07-3, and Seg-D06-2) were identified as candidate chromosome regions for fiber quality, which should be given more attention in future QTL fine mapping, gene cloning, and marker-assisted selection (MAS) breeding.

Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistant VW. However, multiple attempts to improve the VW resistance of the most widely cultivated Upland cotton have brought in little significant progress, and it seems necessary and urgent to develop Chromosome segment substitution lines (CSSLs) for merging the superior genes related with high yield and wide adaptation from G. hirsutum and VW resistance and excellent fiber quality from G. barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed by G. hirsutum CCRI36 and G. barbadense Hai1 to conduct quantitative trait locus (QTL) mapping on VW resistance, and a total of 53 QTLs relevant to VW disease index (DI) were identified together with the phenotypic data of 2 years investigations in two fields with two replications per year. All the QTLs were distributed on 20 chromosomes with phenotypic variation of 3.74-11.89%, of which 29 stable ones were consistent in at least two environments. Based on Meta-analysis on the 53 QTLs, 43 novel ones were identified, while 10 ones consistent to previously identified QTLs. Meanwhile, 32 QTL hotspot regions were detected, including 15 ones were novel. This study concentrates on QTL identification and screening hotspot region related with VW in the 300 CSSLs, which lay a solid platform not only for revealing the genetic and molecular mechanisms of VW resistance, but also for further fine mapping, gene cloning and molecular designing in breeding program for resistant cotton varieties.

Chromosome painting is one of the key technologies in cytogenetic research, which can accurately identify chromosomes or chromosome regions. Oligonucleotide (oligo) probes designed based on genome sequences have both flexibility and specificity, which would be ideal probes for fluorescence in situ hybridization (FISH) analysis of genome structure. In this study, the bulked oligos of the two arms of chromosome seven of cotton were developed based on the genome sequence of Gossypium raimondii (DD, 2n = 2× = 26), and each arm contains 12,544 oligos. Chromosome seven was easily identified in both D genome and AD genome cotton species using the bulked chromosome-specific painting probes. Together with 45S ribosomal DNA (rDNA) probe, the chromosome-specific painting probe was also successfully used to correct the chromosomal localization of 45S rDNA in G. raimondii. The study reveals that bulked oligos specific to a chromosome is a useful tool for chromosome painting in cotton.

Climate warming potentially changes the flowering seasons of terrestrial plants, and thus species interaction, with consequently substantial impacts on ecosystem structure and function. However, the general response patterns of flowering seasons to warming and the underlying mechanisms remain poorly understood. Here, a meta-analysis of data from 26 experimental studies examining 168 species was conducted to quantify the responses of the flowering seasons of terrestrial plants to experimental warming. The results showed that experimental warming prolonged the flowering season by 2.08% across all species included in this study. In addition, flowering season responses were dependent on plant functional types, with a significant extension in herbaceous species (+2.18%) but no change in woody species. The warming impacts on the flowering season of wind-pollinated (-4.53%) and insect-pollinated species (+4.21%) were opposite. Among herbaceous species, the flowering seasons of forb (+4.47%) and specifically legume species (+15.06%) were positive, whereas grass species (-4.53%) showed negative responses to experimental warming. Moreover, experimental warming effects on the flowering season showed quadratic relationships with the latitude and the mean annual temperature but did not change with the mean annual precipitation. The responses of the flowering season to experimental warming also differed in terms of the warming magnitude. These diverse findings indicate the need for additional experimental warming experiments, especially for underrepresented plant functional groups, to better understand the mechanistic relationships between phenology and temperature under future climate warming scenarios.

The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid. In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified from two domesticated tetraploid cottons Gossypium hirsutum, Gossypium barbadense, and 11 MIOX genes were identified from three wild tetraploid cottons Gossypium tomentosum, Gossypium mustelinum and Gossypium darwinii. The number of MIOX genes in tetraploid cotton genome is roughly twice that of diploid cotton genome. Members of MIOX family were classified into six groups based on the phylogenetic analysis. Integrated analysis of collinearity events and chromosome locations suggested that both whole genome duplication and segmental duplication events contributed to the expansion of MIOX genes during cotton evolution. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates revealed that purifying selection was the main force driving the evolution of MIOX genes. Numerous cis-acting elements related to light responsive element, defense and stress responsive element were identified in the promoter of the MIOX genes. Expression analyses of MIOX genes based on RNA-seq data and quantitative real time PCR showed that MIOX genes within the same group shared similar expression patterns with each other. All of these results provide the foundation for further study of the biological functions of MIOX genes in cotton environmental adaptability.

As high-strength cotton fibers are critical components of high quality cotton, developing cotton cultivars with high-strength fibers as well as high yield is a top priority for cotton development. Recently, chromosome segment substitution lines (CSSLs) have been developed from high-yield Upland cotton (Gossypium hirsutum) crossed with high-quality Sea Island cotton (G. barbadense). Here, we constructed a CSSL population by crossing CCRI45, a high-yield Upland cotton cultivar, with Hai1, a Sea Island cotton cultivar with superior fiber quality. We then selected two CSSLs with significantly higher fiber strength than CCRI45 (MBI7747 and MBI7561), and one CSSL with lower fiber strength than CCRI45 (MBI7285), for further analysis. We sequenced all four transcriptomes at four different time points postanthesis, and clustered the 44,678 identified genes by function. We identified 2200 common differentially-expressed genes (DEGs): those that were found in both high quality CSSLs (MBI7747 and MBI7561), but not in the low quality CSSL (MBI7285). Many of these genes were associated with various metabolic pathways that affect fiber strength. Upregulated DEGs were associated with polysaccharide metabolic regulation, single-organism localization, cell wall organization, and biogenesis, while the downregulated DEGs were associated with microtubule regulation, the cellular response to stress, and the cell cycle. Further analyses indicated that three genes, XLOC_036333 [mannosyl-oligosaccharide-α-mannosidase (MNS1)], XLOC_029945 (FLA8), and XLOC_075372 (snakin-1), were potentially important for the regulation of cotton fiber strength. Our results suggest that these genes may be good candidates for future investigation of the molecular mechanisms of fiber strength formation and for the improvement of cotton fiber quality through molecular breeding.

Uridine diphosphate (UDP)-glycosyltransferases (UGTs) involved in many metabolic processes are ubiquitous in plants, animals, microorganisms and other organisms and are essential for their growth and development. Upland cotton contains a large number of UGT genes. In this study, we aimed to identify UGT family members in the genome of upland cotton (Gossypium hirsutum L.) and analyze their expression patterns. Bioinformatics methods were used to identify UGT genes from the whole genome of upland cotton (Gossypium hirsutum L. acc. TM-1). Phylogenetic analysis was conducted based on alignment of UGT proteins from upland cotton, and the gene structure, motif and chromosome localization were analyzed for the H subgroup of the UGT family. And the physical and chemical properties and expressions of the genes in the H subgroup of this family were also analyzed. A total of 274 UGT genes were identified from the whole genome of upland cotton and were divided into nine subgroups based on phylogenetic analyses. In subgroup H, 36 genes were distributed on 18 chromosomes. The subfamily genes were simple in the structure, 19 of its members contained two introns, and the others contained only one intron. The qRT-PCR results and transcriptomic data indicated that most of the genes had a wide range of tissue expression characteristics. And the phylogenetic analysis results and expression profiles of these genes revealed tissues and different UGT genes from this crop. Taking RNA-seq, RT-qPCR, and quantitative trait locus (QTL) mapping together, our results suggested that GhUGT6 and GhUGT105 in subgroup H of the GhUGT gene family could be potential candidate genes for cotton yield, and GhUGT16, GhUGT103 might play a vital role in fiber development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1984-1) contains supplementary material, which is available to authorized users.

Background Verticillium wilt (VW), also known as “cotton cancer,” is one of the most destructive diseases in global cotton production that seriously impacts fiber yield and quality. Despite numerous attempts, little significant progress has been made in improving the VW resistance of upland cotton. The development of chromosome segment substitution lines (CSSLs) from Gossypium hirsutum × G. barbadense has emerged as a means of simultaneously developing new cotton varieties with high-yield, superior fiber, and resistance to VW. Results In this study, VW-resistant investigations were first conducted in an artificial greenhouse, a natural field, and diseased nursery conditions, resulting in the identification of one stably VW-resistant CSSL, MBI8255, and one VW-susceptible G. hirsutum, CCRI36, which were subsequently subjected to biochemical tests and transcriptome sequencing during V991 infection (0, 1, and 2 days after inoculation). Eighteen root samples with three replications were collected to perform multiple comparisons of enzyme activity and biochemical substance contents. The findings indicated that VW resistance was positively correlated with peroxidase and polyphenol oxidase activity, but negatively correlated with malondialdehyde content. Additionally, RNA sequencing was used for the same root samples, resulting in a total of 77,412 genes, of which 23,180 differentially expressed genes were identified from multiple comparisons between samples. After Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the expression profiles identified using Short Time-series Expression Miner, we found that the metabolic process in the biological process, as well as the pathways of phenylpropanoid biosynthesis and plant hormone signal transduction, participated significantly in the response to VW. Gene functional annotation and expression quantity analysis indicated the important roles of the phenylpropanoid metabolic pathway and oxidation-reduction process in response to VW, which also provided plenty of candidate genes related to plant resistance. Conclusions This study concentrates on the preliminary response to V991 infection by comparing the VW-resistant CSSL and its VW-susceptible recurrent parent. Not only do our findings facilitate the culturing of new resistant varieties with high yield and superior performance, but they also broaden our understanding of the mechanisms of cotton resistance to VW. Electronic supplementary material The online version of this article (10.1186/s12870-018-1619-4) contains supplementary material, which is available to authorized users.

Fiber quality and yield are important traits of cotton. Quantitative trait locus (QTL) mapping is a prerequisite for marker-assisted selection (MAS) in cotton breeding. To identify QTLs for fiber quality and yield traits, 4 backcross-generation populations (BC1F1, BC1S1, BC2F1, and BC3F0) were developed from an interspecific cross between CCRI36 (Gossypium hirsutum L.) and Hai1 (G. barbadense L.). A total of 153 QTLs for fiber quality and yield traits were identified based on data from the BC1F1, BC1S1, BC2F1 and BC3F0 populations in the field and from the BC2F1 population in an artificial disease nursery using a high-density genetic linkage map with 2292 marker loci covering 5115.16 centimorgans (cM) from the BC1F1 population. These QTLs were located on 24 chromosomes, and each could explain 4.98–19.80% of the observed phenotypic variations. Among the 153 QTLs, 30 were consistent with those identified previously. Specifically, 23 QTLs were stably detected in 2 or 3 environments or generations, 6 of which were consistent with those identified previously and the other 17 of which were stable and novel. Ten QTL clusters for different traits were found and 9 of them were novel, which explained the significant correlations among some phenotypic traits in the populations. The results including these stable or consensus QTLs provide valuable information for marker-assisted selection (MAS) in cotton breeding and will help better understand the genetic basis of fiber quality and yield traits, which can then be used in QTL cloning.

Superoxide dismutases (SODs) play important roles in plant growth, development, and response to abiotic stresses. Despite SOD gene families have been identified in various plant species, little is known in foxtail millet (Setaria italica L.). In this study, a systematic analysis of SOD gene family was performed in foxtail millet and the expression pattern of SOD genes in response to abiotic stressors was analyzed at the whole-genomic level. Eight SOD genes were identified in foxtail millet, including 4 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. These SiSODs are unevenly distributed across 5 of the 9 chromosomes. Phylogenetic analysis showed that SOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs), containing seven subgroups, from foxtail millet and other plant species. SOD genes have conserved motif and exon/intron composition in the same subgroup among Setaria italica, Setaria viridis, and Oryza sativa. Additionally, many cis-elements that respond to different stressors were distributed at different densities in the promoters of 8 SiSODs. The expression patterns of SiSODs in different tissues and different abiotic stressors indicated that the SiSODs may play important roles in reactive oxygen species scavenging, caused by various stressors in foxtail millet. This study provides a foundation for the further cloning and functional verification of the SOD gene family response to environmental stimuli in foxtail millet.

It is of great importance to identify quantitative trait loci (QTL) controlling fiber quality traits and yield components for future marker-assisted selection (MAS) and candidate gene function identifications. In this study, two kinds of traits in 231 F6:8 recombinant inbred lines (RILs), derived from an intraspecific cross between Xinluzao24, a cultivar with elite fiber quality, and Lumianyan28, a cultivar with wide adaptability and high yield potential, were measured in nine environments. This RIL population was genotyped by 122 SSR and 4729 SNP markers, which were also used to construct the genetic map. The map covered 2477.99 cM of hirsutum genome, with an average marker interval of 0.51 cM between adjacent markers. As a result, a total of 134 QTLs for fiber quality traits and 122 QTLs for yield components were detected, with 2.18–24.45 and 1.68–28.27% proportions of the phenotypic variance explained by each QTL, respectively. Among these QTLs, 57 were detected in at least two environments, named stable QTLs. A total of 209 and 139 quantitative trait nucleotides (QTNs) were associated with fiber quality traits and yield components by four multilocus genome-wide association studies methods, respectively. Among these QTNs, 74 were detected by at least two algorithms or in two environments. The candidate genes harbored by 57 stable QTLs were compared with the ones associated with QTN, and 35 common candidate genes were found. Among these common candidate genes, four were possibly “pleiotropic.” This study provided important information for MAS and candidate gene functional studies.

Long terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome. Some LTR retrotransposon families that insert after polyploid formation may still distribute the majority of its copies in one of the subgenomes. The data also shows that families of 10~200 copies are abundant and they have a great influence on the Gossypium genome size; on the contrary, a small number of high copy LTR retrotransposon families have less contribution to the genome size. Kimura distance distribution indicates that high copy number family is not a recent outbreak, and there is no obvious relationship between family copy number and the period of evolution. Further analysis reveals that each LTR retrotransposon family may have their own distribution characteristics in cotton.

A bacterial artificial chromosome (BAC) library for G. mustelinum Miers ex G. Watt (AD4) was constructed. Intact nuclei from G. mustelinum (AD4) were used to isolate high molecular weight DNA, which was partially cleaved with Hind III and cloned into pSMART BAC (Hind III) vectors. The BAC library consisted of 208,182 clones arrayed in 542 384-microtiter plates, with an average insert size of 121.72 kb ranging from 100 to 150 kb. About 2% of the clones did not contain inserts. Based on an estimated genome size of 2372 Mb for G. mustelinum, the BAC library was estimated to have a total coverage of 10.50 × genome equivalents. The high capacity library of G. mustelinum will serve as a giant gene resource for map-based cloning of quantitative trait loci or genes associated with important agronomic traits or resistance to Verticillium wilt, physical mapping and comparative genome analysis.

Developing chromosome segments substitution lines (CSSLs) is an effective method for broadening the cotton germplasm resource, and improving the fiber quality and yield traits. In this study, the 1054 F2 individual plants and 116 F2:3 lineages were generated from the two parents of MBI9749 and MBI9915 selected from BC5F3:5 lines which originated from hybridization of CCRI36 and Hai1, and advanced backcrossing and repeated selfing. Genotypes of the parents and F2 population were analyzed. The results showed that 19 segments were introgressed for MBI9749 and 12 segments were introgressed for MBI9915, distributing on 17 linkage groups. The average background recovery rate to the recurrent parent CCRI36 was 96.70% for the two parents. An average of 16.46 segments was introgressed in F2 population. The average recovery rate of 1054 individual plants was 96.85%, and the mean length of sea island introgression segments was 157.18 cM, accounting for 3.15% of detection length. QTL mapping analysis detected 22 QTLs associated with fiber quality and yield traits in the F2 and F2:3 populations. These QTLs distributed on seven chromosomes, and the phenotypic variation was explained ranging from 1.20 to 14.61%. Four stable QTLs were detected in F2 and F2:3 populations, simultaneously. We found that eight QTLs were in agreement with the previous research. Six QTL-clusters were identified for fiber quality and yield traits, in which five QTL-clusters were on chromosome20. The results indicated that most of QTL-clusters always improve the fiber quality and have negative additive effect for yield related traits. This study demonstrated that CSSLs provide basis for fine mapping of the fiber quality and yield traits in future, and could be efficiently used for pyramiding favourable alleles to develop the new germplasms for breeding by molecular marker-assisted selection.

Background How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton. Results In total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the “oxidation-reduction process”, which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes. Conclusions The present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4077-8) contains supplementary material, which is available to authorized users.

MBI9915 is an introgression cotton line with excellent fiber quality. It was obtained by advanced backcrossing and continuous inbreeding from an interspecific cross between the upland cotton (Gossypium hirsutum) cultivar CCRI36 as the recurrent parent and the sea island cotton (G. barbadense) cultivar Hai1, as the donor parent. To study the genetic effects of the introgressed chromosome segments in G. hirsutum, an F2 secondary segregating population of 1537 individuals was created by crossing MBI9915 and CCRI36, and an F2:3 population was created by randomly selecting 347 individuals from the F2 generation. Quantitative trait locus (QTL) mapping and interaction for fiber length and strength were identified using IciMapping software. The genotype analysis showed that the recovery rate for MBI9915 was 97.9%, with a total 6 heterozygous segments and 13 homozygous segments. A total of 18 QTLs for fiber quality and 6 QTLs for yield related traits were detected using the two segregating generations. These QTLs were distributed across 7 chromosomes and collectively explained 0.81%–9.51% of the observed phenotypic variations. Six QTLs were consistently detected in two generations and 6 QTLs were identified in previous studies. A total of 13 pairs of interaction for fiber length and 13 pairs of interaction for fiber strength were identified in two generations. Among them, 3 pairs of interaction for fiber length and 3 pairs of interaction for fiber strength could be identified in all generations; 4 pairs of interactions affected fiber length and fiber strength simultaneously. The results clearly showed that 5 chromosome segments (Seg-5-1, Seg-7-1, Seg-8-1, Seg-20-2 and Seg-20-3) have important effects on fiber yield and quality. This study provides the useful information for gene cloning and marker-assisted breeding for excellent fiber related quality.

Background Pectin methylesterase (PME, EC 3.1.1.11) is a hydrolytic enzyme that utilizes pectin as substrates, and plays a significant role in regulating pectin reconstruction thereby regulating plant growth. Pectin is one of the important components of the plant cell wall, which forms the main structural material of cotton fiber. In this research, cotton genome information was used to identify PMEs. Results We identified 80 (GaPME01-GaPME80) PME genes from diploid G. arboreum (A genome), 78 (GrPME01-GrPME78) PME genes from G. raimondii (D genome), and 135 (GhPME001-GhPME135) PME genes from tetraploid cotton G. hirsutum (AD genome). We further analyzed their gene structure, conserved domain, gene expression, and systematic evolution to lay the foundation for deeper research on the function of PMEs. Phylogenetic data indicated that members from the same species demonstrated relatively high sequence identities and genetic similarities. Analysis of gene structures showed that most of the PMEs genes had 2–3 exons, with a few having a variable number of exons from 4 to 6. There are nearly no differences in the gene structure of PMEs among the three (two diploid and one tetraploid) cotton species. Selective pressure analysis showed that the Ka/Ks value for each of the three cotton species PME families was less than one. Conclusion Conserved domain analysis showed that PMEs members had a relatively conserved C-terminal pectinesterase domain (PME) while the N-terminus was less conserved. Moreover, some of the family members contained a pectin methylesterase inhibitor (PMEI) domain. The Ka/Ks ratios suggested that the duplicated PMEs underwent purifying selection after the duplication events. This study provided an important basis for further research on the functions of cotton PMEs. Results from qRT-PCR indicated that the expression level of different PMEs at various fiber developmental stages was different. Moreover, some of the PMEs showed fiber predominant expression in secondary wall thickening indicating tissue-specific expression patterns. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3365-z) contains supplementary material, which is available to authorized users.

Cotton fiber strength is a critical property determining fiber qualities, and determined by the secondary cell wall development. Understanding the mechanism of fiber development will provide a way to improvement of fiber strength. In this study, the introgression lines of upland and sea island cotton, and have experience of four generations of backcross with upland parent, and have significant higher fiber strength than their upland parent, and the transcriptome were analyzed and compared between the introgression lines and their upland parent. There were 2201 differentially expressed genes (DEG) identified by comparing two introgression lines with their recurrent parent CCRI45, in different development stages from 15 days post-anthesis (DPA) to 28 DPA. The up-regulated genes regulated the polysaccharide metabolic process, single-organism localization, cell wall organization or biogenesis and so on. The down-regulated genes involved in the microtubule-based process, cellular response to stress, cell cycle process and so on. Further functional analysis revealed three significant functional genes, XLOC_036333 (mannosyl-oligosaccharide-alpha-mannosidase mns1), XLOC_029945 (FLA8) and XLOC_075372 (snakin-1), playing important roles in the regulation of cotton fiber strength. Our results provide important candidates genes and inspirations for the future investigation of the molecular mechanism of fiber quality formation, and improvement of cotton fiber quality in breeding.

Background Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. Results In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0–153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15–16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. Conclusions This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0741-4) contains supplementary material, which is available to authorized users.

Background The identification of quantitative trait loci (QTLs) that are stable and consistent across multiple environments and populations plays an essential role in marker-assisted selection (MAS). In the present study, we used 28,861 simple sequence repeat (SSR) markers, which included 12,560 Gossypium raimondii (D genome) sequence-based SSR markers to identify polymorphism between two upland cotton strains 0–153 and sGK9708. A total of 851 polymorphic primers were finally selected and used to genotype 196 recombinant inbred lines (RIL) derived from a cross between 0 and 153 and sGK9708 and used to construct a linkage map. The RIL population was evaluated for fiber quality traits in six locations in China for five years. Stable QTLs identified in this intraspecific cross could be used in future cotton breeding program and with fewer obstacles. Results The map covered a distance of 4,110 cM, which represents about 93.2 % of the upland cotton genome, and with an average distance of 5.2 cM between adjacent markers. We identified 165 QTLs for fiber quality traits, of which 47 QTLs were determined to be stable across multiple environments. Most of these QTLs aggregated into clusters with two or more traits. A total of 30 QTL clusters were identified which consisted of 103 QTLs. Sixteen clusters in the At sub-genome comprised 44 QTLs, whereas 14 clusters in the Dt sub-genome that included 59 QTLs for fiber quality were identified. Four chromosomes, including chromosome 4 (c4), c7, c14, and c25 were rich in clusters harboring 5, 4, 5, and 6 clusters respectively. A meta-analysis was performed using Biomercator V4.2 to integrate QTLs from 11 environmental datasets on the RIL populations of the above mentioned parents and previous QTL reports. Among the 165 identified QTLs, 90 were identified as common QTLs, whereas the remaining 75 QTLs were determined to be novel QTLs. The broad sense heritability estimates of fiber quality traits were high for fiber length (0.93), fiber strength (0.92), fiber micronaire (0.85), and fiber uniformity (0.80), but low for fiber elongation (0.27). Meta-clusters on c4, c7, c14 and c25 were identified as stable QTL clusters and were considered more valuable in MAS for the improvement of fiber quality of upland cotton. Conclusion Multiple environmental evaluations of an intraspecific RIL population were conducted to identify stable QTLs. Meta-QTL analyses identified a common chromosomal region that plays an important role in fiber development. Therefore, QTLs identified in the present study are an ideal candidate for MAS in cotton breeding programs to improve fiber quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2560-2) contains supplementary material, which is available to authorized users.

Background Verticillium wilt (VW) caused by Verticillium dahliae (Kleb) is one of the most destructive diseases of cotton. The identification of highly resistant QTLs or genes in the whole cotton genome is quite important for developing a VW-resistant variety and for further molecular design breeding. Results In the present study, BC1F1, BC1S1, and BC2F1 populations derived from an interspecific backcross between the highly resistant line Hai1 (Gossypium barbadense L.) and the susceptible variety CCRI36 (G. hirsutum L.) as the recurrent parent were constructed. Quantitative trait loci (QTL) related to VW resistance were detected in the whole cotton genome using a high-density simple sequence repeat (SSR) genetic linkage map from the BC1F1 population, with 2292 loci covering 5115.16 centiMorgan (cM) of the cotton (AD) genome, and the data concerning VW resistance that were obtained from four dates of BC2F1 in the artificial disease nursery and one date of BC1S1 and BC2F1 in the field. A total of 48 QTLs for VW resistance were identified, and 37 of these QTLs had positive additive effects, which indicated that the G. barbadense alleles increased resistance to VW and decreased the disease index (DI) by about 2.2–10.7. These QTLs were located on 19 chromosomes, in which 33 in the A subgenome and 15 QTLs in the D subgenome. The 6 QTLs were found to be stable. The 6 QTLs were consistent with those identified previously, and another 42 were new, unreported QTLs, of which 31 QTLs were from G. barbadense. By meta-analysis, 17 QTL hotspot regions were identified and 10 of them were new, unreported hotspot regions. 29 QTLs in this paper were in 12 hotspot regions and were all from G. barbadense. Conclusions These stable or consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying VW resistance. This study provides useful information for further comparative analysis and marker-assisted selection in the breeding of disease-resistant cotton. It may also lay an important foundation for gene cloning and further molecular design breeding for the entire cotton genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3128-x) contains supplementary material, which is available to authorized users.