Phytosterol content and the campesterol:sitosterol ratio influence cotton fiber development: role of phytosterols in cell elongation

Phytosterols play an important role in plant growth and development, including cell division, cell elongation, embryogenesis, cellulose biosynthesis, and cell wall formation. Cotton fiber, which undergoes synchronous cell elongation and a large amount of cellulose synthesis, is an ideal model for the study of plant cell elongation and cell wall biogenesis. The role of phytosterols in fiber growth was investigated by treating the fibers with tridemorph, a sterol biosynthetic inhibitor. The inhibition of phytosterol biosynthesis resulted in an apparent suppression of fiber elongation in vitro or in planta. The determination of phytosterol quantity indicated that sitosterol and campesterol were the major phytosterols in cotton fibers; moreover, higher concentrations of these phytosterols were observed during the period of rapid elongation of fibers. Furthermore, the decrease and increase in campesterol:sitosterol ratio was associated with the increase and decease in speed of elongation, respectively, during the elongation stage. The increase in the ratio was associated with the transition from cell elongation to secondary cell wall synthesis. In addition, a number of phytosterol biosynthetic genes were down-regulated in the short fibers of ligon lintless-1 mutant, compared to its near-isogenic wild-type TM-1. These results demonstrated that phytosterols play a crucial role in cotton fiber development, and particularly in fiber elongation.     

SSR marker-assisted improvement of fiber qualities in Gossypium hirsutum using G. barbadense introgression lines

Key message

This study demonstrates the first practical use of CSILs for the transfer of fiber quality QTLs into Upland cotton cultivars using SSR markers without detrimentally affecting desirable agronomic characteristics.

Abstract

Gossypium hirsutum is characterized by its high lint production and medium fiber quality compared to extra-long staple cotton G. barbadense. Transferring valuable traits or genes from G. barbadense into G. hirsutum is a promising but challenging approach through a traditional interspecific introgression strategy. We developed one set of chromosome segment introgression lines (CSILs), where TM-1, the genetic standard in G. hirsutum, was used as the recipient parent and the long staple cotton G. barbadense cv. Hai7124 was used as the donor parent by molecular marker-assisted selection (MAS). Among them, four CSILs, IL040-A4-1, IL080-D6-1, IL088-A7-3 and IL019-A2-6, found to be associated with superior fiber qualities including fiber length, strength and fineness QTL in Xinjiang were selected and backcrossed, and transferred these QTLs into three commercial Upland cotton cultivars such as Xinluzao (XLZ) 26, 41 and 42 grown in Xinjiang. By backcrossing and self-pollinating twice, five improved lines (3262-4, 3389-2, 3326-3, 3380-4 and 3426-5) were developed by MAS of background and introgressed segments. In diverse field trials, these QTLs consistently and significantly offered additive effects on the target phenotype. Furthermore, we also pyramided two segments from different CSILs (IL080-D6-1 and IL019-A2-6) into cultivar 0768 to accelerate breeding process purposefully with MAS. The improved lines pyramided by these two introgressed segments showed significant additive epistatic effects in four separate field trials. No significant alteration in yield components was observed in these modified lines. In summary, we first report that these CSILs have great potential to improve fiber qualities in Upland cotton MAS breeding programs.     

Simple sequence repeat (SSR) markers linked to the Ligon lintless (Li(1)) mutant in cotton

Ligon lintless (Li(1)) is a monogenic, dominant mutant in cotton, whose expression results in extreme reductions in fiber length on mature seed. The objectives of this research were to compare fiber initiation between the Li(1) mutant and TM-1 to reveal the fiber initiation differences between normal and mutant phenotypes, to develop a linkage map of simple sequence repeat (SSR) markers with the Li(1) locus, and to identify the chromosomal location of the Li(1) locus. Comparative scanning electron microscopy studies of fiber development in a normal TM-1 genotype and the near-isogenic Li(1) mutant at 1 and 3 days postanthesis revealed little differences between the two during early stages of development, suggesting that Li(1) gene expression occurs later, probably during the elongation phase. Thirty-eight SSR loci were found to be polymorphic between TM-1 and Li(1) and were used for mapping in an F(2) population. Twenty-two SSR loci, along with Li(1), were located on eight linkage groups, covering a total genetic distance of 218.3 cM. Analysis of individual monosomic and monotelodisomic plants indicated that two SSR loci (MP4030 and MP673) from the Li(1) linkage group were located on chromosome 22.     

Alleles conferring improved fiber quality from EMS mutagenesis of elite cotton genotypes

Key message

Genetic improvements for many fiber traits are obtained by mutagenesis of elite cottons, mitigating genetic uniformity in this inbred polyploid by contributing novel alleles important to ongoing crop improvement.

Abstract

The elite gene pool of cotton (Gossypium spp.) has less diversity than those of most other major crops, making identification of novel alleles important to ongoing crop improvement. A total of 3,164 M₅ lines resulting from ethyl methanesulfonate (EMS) mutagenesis of two G. hirsutum breeding lines, TAM 94L-25 and Acala 1517-99, were characterized for basic components of fiber quality and selected yield components. Across all measured traits, the ranges of phenotypic values among the mutant lines were consistently larger than could be explained by chance (5.27–10.1 for TAM 94 L-25 and 5.29–7.94 standard deviations for Acala 1517-99-derived lines). Multi-year replicated studies confirmed a genetic basis for these differences, showing significant correlations between lines across years and environments. A subset of 157 lines selected for superior fiber qualities, including fiber elongation (22 lines), length (22), lint percent (17), fineness (23), Rd value (21), strength (19), uniformity (21) and multiple attributes in a selection index (26) were compared to 55 control lines in replicated trials in both Texas and Georgia. For all traits, mutant lines showing substantial and statistically significant improvements over control lines were found, in most cases from each of the two genetic backgrounds. This indicates that genetic improvements for a wide range of fiber traits may be obtained from mutagenesis of elite cottons. Indeed, lines selected for one fiber trait sometimes conferred additional attributes, suggesting pleiotropic effects of some mutations and offering multiple benefits for the incorporation of some alleles into mainstream breeding programs.     

Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing two parameters reflecting lint fiber fineness and to compare the precision of these two measurements. By applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC₃F₂ plants from 24 independently derived BC₃ families, we were able to detect 32 and nine quantitative trait loci (QTLs) for fiber fineness and micronaire (MIC), respectively. The discovery of larger numbers of QTLs in this study than previously found in other studies based on F₂ populations grown in favorable environments reflects the ability of the backcross-self design to resolve smaller QTL effects. Although the two measurements differed dramatically in the number of QTLs detected, seven of the nine MIC QTLs were also associated with fiber fineness. This supports other data in suggesting that fiber fineness more accurately reflects the underlying physical properties of cotton fibers and, consequently, is a preferable trait for selection. Negative transgression, with the majority of BC₃F₂ families showing average phenotypes that were poorer than that of the inferior parent, suggests that many of the new gene combinations formed by interspecific hybridization are maladaptive and may contribute to the lack of progress in utilizing G. barbadense in conventional breeding programs to improve upland cotton.Electronic Supplementary Material Supplementary material is available for this article at     

Quantitative trait loci affecting cotton fiber are linked to the t1 locus in upland cotton

Pilose (T ₁), a dominant marker in upland cotton, has been associated with coarse, short fibers. Pilose was, thereby, considered to be pleiotropic on fiber fineness and length. However, a pilose-expressing line with a fiber of average fineness was recently identified. This finding does not support pleiotropy between T ₁ and fiber traits, but is indicative of linkage between pilose and loci influencing fiber characteristics. To understand the relationship between T ₁ and fiber traits, a pilose line with short, coarse fiber was crossed to two t ₁ lines with standard fiber characteristics. One hundred and forty-nine F₂-derived F₃ lines were developed from one cross, and 60 F₂-derived F₃ lines from the other. Seven fiber traits (elongation, maturity, micronaire reading, perimeter, 2.5% span length, strength, and wall thickness) were measured. Segregation was normal, as indicated by allelic frequencies of 0.5 for T ₁ and t ₁, and segregation ratios of 121 for marker genotypes. The association of homozygous T ₁ lines with fibers of average fineness was again observed. Linkage between T ₁ and loci affecting micronaire, perimeter, 2.5% span length, strength, and wall thickness was found in both populations. Significant additive and non-additive gene effects for each of these traits at the marker locus were found as well. The pilose marker accounted for 10–75% of the phenotypic variation associated with each trait. In conclusion, the t ₁ locus is linked to numerous loci that influence fiber traits, and this linkage has previously been misinterpreted as pleiotropy.     

Delineation of interspecific epistasis on fiber quality traits in Gossypium hirsutum by ADAA analysis of intermated G. barbadense chromosome substitution lines

Genetic diversity is the foundation of any crop improvement program, but the most cultivated Upland cotton [Gossypium hirsutum L., 2n?=?52, genomic formula?2(AD)₁] has a very narrow gene pool resulting from its evolutionary origin and domestication history. Cultivars of this cotton species (G. hirsutum L.) are prized for their combination of exceptional yield, other agronomic traits, and good fiber properties, whereas the other cultivated 52-chromosome species, G. barbadense L. [2n?=?52, genomic formula?2(AD)₂], is widely regarded as having the opposite attributes. It has exceptionally good fiber qualities, but generally lower yield and less desirable agronomic traits. Breeders have long aspired to combine the best attributes of G. hirsutum and G. barbadense, but have had limited success. F₁ hybrids are readily created and largely fertile, so the limited success may be due to cryptic biological and technical challenges associated with the conventional methods of interspecific introgression. We have developed a complementary alternative approach for introgression based on chromosome substitution line, followed by increasingly sophisticated genetic analyses of chromosome-derived families to describe the inheritance and breeding values of the chromosome substitution lines. Here, we analyze fiber quality traits of progeny families from a partial diallel crossing scheme among selected chromosome substitution lines (CS-B lines). The results provide a more detailed and precise QTL dissection of fiber traits, and an opportunity to examine allelic interaction effects between two substituted chromosomes versus one substituted chromosome. This approach creates new germplasm based on pair wise combinations of quasi-isogenic chromosome substitutions. The relative genetic simplicity of two-chromosome interactions departs significantly from complex or RIL-based populations, in which huge numbers of loci are segregating in all 26 chromosome pairs. Data were analyzed according to the ADAA genetic model, which revealed significant additive, dominance, and additive-by-additive epistasis effects on all of the fiber quality traits associated with the substituted chromosome or chromosome arm of CS-B lines. Fiber of line 3-79, the donor parent for the substituted chromosomes, had the highest Upper Half Mean length (UHM), uniformity ratio, strength, elongation, and lowest micronaire among all parents and hybrids. CS-B16 and CS-B25 had significant additive effects for all fiber traits. Assuming a uniform genetic background of the CS-B lines, the comparative analysis of the double-heterozygous hybrid combinations (CS-B?×?CS-B) versus their respective single heterozygous combinations (CS-B?×?TM-1) demonstrated that interspecific epistatic effects between the genes in the chromosomes played a major role in most of the fiber quality traits. Results showed that fiber of several hybrids including CS-B16?×?CS-B22Lo, CS-B16?×?CS-B25 and CS-B16?×?TM-1 had significantly greater dominance effects for elongation and hybrid CS-B16?×?CS-B17 had higher fiber strength than their parental lines. Multiple antagonistic genetic effects were also present for fiber quality traits associated with most of the substituted chromosomes and chromosome arms. Results from this study highlight the vital importance of epistasis in fiber quality traits and detected novel effects of some cryptic beneficial alleles affecting fiber quality on the 3-79 chromosomes, whose effects were not detected in the 3-79 parental lines.     

Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics

Cotton fiber qualities including length, strength and fineness are known to be controlled by genes affecting cell elongation and secondary cell wall (SCW) biosynthesis, but the molecular mechanisms that govern development of fiber traits are largely unknown. Here, we evaluated an interspecific backcrossed population from G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 for fiber characteristics in four-year environments under field conditions, and detected 12 quantitative trait loci (QTL) and QTL-by-environment interactions by multi-QTL joint analysis. Further analysis of fiber growth and gene expression between TM-1 and Hai7124 showed greater differences at 10 and 25 days post-anthesis (DPA). In this two period important for fiber performances, we integrated genome-wide expression profiling with linkage analysis using the same genetic materials and identified in total 916 expression QTL (eQTL) significantly (P<0.05) affecting the expression of 394 differential genes. Many positional cis-/trans-acting eQTL and eQTL hotspots were detected across the genome. By comparative mapping of eQTL and fiber QTL, a dataset of candidate genes affecting fiber qualities was generated. Real-time quantitative RT-PCR (qRT-PCR) analysis confirmed the major differential genes regulating fiber cell elongation or SCW synthesis. These data collectively support molecular mechanism for G. hirsutum and G. barbadense through differential gene regulation causing difference of fiber qualities. The down-regulated expression of abscisic acid (ABA) and ethylene signaling pathway genes and high-level and long-term expression of positive regulators including auxin and cell wall enzyme genes for fiber cell elongation at the fiber developmental transition stage may account for superior fiber qualities.     

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

Background

Cotton fibers (produced by Gossypium species) are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb) and G. hirsutum (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh × Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years.

Results

The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3.

Conclusions

Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.     

Disruption of interfascicular fiber differentiation in an Arabidopsis mutant.

Arabidopsis develops interfascicular fibers in stems for needed support of shoots. To study the molecular mechanisms controlling fiber differentiation, we isolated an interfascicular fiber mutant (ifl1) by screening ethyl methanesulfonate-mutagenized Arabidopsis populations. This mutant lacks normal interfascicular fibers in stems. Interestingly, some interfascicular cells were sclerified in the upper parts but not in the basal parts of the ifl1 stems. These sclerified cells were differentiated at a position different from that of interfascicular fibers in the wild type. Lack of interfascicular fibers correlated with a dramatic change of stem strength. Stems of the mutant could not stand erect and were easily broken by bending. Quantitative measurement showed that it took approximately six times less force to break basal stems of the mutant than of the wild type. In addition, noticeable morphological changes were associated with the mutant, including long stems, dark green leaves with delayed senescence, and reduced numbers of cauline leaves and branches. Genetic analysis showed that the ifl1 mutation was monogenic and recessive. The ifl1 locus was mapped to a region between the 17C2 and 7H9L markers on chromosome 5. Isolation of the ifl1 mutant provides a novel means to study the genetic control of fiber differentiation.     

Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.)

Background

Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy.

Results

Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel.

Conclusions

The 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-397) contains supplementary material, which is available to authorized users.     

Using three overlapped RILs to dissect genetically clustered QTL for fiber strength on Chro.D8 in Upland cotton

Fiber strength is an important trait among cotton fiber qualities due to ongoing changes in spinning technology. Major quantitative trait loci (QTL) for fiber quality enable molecular marker-assisted selection (MAS) to effectively improve fiber quality of cotton cultivars. We previously identified a major QTL for fiber strength derived from 7235 in Upland cotton. In the present study, in order to fine-map fiber strength QTL, we chose three recombinant inbred lines (RIL), 7TR-133, 7TR-132, and 7TR-214, developed from a cross between 7235 and TM-1 for backcrossing to TM-1 to develop three large mapping populations. Phenotypic data for fiber strength traits were collected in Nanjing (JES/NAU) and Xinjiang (BES/XJ) in 2006 and 2007. Three simple sequence repeat (SSR) genetic linkage maps on Chro.24(D8) were constructed using these three backcrossed populations. The SSR genetic maps were constructed using 907 individuals in (7TR-133 × TM-1)F₂ (Pop A), 670 in (7TR-132 × TM-1)F₂ (Pop B), and 940 in (7TR-214 × TM-1)F₂ (Pop C). The average distance between SSR loci was 0.62, 1.7, and 0.56 cM for the three maps. MapQTL 5 software detected five-clustered QTL (2.5 < LOD < 29.8) on Chro.D8 for fiber strength following analysis of three RIL backcrossed F₂/F_2:3 progenies at JES/NAU and BES/XJ over 2 years. Five QTL for fiber strength exhibited a total phenotypic variance (PV) of 28.8–59.6%.     

The R3-MYB Gene GhCPC Negatively Regulates Cotton Fiber Elongation

Cotton (Gossypium spp.) fibers are single-cell trichomes that arise from the outer epidermal layer of seed coat. Here, we isolated a R3-MYB gene GhCPC, identified by cDNA microarray analysis. The only conserved R3 motif and different expression between TM-1 and fuzzless-lintless mutants suggested that it might be a negative regulator in fiber development. Transgenic evidence showed that GhCPC overexpression not only delayed fiber initiation but also led to significant decreases in fiber length. Interestingly, Yeast two-hybrid analysis revealed an interaction complex, in which GhCPC and GhTTG1/4 separately interacted with GhMYC1. In transgenic plants, Q-PCR analysis showed that GhHOX3 (GL2) and GhRDL1 were significantly down regulated in −1–5 DPA ovules and fibers. In addition, Yeast one-hybrid analysis demonstrated that GhMYC1 could bind to the E-box cis-elements and the promoter of GhHOX3. These results suggested that GhHOX3 (GL2) might be downstream gene of the regulatory complex. Also, overexpression of GhCPC in tobacco led to differential loss of pigmentation. Taken together, the results suggested that GhCPC might negatively regulate cotton fiber initiation and early elongation by a potential CPC-MYC1-TTG1/4 complex. Although the fibers were shorter in transgenic cotton lines than in the wild type, no significant difference was detected in stem or leaf trichomes, even in cotton mutants (five naked seed or fuzzless), suggesting that fiber and trichome development might be regulated by two sets of genes sharing a similar model.