Unravelling the genetic basis and regulation networks related to fibre quality improvement using chromosome segment substitution lines in cotton.

The elucidation of genetic architecture and molecular regulatory networks underlying complex traits remains a significant challenge in life science, largely due to the substantial background effects that arise from epistasis and gene-environment interactions. The chromosome segment substitution line (CSSL) is an ideal material for genetic and molecular dissection of complex traits due to its near-isogenic properties; yet a comprehensive analysis, from the basic identification of substitution segments to advanced regulatory network, is still insufficient. Here, we developed two cotton CSSL populations on the Gossypium hirsutum background, representing wide adaptation and high lint yield, with introgression from G. barbadense, representing superior fibre quality. We sequenced 99 CSSLs that demonstrated significant differences from G. hirsutum in fibre, and characterized 836 dynamic fibre transcriptomes in three crucial developmental stages. We developed a workflow for precise resolution of chromosomal substitution segments; the genome sequencing revealed substitutions collectively representing 87.25% of the G. barbadense genome. Together, the genomic and transcriptomic survey identified 18 novel fibre-quality-related quantitative trait loci with high genetic contributions and the comprehensive landscape of fibre development regulation. Furthermore, analysis determined unique cis-expression patterns in CSSLs to be the driving force for fibre quality alteration; building upon this, the co-expression regulatory network revealed biological relationships among the noted pathways and accurately described the molecular interactions of GhHOX3, GhRDL1 and GhEXPA1 during fibre elongation, along with reliable predictions for their interactions with GhTBA8A5. Our study will enhance more strategic employment of CSSL in crop molecular biology and breeding programmes.

Characteristics of sudanese camel-hair fibres under subtropical desert condition.

The study assessed the quality and variability of camel hair fibres in arid regions of Egypt. Raw camel-hair samples were collected from fifteen Sudanese camels divided into seven males (414.60 ± 38.19 kg, BW) and eight females (401.67 ± 26.76 kg BW), and the study investigated the influences of animal sex on both the physical and chemical traits of camel-hair fibers. The relationships among physical properties and both mineral and amino acid content were studied. Camel's sex had no significant effect on any of the studied traits including fibre diameter (FD), prickle factor (PF), medullated fibre (MF), staple length (SL) and staple strength (SS). In the meantime, no significant differences were found between males and females in fibers' minerals contents except potassium, where fibres of females had significantly higher potassium content than those of males. For amino acids contents in camel fibres, camel sex had a significant effect only on glutamic acid, since fibres of males showed higher (P < 0.05) content than females. Fibre diameter had positive (P < 0.01) correlations with prickle factor (r = 0.83) and medullated fibres (r = 0.73). Zinc content in camel fibres was positively correlated with fibre diameter (r = 0.57; P < 0.05) and medullated fibres (r = 0.73; P < 0.01). Moreover, a significant (negative correlation coefficient P < 0.05) was found between fibre diameter and both sulfur and proline contents (r=-0.39 and - 0.56). Ammonia content in fibres was correlated negatively (P < 0.05) with prickle factor and elongation (r=-0.62 and - 0.58, respectively). The variability in the physical properties and chemical composition of Sudanese camel-hair fibers under subtropical desert conditions may shed light on the possibility of improving fiber quality.

Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance.

Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.

Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions.

Fine mapping QTLs and identifying candidate genes for cotton fibre-quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high-density genetic map by specific-locus amplified fragment sequencing (SLAF-seq) to identify QTLs associated with fibre-quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high-yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre-quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF-based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co-located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre-related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre-length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint-percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre-related traits and would be helpful for cloning fibre-development-related genes as well as for marker-assisted genetic improvement in cotton.

Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population.

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.

Improved lint yield under field conditions in cotton over-expressing transcription factors regulating fibre initiation.

Only a few transcription factors (TFs) regulating which cells of the ovule epidermis differentiate into lint fibres have been identified in cotton (Gossypium hirsutum L.). In this study, the effect on lint yield and fibre quality of over-expressing three TFs in cotton, GhHD-1, GhMYB25 and GhMYB25Like, and their double and triple combinations, were evaluated in field experiments over two seasons. The expression of single or stacked TFs were all driven either by an ovule-specific promoter, FBP 7, or a constitutive promoter, Stunt 7, in a Coker 315 background. TF type, either singly or in combination, was found to be the most significant factor affecting lint yield. Among 64 transgenic lines tested, seven were higher yielding than null segregant lines in one or both seasons and were all from the sets with single and double over-expressed TF combinations. A reduced yield was associated with the set of triple combinations. The two most stable high yielding lines across the seasons recorded 12-22% higher yields than the nulls, although were not competitive to locally adapted commercial controls. Over-expression of TFs singly or in combination did not significantly alter fibre length and strength, but sometimes increased fibre micronaire. There were positive relationships between lint yield and lint percentage and lint yield and fibre density amongst the transgenic lines. Our preliminary results suggest that manipulating TF expression, either singly or in pairs, can increase the density of fibres initiated on developing seeds and fibre yields under field conditions while maintaining overall fibre quality.

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum).

Brown fibre cotton is an environmental-friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine-mapped the brown fibre region, Lc1 , and dissected it into 2 loci, qBF-A07-1 and qBF-A07-2. The qBF-A07-1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF-A07-1 and qBF-A07-2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF-A07-1 and qBF-A07-2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome-wide association study (GWAS) and found that qBF-A07-2 negatively affects fibre yield and quality through an epistatic interaction with qBF-A07-1. This study sheds light on the genetics of fibre colour and lint-related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.

Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.

Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome-wide association study (GWAS) of fibre quality traits. A total of 10 511 polymorphic SNPs distributed in 26 chromosomes were screened across the cotton germplasms, and forty-six significant SNPs associated with five fibre quality traits were detected. These significant SNPs were scattered over 15 chromosomes and were involved in 612 unique candidate genes, many related to polysaccharide biosynthesis, signal transduction and protein translocation. Two major haplotypes for fibre length and strength were identified on chromosomes Dt11 and At07. Furthermore, by combining GWAS and transcriptome analysis, we identified 163 and 120 fibre developmental genes related to length and strength, respectively, of which a number of novel genes and 19 promising genes were screened. These results provide new insight into the genetic basis of fibre quality in G. hirsutum and provide candidate SNPs and genes to accelerate the improvement of upland cotton.

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs.

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton-producing and cotton-consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single-nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty-eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high-resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.

Interactive effects of protein and carbohydrates on production of microbial metabolites in the large intestine of growing pigs.

The study aimed at determining the effect of protein type and indigestible carbohydrates on the concentration of microbial metabolites in the large intestine of pigs. The experiment involved 36 pigs (15 kg initial body weight) divided into six groups, fed cereal-based diets with highly digestible casein (CAS) or potato protein concentrate (PPC) of lower ileal digestibility. Each diet was supplemented with cellulose, raw potato starch or pectin. After 2 weeks of feeding, pigs were sacrificed and samples of caecal and ascending, transverse and descending colon digesta were collected for analyses of microbial metabolites. PPC increased the concentration of ammonia, p-cresol, indole, n-butyrate, isovalerate and most of the amines in comparison with CAS. Pectin reduced the production of p-cresol, indole, phenylethylamine and isovalerate in the large intestine compared with potato starch. Starch and pectin increased mainly the concentration of n-butyrate and n-valerate in the colon compared to cellulose. Interaction affected mainly amines. Feeding PPC diet with potato starch considerably increased putrescine, cadaverine, tyramine and total amines concentrations compared with PPC diets with pectin and cellulose, whereas feeding CAS diet with starch reduced their concentrations. There was also a significant effect of interaction between diet and intestinal segment on microbial metabolites. In conclusion, PPC intensifies proteolysis in the large intestine and also n-butyrate production. Raw starch and pectin similarly increase n-butyrate concentration but pectin inhibits proteolysis more efficiently than starch. The interactive effects of both factors indicate that pectin and cellulose may beneficially affect fermentative processes in case of greater protein flow to the large intestine.

Leveraging transcriptomics-based approaches to enhance genomic prediction: integrating SNPs and gene networks for cotton fibre quality improvement.

Cultivated cotton plants are the world's largest source of natural fibre, where yield and quality are key traits for this renewable and biodegradable commodity. The Gossypium hirsutum cotton genome contains ~80K protein-coding genes, making precision breeding of complex traits a challenge. This study tested approaches to improving the genomic prediction (GP) accuracy of valuable cotton fibre traits to help accelerate precision breeding. With a biology-informed basis, a novel approach was tested for improving GP for key cotton fibre traits with transcriptomics of key time points during fibre development, namely, fibre cells undergoing primary, transition, and secondary wall development. Three test approaches included weighting of SNPs in DE genes overall, in target DE gene lists informed by gene annotation, and in a novel approach of gene co-expression network (GCN) clusters created with partial correlation and information theory (PCIT) as the prior information in GP models. The GCN clusters were nucleated with known genes for fibre biomechanics, i.e., fasciclin-like arabinogalactan proteins, and cluster size effects were evaluated. The most promising improvements in GP accuracy were achieved by using GCN clusters for cotton fibre elongation by 4.6%, and strength by 4.7%, where cluster sizes of two and three neighbours proved most effective. Furthermore, the improvements in GP were due to only a small number of SNPs, in the order of 30 per trait using the GCN cluster approach. Non-trait-specific biological time points, and genes, were found to have neutral effects, or even reduced GP accuracy for certain traits. As the GCN clusters were generated based on known genes for fibre biomechanics, additional candidate genes were identified for fibre elongation and strength. These results demonstrate that GCN clusters make a specific and unique contribution in improving the GP of cotton fibre traits. The findings also indicate that there is room for incorporating biology-based GCNs into GP models of genomic selection pipelines for cotton breeding to help improve precision breeding of target traits. The PCIT-GCN cluster approach may also hold potential application in other crops and trees for enhancing breeding of complex traits.

Consequences of Drought Stress Encountered During Seedling Stage on Physiology and Yield of Cultivated Cotton.

Survival of living organisms depends on the availability of water resources required for agriculture. In the current scenario of limited water resources, it is our priority to maximise the yield potential of crops with a minimum supply of available water. In this study, we evaluated seven cultivated varieties of Gossypium hirsutum (FH-114, FH-152, FH-326, FH-492, FH-942, VH-327 and FH-NOOR) for their tolerance, yield potential and fibre quality under water shortages. We also studied the effect of drought stress on osmoregulation, chlorophyll content, antioxidant (peroxidase and catalase) activity, lipid peroxidation and secondary metabolite accumulation in the varieties under study. It was revealed that three varieties (FH-114, FH-152 and VH-327) exhibited a lower stress susceptibility index and more tolerance to drought stress. All the varieties demonstrated enhanced proline and malondialdehyde content, but no significant change in chlorophyll content was observed under limited water supply. Antioxidant activity offered by catalase and phenolic content was enhanced in FH-492 whilst peroxidase activity increased in FH-114 and FH-326. Phenolic content was highest in FH-942 and decreased significantly in the remaining varieties. Ginning outturn of the cotton varieties increased in VH-327 (19.8%) and FH-326 (3.7%), was not affected in FH-114 and FH-492 and was reduced in FH-152, FH-942 and FH-NOOR. All cotton varieties tested showed an increase in micronaire thickness when exposed to drought stress as early as the seedling stage. This study highlights the evaluation and screening of cotton varieties for their response to drought stress in terms of yield and fibre quality when exposed to water shortages during plant development and can help in devising irrigation plans.

Influence of phosphorus on copper phytoextraction via modulating cellular organelles in two jute (Corchorus capsularis L.) varieties grown in a copper mining soil of Hubei Province, China.

Soil in mining areas is typically highly contaminated with heavy metals and lack essential nutrients for plants. Phosphorus reduces oxidative stress, improves plant growth, composition, and cellular structure, as well as facilitates the phytoremediation potential of fibrous crop plant species. In this study, we investigated two jute (Corchorus capsularis) varieties HongTieGuXuan and GuBaChangJia cultivated in copper (Cu)-contaminated soil (2221 mg kg-1), under different applications of phosphorus (0, 30, 60, and 120 kg ha-1) at both anatomical and physiological levels. At the same Cu concentration, the tolerance index of HongTieGuXuan was higher than that of GuBaChangJia, indicating that HongTieGuXuan may be more tolerant to Cu stress. Although the normal concentration of P (60 kg ha-1) in the soil improved plant growth, biomass, chlorophyll content, fibre yield and quality, and gaseous exchange attributes. However, high concentration of P (120 kg ha-1) was toxic to both jute varieties affected morphological and physiological attributes of the plants under same level of Cu. Moreover, Cu toxicity increased the oxidative stress in the leaves of both jute varieties was overcome by the activities of antioxidant enzymes. Furthermore, the high concentration of Cu altered the ultrastructure of chloroplasts, plastoglobuli, mitochondria, and many other cellular organelles in both jute varieties. Thus, phytoextraction of Cu by both jute varieties increased with the increase in P application in the Cu-contaminated soil. This suggests that P application enhanced the phytoremediation potential jute plants and can be cultivated as fibrous crop in Cu-contaminated sites.

Characterisation of white and black merino wools: a proteomics study.

Wool is an important agricultural commodity with merino wool being rated alongside the finest quality fibres, which include the goat fibres Mohair and Cashmere. Although pigmented wool merinos have become extremely rare, the market for this wool is increasing. In Portugal, there are two merino breeds: white and black, descendants of animals originally bred on the Iberian Peninsula. These breeds have the potential to assist in our understanding of how protein expression relates to wool traits of importance to the textile industry. Herein, we study the characteristics and protein expression profiles of wool from ewes of the Portuguese black and white merino (n=15). Both breeds had very similar results for fibre diameter (25 µm) and curvature (105 to 111°/mm). Significant between-breed differences were found in the two types of keratin-associated proteins (KAPs): high-sulphur proteins (HSPs) and high-glycine-tyrosine proteins (HGTPs). The expression of HSPs, KAP2-3 and KAP2-4, decreased expression in the pigmented animals, whereas KAP13-1 was found in higher amounts. Likewise, the expression of the ultra-high-sulphur proteins, KAP4-3 and KAP4-7-like, was reduced in black sheep to half the levels of the white wools, whereas the HGTPs, KAP6, KAP6-1, KAP6-2 and KAP16-2, were more abundant in black sheep. These results suggest structural differences between the black and white merino wool, because of differences among some KAPs. These differences have important implications for the textile industry.

Extensin arabinoside chain length is modulated in elongating cotton fibre.

Cotton fibre provides a unicellular model system for studying cell expansion and secondary cell wall deposition. Mature cotton fibres are mainly composed of cellulose while the walls of developing fibre cells contain a variety of polysaccharides and proteoglycans required for cell expansion. This includes hydroxyproline-rich glycoproteins (HRGPs) comprising the subgroup, extensins. In this study, extensin occurrence in cotton fibres was assessed using carbohydrate immunomicroarrays, mass spectrometry and monosaccharide profiling. Extensin amounts in three species appeared to correlate with fibre quality. Fibre cell expression profiling of the four cotton cultivars, combined with extensin arabinoside chain length measurements during fibre development, demonstrated that arabinoside side-chain length is modulated during development. Implications and mechanisms of extensin side-chain length dynamics during development are discussed.