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Improvement of cotton fibre yield and quality is challenging due to the narrow genetic base of modern cotton cultivars, which emphasizes the great need to effectively explore the existing germplasm resources. With major objective to assess the genetic diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions (253 Chinese and 49 different exotic origins), were genotyped using 198 simple sequence repeats (SSRs) markers. Each of the 198 markers differed greatly in its ability to detect variations in the panel of cotton germplasm. The SSRs amplified 897 alleles, of which 77.7% were polymorphic. The number of alleles varied from 2 to 12 (mean 4.53). Gene diversity ranged from 0.020 to 0.492 with a mean of 0.279. The polymorphic information content (PIC) values ranged from 0.371 to 0.019 (mean 0.225). Genetic distances in the whole cotton germplasm ranged from 0.451 to 0.052 (mean 0.270), demonstrating relatively wider genetic diversity range. Chinese-origin cotton germplasm showed the highest level of SSR polymorphisms (gene diversity $$=$$ 0.268, PIC $$=$$ 0.218), whereas American-origin revealed the highest mean genetic distance (0.274). Model-based Bayesian analysis clustered the whole cotton germplasm into three subpopulations, and the highest molecular variation ws revealed between subpopulations (4%, $$P{

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium (LD). This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism (PIC=0.53) was found, and three groups were detected ( K =3) with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r 2 ≥0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model (GLM) and mixed linear model (MLM) ( P ≤0.01). The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci (QTLs) information for marker-assisted selection.

Cotton is the most important textile crop in the world due to its cellulose-enriched fibers. Sucrose synthase genes (Sus) play pivotal roles in cotton fiber and seed development. To mine and pyramid more favorable alleles for cotton molecular breeding, single nucleotide polymorphisms (SNPs) of GhSus family genes were investigated across 277 upland cotton accessions by EcoTILLING. As a result, a total of 24 SNPs in the amplified regions of eight GhSus genes were identified. These SNPs were significantly associated with at least one fiber- or seed-related trait measured in Nanjing, Anyang and Kuche in 2007–2009. Four main-effect quantitative trait nucleotides (QTNs) and five epistatic QTNs, with 0.76–3.56% of phenotypic variances explained by each QTN (PVE), were found to be associated with yield-related traits; six epistatic QTNs, with the 0.43–3.48% PVE, were found to be associated with fiber quality-related traits; and one main-effect QTN and one epistatic QTN, with the PVE of 1.96% and 2.53%, were found to be associated with seed oil content and protein content, respectively. Therefore, this study provides new information for molecular breeding in cotton.

The impact of alien DNA fragments on plant genome has been studied in many species. However, little is known about the introgression lines of Gossypium. To study the consequences of introgression in Gossypium, we investigated 2000 genomic and 800 epigenetic sites in three typical cotton introgression lines, as well as their cultivar (Gossypium hirsutum) and wild parents (Gossypium bickii), by amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP). The results demonstrate that an average of 0.5% of exotic DNA segments from wild cotton is transmitted into the genome of each introgression line, with the addition of other forms of genetic variation. In total, an average of 0.7% of genetic variation sites is identified in introgression lines. Simultaneously, the overall cytosine methylation level in each introgression line is very close to that of the upland cotton parent (an average of 22.6%). Further dividing patterns reveal that both hypomethylation and hypermethylation occurred in introgression lines in comparison with the upland cotton parent. Sequencing of nine methylation polymorphism fragments showed that most (7 of 9) of the methylation alternations occurred in the noncoding sequences. The molecular evidence of introgression from wild cotton into introgression lines in our study is identified by AFLP. Moreover, the causes of petal variation in introgression lines are discussed.

With 1 figure and 8 tables Abstract The genetic effects and heterosis of the colour and quality of brown fibres were analysed in this paper through the complete 5 × 5 diallel crossing among two brown cotton cultivars and three white cotton cultivars in upland cotton (Gossypium hirsutum). Parents and F1 were arranged in a randomized block design in three locations. The results showed that the inheritability for all the traits has exceeded 50%, with significant dominance effect at the 0.01 level. The additive effect of fibre colour, lint percentage, elongation and strength was also significant at the 0.01 level, reaching 85.6%, 29.7%, 16.1% and 19.1%, respectively. The ratio of residual variance of lint percentage and fibre qualities was 29.5 – 45.9%, that of colour was only 1.1%. Fibre colour had significant negative correlation with lint percentage, fibre length, uniformity, elongation and strength. The mid-parent heterosis of fibre colour was negative, which was −0.7%; those of lint percentage, fibre length, uniformity and strength were 3.5%, 4.2%, 1.7% and 2.6%, respectively, reaching the significant level. The simple correlation coefficient between heterosis of fibre length and strength and SSR genetic distance was 0.718 and 0.724, respectively, with a significant level. For the heterosis utilizing, the fibre quality of F1 could be predicted via the mean value of the fibre qualities of parents or the SSR genetic difference among varieties (lines). Selection among the early hybrid generations was suggested. Regional planning could be applied to improve lint percentage and fibre qualities by taking advantage of environmental variation.

With 2 figures and 4 tables Abstract A novel super-dwarf mutant, named AS98, was discovered from an interspecific hybrid in 1998. Compared to the normal line LHF10W99, plant height and internode length were significantly shorter in AS98, but it had only slightly (3–5%) fewer internodes. Therefore, the shorter plant height was the result of shorter internodal length. AS98 was crossed with LHF10W99, and the F1, F2, BC1, and BC2 populations were used for genetic analysis of the dwarf trait. The results showed that the trait was controlled by a single incomplete-dominant gene. Exogenous application of gibberellin acid (GA3), brassinosteroid and indol acetic acid showed a significant response to GA3, which could restore plant height in AS98. The results thus provide a basis for utilizing the dwarf trait in breeding and studying the biosynthesis of GA or signal transduction in cotton.