Association Analysis Between Yield, Fiber Quality Traits And SSR Markers In Upland Cotton

As the most important natural fiber crop in the world, cotton makes a significantcontribution to the development of textile industry in China. At present, increasing yield andimproving fiber quality are the targets on cotton breeding. It is enormously significant towiden genetic bases and prove efficiency of cotton breeding which screens SSR markersassociated with yield, fiber quality of cotton on the base of fully acquainting genetic diversityof cotton.1. The genetic diversity, population structure and the linkage disequilibrium (LD) ofchromosomes of126upland cotton varieties was analyzed by125SSR markers that werewell-distributed on26chromosomes. In addition, association analysis between SSR markerswith yield, fiber quality phenotype variation was showed to any alleles with good variation ofdifferent markers. The results are as follows.(1) Analysis of genetics diversity detected125loci, a total of424allelic variations,with an average allele number of3.38. The average GDC (Genetic Diversity Content) was0.49and PIC (Polymorphism Information Content) was0.41. The results showed that thegenetic diversity of material was relatively abundant.(2) Population structure of126upland cotton materials analyzed by Structure softwareshowed that cotton materials divided into two groups which have region. The result of clusterby nei’s distance was similar to population structure analysis at great degree.(3) The linkage disequilibrium (LD) analyzed by TASEEL2.0software, showed thatonly11.95%combinations of sites was D’>0.5.and7.13%combinations of sites supposedlinkage disequilibrium (P <0.01). So it meaned upland cotton had a lower level of LDHowever, matrix plot of linkage disequilibrium showed LD of upland cotton wasunwell-distributed on chromosome and had higher level on A13, D1and D8.(4) Marker-trait association analysis showed that55SSR loci were detectedsignificantly （P<0.001） associated with14traits. In which,11SSR loci are associated withboll number,1SSR loci are associated with fruit branch,1SSR loci are associated with plantheight,1SSR loci are associated with boll weight,4SSR loci are associated with lintpercentage,7SSR loci are associated with the protein content of seed,4SSR loci areassociated with the fat content of seed,6SSR loci are associated with fiber length,4SSR lociare associated with strength,1SSR loci are associated with fiber micronaire,2SSR loci areassociated with short fiber index,1SSR loci are associated with uniformity,10SSR loci are associated with Elongation,3SSR loci are associated with radiant reflectance. The results canlay the foundations for marker-assisted selection of cotton.(5) Good variation of different markers by association analysis detected numerousassociations between marker sites and yield, fiber quality traits. And found a batch of excellentassociated sites, allele’s variety and carrier materials of association excellent sites whichprovided significant information for parental selection, the combination of matching andallele variations of offspring on cotton breeding.2. Synonymous codon usage bias (SCUB) of coding DNA sequences of proteins innuclear genome of13diploid (A, D genome) and2allotetraploid (AD genome) cotton specieswere analyzed by CodonW program. The main results are as follows.(1) The results showed that15cotton species have similar base composition of codonswhich possess more pyrimidines (A and C) than purines (T and G) at the third codon position.Relative synonymous codon usage analyses (RSCU) found significant and highly concurrentcodon usage bias among the15cotton species. Twenty high frequency codons were useduniversally in15cotton species. Inconsistent with such concurrence, quite different preferredcodons (ΔRSCU≧0.3) were determined among the15cotton species. Compared with aprevious study (Shang et al.,2011), the nuclear genome and chloroplast genome showedsimilar codon composition especially at the third codon position but quite differenthigh-frequency codons of8amino acids.(2) ENC-plot analysis indicated that the SCUB is related to mutation and selection, inwhich selection plays a leading role.(3) The relationship of the15cotton species revealed by cluster analysis based on RSCUvalue was highly consistent with their taxonomic results widely accepted, suggesting thecodon usage bias pattern could reflect the relationship of the origin and evolution of differentcotton species at a certain degree.