| Cotton is the world's most important natural textile fiber. With the changes in spinning technology, the improvement of cotton fiber quality is becoming extremely important. The combination of conventional breeding techniques with MAS (molecular-assisted selection) will become a basic approach for cotton fiber improvement. The cross of 1138×NM03102 was made, which included one parent, NM03102 with elite fiber quality from New Mexico State University, USA, and the another parent, 1138 as commercial cultivation transgenic variety resistant to budworm from Shandong Cotton Research Center. It could be very useful to identify the quantitative trait loci (QTL) of fiber quality and yield traits for revealing the genetic basis of the main characters and their genetic relationships, and increasing the selective effeciency of cotton breeding.The fiber quality and yield traits were tested or observed systematically. The results showed that: there were significant or extremely significant difference for boll size,lint percent, fiber length, fiber strength and Micronaire value between the two parents, And all the traits in F2 and F2:3 populations were distributed in normal distribution with the phenomenon of two-way transgressive segregation, which match to the phenotypes conditioned by multiple micro-effect genes.The correlation analysis indicated that fiber length was very significantly positive correlation with fiber strength, fiber elongation and fiber uniformity, not correlation with Micronaire value. Fiber strength was very significantly positive correlation with fiber elongation and fiber uniformity, and very significantly negative correlation with Micronaire value. Micronaire was very significantly positive correlation with fiber elongation and fiber uniformity. Boll size was significantly negative correlation with lint percent, and very significantly positive correlation with fiber length, fiber uniformity, Micronaire value and fiber elongation. Lint percent was significant negative correlation with fiber length, fiber uniformity, fiber elongation and fiber strength, which indicated it's still difficult to improve fiber quality and lint percent simultaneously. These correlations could be partly explained by QTLs clusters or co-location in the experiment.In the present study,225 pairs of polymorphic primer were obtained for the two parents from 7892 pairs of SSR primer , and the polymorphic primers were used to genotype the 195 individual plants in F2 population derived from 1138×NM03102,242 loci were obtained. With the software of Joinmap3.0 with LOD of 5.0, Linkage test indicated that 182 loci could be mapped to 37 linkage groups, which covered a total genetic distance of 1661.6cM, approximately 37.34 % of cotton genome. The average distance of neighbor markers was 9.1cM. 35 linkage groups were assigned to corresponding chromosome.Based on Composite Interval Mapping (CIM) method of WinQTLCartographer2.5, the result showed that 20 QTLs for fiber quality were detected in F2 and F2:3 populations, 4 for fiber length , 4 for fiber strength , 5 for Micronaire value, 4 for fiber uniformity and 3 for fiber elongation,respectively. These QTLs expained 5.10%-28.49% of the corresponding phenotypic variations. 27 QTLs for the yield traits were identified, 3 for plant seedcotton yield, 4 for plant lint yield, one for boll size, 6 for seed index, 6 for lint percent , 4 for plant height and 3 for fruit branchs, respectively. These QTLs expained 5.93%-44.29% of the corresponding phenotypic variations.10 favorable alleles for fiber quality originate from donor parent NM03102. In addition, 2 QTLs with one for fiber strength and another for Micronaire value could be detected in two generations. And 2 QTLs with one for fiber strength and another for fiber uniformity could be detected in different genetic background previously published in other reports. Fourteen favorable alleles for the yield traits originate from donor parent 1138. 1 QTL for fruit branch could be detected in two generations and 2 QTLs with 1 for seed index and 1 QTL for lint percent were same as previously published reports. In particular, 1QTL for fiber strength could be detected in different generations and different genetic background. The molecular markers linked closely to the stable major QTL could be used in MAS to improve cotton fiber quality.
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