Genetic Diversity And Association Analysis Of Agronomic Traits For Upland Cotton Core Germplasm Based On SSR Markers

This study constructed the Chinese upland cotton core germplasm based on the phenotypic traits then further analyzed the genetic diversity and population structure of the core germplasm, and investigated the QTLs for major agronomic traits by simple sequence repeats （SSRs） association study. The main results were listed as following:1. The construction of Core Collection of Upland Cotton in ChinaA total 5963 of upland cotton germplasm collection were sampled for constructing a core collection. The whole collection was firstly divided into 11 groups based on the major genotypes. The constructed core collection included 281 accessions based on 21 traits in each subset by unweighted pair-group method with arithmetic means （UPGMA）, which accounted for 4.71% number of total collection. Furthermore the representativeness between core collection and total collections was assessed by the t test, F test of variance, coefficient of variation, the diversity index t test, average, range, phenotypic variance and variation coefficient, mean difference percentage, variance difference percentage, coincidence rate of range, changeable rate of coefficient of variation, the percentage of phenotypic variationand principal component analysis. The results demonstrated that the selected core collection could represent the genetic diversity of whole collection. Considering the other types of upland cotton germplasm, the rate of phenotypic variation explanation reached 80.67%, so, we contracted the final upland cotton core collection with total 419 accessions by similar principle.2. Comprehensive evaluation and genetic diversity analysis of phenotypic traits of core collection in upland cottonWe analyzed the genetic diversity, change pattern of genetic variation for 17 phenotypic traits and explored the comprehensive evaluation techniques for 419 core collection in upland cotton. Genetic diversity indices of phenotypic traits were ranged from 0.351 to 3.796, with an average of 1.715. The result for the genetic diversity and genetic richness of different geographical origin indicated that the comprehensive properties of accessions from the Yellow River, Yangtze River and the Northwest regions were the best. Different periods of the genetic diversity and genetic richness with the passage of time gradually reduce. The clustering analysis shown that no obvious group divergence existed in upland cotton, however, the accessions with patial similar characteristics clustered into 13 subgroups. By performing the principal component analysis （PCA） and step regression analysis based on comprehensive assessment of phenotypic traits, the results demonstrated that N74-250 from Australia was the best accession with comprehensive traits while the accession Liaoyanglvrongmian was the worst. We also found that the traits inculding boll weight, fiber elongation, flowering date, micronaire, plant height, number of fruit branches and spinning consistent index could be suitable used as comprehensive standards for assessing upland cotton core collection.Generally, the Chinese upland cotton core collection has a rich genetic diversity; genetic variation of the germplasm from different geographical origin was great; The accessions from different ecological zones have unique characteristics, which provided the basis for geographically distant hybridization and widening the genetic diversity of current germplasm. Meanwhile, in this study, the construction of comprehensive evaluation methods for core of upland cotton germplasm could lay a foundation for high efficient evaluation of overall characteristic of cotton germplasm in future.3. The genetic diversity analysis of upland cotton core collectionTotal 1046 allelic variation were detected from 299 polymorphic SSR markers were used to assess the generic diversity of 419 upland cotton, Each marker generated average 3.5 allelic variation, and The polymorphism information content （PIC） value of markers were ranged from 0.02 to 0.85, with an average of 0.54, showed that the selected primers could provide relatively abundant genetic information. Calculation of similarity coefficient（SM） among all core material and the adjacent method based on Nei’s genetic distance cluster analysis showed that the pairwised coefficient of similarity between in 419 accessions was ranged from 0.505 to 0.941, with an average of 0.651, the number of accessions with similarity coefficient less than 0.669 was accounted for 88.69%; The average similarity coefficient among different breeding stages was small; From the perspective of different geographic origin, the maximum similarity coefficient of accessions from Yangtze River basin reached 0.671, followed by the Yellow River basin （0.664） and Southern China （0.624）; We found that the average similarity coefficient of foreign accessions （0.643） was slightly lower than that in domestic accessions （0.655）, and the domestic core germplasm domestic upland cotton core germplasm （0.506 0.941） is greater than the foreign germplasm resources （0.532 0.901）. Cluster analysis based on SSR marker results revealed that the existing germplasm upland cotton core germplasm resources in China and introduced the development trend of law; Will be in accordance with the approved s 419 core germplasm in installment, it found that early introduction of core materials related to geographic origin, introduced some of the more match the local planting environment variety.4. The associated study for major agronomic traits in Upland cotton core collectionAssociated analysis of mixed linear model was used to detect the excellent correlated loci, a total of 141 marker loci associated with yield, fiber quality traits and other traits were found, thirty-two of them were simultaneously detected in all 6 environments for 15 of the traits; Total 32 loci were simultaneously detected in 2 environments. Marker CM0043₁ simultaneously associated with uniformity index, spinning evenness index and the fiber length, which all showed positive effects, indicating this marker could improve fiber quality; JESPR0190 associated with boll opening period, flowering period and branch number showed the negative effects, indicating this marker could shorten the growth period and reduce the number of branch to regulate the maturity; NAU3434₃ and NAU3587₃ were both associated with the first fruit and bell weight, this type of marker which associated with multiple traits might be caused by the gene （or QTL） pleiotropy; Additionally, there were three markers with-logP> 10, including NAU0874, NAU5433 and NAU5192₄, and NAU5433 associated with leaf trichome was located at the same gene of the known gene T1.