| Almost all of agronomically important traits of cotton are quantitatively inherited,which are controlled by genotype as well as affected by environments.At the same time,there is a complex relationship among these traits,so it is difficult to synchronously improve the target traits by traditional breeding methods.Association analysis has become an important means to dissect complex quantitative traits,and it can improve the breeding efficiency by identifying the marker loci associated with target traits.The important information can be provided for genetic improvement of upland cotton varieties by genetic diversity analysis of upland cotton varieties in natural populations and association analysis of target traits.With the application of transgenic technology,there are differences in only a few phenotypic traits or no differences,so it is important to detect the authenticity and purity of varieties by using effective methods.In this study,180 superior upland cotton cultivars and breeding lines were selected as a natural population from association panel previously constructed in our laboratory.The accessions were genotyped with 560 SSR markers which uniformly distributed in the whole-genome of tetraploid cotton(selecting a SSR marker for each 10 cM)and linked or associated with important traits in Upland Cotton.At the same time,the important characters of cotton including yield,fiber quality,early maturity,agronomic traits and seed quality traits were identified in mutiple experimental sites over the years.Genetic diversity analysis was performed for the experimental materials with phenotypic and SSR markers data.Marker loci associated with important traits of cotton were detected by the method of association analysis.With the molecular markers associated significantly with at least two phenotypic characters and the first and alternative primers previously provided as the core primers DNA barcoding of 180 upland cotton cultivars(lines)was constructed,and it lay the foundation for molecular identification of cotton cultivars authenticity and purity.1.Analysis of genetic diversity of upland cotton varieties in china560 SSR markers selected were used to scan the whole-genome of upland cotton varieties,and 228 polymorphic markers were obtained.The 228 polymorphic markers loci had 601 alleles,with allelic variation ranged from 2-11 and a mean of 2.64.Among them,86 percent of the total polymorphic markers loci,198 had two or three alleles.The means of gene diversity index and the polymorphic information content(PIC)of 228 markers loci were 0.37 and 0.31,respectively.The results indicated that the upland cotton varieties tested possessed ittle genetic diversity.Clustering analysis based on phenotypic genetic distance was performed,and the 180 upland cotton cultivars could be categorized into five major groups at the genetic distance of 6.30.Among the five groups,the first group could be categorized into six subgroups at the genetic distance of 5.13.By clustering analysis of genetic distance based on SSR markers the 180 upland cotton cultivars could be categorized into 10 major groups.Some varieties were categorized into the same group in the two kinds of clustering analysis,but there were large differences in some varieties between the two kinds of clustering analysis.Therefore,the evaluation of the genetic diversity of germplasm can be more comprehensive and accurate combining different kinds of clustering analysis data.The results in this study provide important information for further association analysis.2.Association analysis of important traits of upland cottonAssociation analysis of 17 traits was performed using the Tassel 2.1 MLM(mixed linear model)program.A total of 291 marker loci significantly associated with QTL of importment traits were detected in at least two environments.Among them,there were 20 marker loci detected for yield traits,125 for fiber quality traits,67 for early maturing traits,52 for agronormic traits and 27 for seed quality traits.The majority of the 291 loci were able to coincide with the QTL genome segments located in other studies.The markers in two sides of NAU3212 and NAU4926,associated with fiber length and fiber strength respectively,were completely consistent with the corresponding QTL previously located.Not only the same trait existed many association loci,but also the same locus may be associated with multiple traits.In total 291 loci,there were 79 repeat loci which associated simultaneously with at least two traits.For each kind of character,three repeat loci for yield traits were detected,such as cgr5675 associated with lint percentage and seed index,CIR286 associated with boll weight lint yield and NAU2741 associated with boll weight and seed index.There were 26 repeat loci detected for fiber quality,11 for early maturing,10 for agronomic traits,9 for seed quality.These results indicated that the phenotypic variation of the related traits is regulated by the same gene nearby the same site at a certainextent,or the genes controlling these traits are closely linked to the chromosome.These results indicate that the phenotypic variation of the related traits is regulated at a certain extent by the same gene at the same site,or the genes controlling these traits are closely linked on chromosome.3.DNA fingerprinting barcode constrution of upland cotton varieties in chinaFurther repeat determination was performed for 79 repeat loci associated simultaneously with at least two traits,and 21 primer pairs with clear and high polymorphism information content were screened.The 21 primer pairs covering 21 chromosomes are as follows,NAU2741 on A1,NAU3016 on A3,NAU3212 on A5,NAU3427 on A6,NAU3654 on A7,BNL3792 on A8,NAU3414 on A9,NAU2508 on A10,BNL1231 on All,BNL3261 on A12,BNL1707 on A13,BNL2646 on D1,NAU5467 on D2,NAU5260 on D3,NAU6966 on D4,NAU2816 on D5,BNL3359 on D6,NAU6468 on D7,NAU3100 on D9,NAU2776 on D10 and NAU6582 on D13.And 23 pairs of primers as core primers were determined together with the selected SSR markers NAU0478 on D8 and NAU2251 on D12 from the first and alternative primers previously provided.The 23 pairs of core primers had 64 alleles in the 180 upland cotton varieties,with an average of 2.83 alleles per SSR marker(range,2-5).The gene diversity ranged from 0.15 to 0.61 with a mean of 0.38.The polymorphic information content ranged from 0.14 to 0.53 with a mean of 0.32.Most of the 23 core primer pairs are expressed sequence tags(EST),and they were associated with multiple traits,so it is very useful for fingerprinting analysis with the 23 core primer pairs.The genetic distance matrix based on 23 core primer pairs had a highly significant positive correlation with that based on 228 primer pairs,and a significant positive correlation with that based on phenotype,which showed the evaluation of the experimental materials was reliable by using the 23 core primer pairs.The microsatellite loci electrophoresis band type of 23 primer’pairs in the control TM-1 were recorded as 1,and electrophoresis band types in other 179 upland cotton cultivars were obtained.Microsatellite loci code combination in the 23 chromosome for each species,a total of 23 digital codes,was obtained through putting the electrophoresis band type code together in series according to chromosome number from small to large,Dt subgroup,At subgroup.Thus SSR molecular identity card for each species was formed.Each number in molecular identity card indicated the microsatellite loci code in each species relative to the control species in different chromosomal locations,and the relative DNA barcode of a variety was formed and used for cultivar DUS tests. |
PDF Full Text Request