Genetic Diversity Evaluation Of Shorted-season Upland Cotton Cultivars And Localization Of QTLs For Important Agriculture And Economic Traits

Cotton is one of the most important economic crops in the world; it provides the mostimportant material, natural fiber, for textile industry. So, cotton has an important strategicstatus in national economy. Short-season upland cotton plays an important role in thecultivation reform in china. We used molecular marker to detect the genetic diversityamong the short-season upland cotton varieties.In this research, RAPDs analysis was used to assess the genetic diversity of 29 eliteshort-seasoned cotton cultivars. From 600 10-mer arbitrary primers, we selected 122primers that could produce legible and repetitive bands. 29 cotton varieties were screenedwith these 122 primers to generate 181 polymorphism loci. Cluster analysis and UPGMA(with NTSYS-PC2.10) showed that these 29 varieties could be classified into two groups.The correlation coefficients between species mostly range from 0.60 to 0.79; only 0.99percent was between 0.30 and 0.39. And this is agreed with the pedigree. In a word, thegenetic basis of popular short season upland cotton in China is narrow, and the Kings isthe main sources of earliness gene.For cotton breeders, the major task is to improve the yield and the fiber quality, andduring the past decades of years, under the continuous efforts of the breeders, the yieldand fiber quality has been greatly improved. But, with the development of textile industryand increased consumption demands on cotton fiber commodity, most of the cottoncultivars are out of date, especially for cotton quantity. Consequently, it is eager to breedthe cultivars with high yield and good quality. However, cotton yield traits and qualitytraits are complicated quantitative traits; what is more, yield traits are negativelyassociated with quality trait, so it is difficult to improve yield and quantity simultaneity bytraditional breeding ways. The appearance of molecular markers and the development ofthe molecular quantitative genetics, make it possible to build high density linkage mapand QTL mapping, and then by using the linked markers, marker-assisted selection can beperformed during breeding process.Based on a F₂ population from cross between Ghirsutum L.×G.barbadense L., acombined TRAP-SSR-AFLP-SRAP genetic map of tetraploid cotton was constructed andQTL mapping was performed. The main results were summarized as follows:1. An interspecific F₂ population of 222 individuals between Ghirsutum L. cv CRI36×G.barbadense L. cv Hai7124 was planted in Hainan, from which 186 individuals werepicked out and used as mapping population. 2. Four kinds of molecular markers were used to identify polymorphism between twoparents. Finally, a total of 1250 polymorphic loci were obtained including 198TRAPs, 758 SSRs, 143 AFLPs and 151 SRAPs. Also, two morphologic markers,yellow pollen and red spot, were investigated. The 1252 polymorphic loci weresubsequently analyzed by X² test, at the 5% significant level, 249 loci deviated fromthe expected ratio (1:2:1 or 3:1), which included 124 SSRs (19.2%), 38 TRAPs(18.9%), 24 SRAPs (15.9) and 27 AFLPs (16.3%).3. 1252(A thousand two hundred and fifty-two) marker loci were used to constructgenetic linkage groups using MapMaker/EXP. 3.0. The map consisted of 1097markers mapped into 35 linkage groups, including 697 SSRs, 171 TRAPs, 129SRAPs, 98 AFLPs, and two morphological markers, and spanned 4,536.7 cM with anaverage genetic distance of 4.1 cM per marker. According to the assigned SSRs orcommon loci, linkage groups were assigned to the 26 chromosomes of the tertraploidgenome and eight novel small linkage groups. The distance of single linkage groupwas from 106.5 cM to 235.1 cM, the loci number in every group was from 2 to 63,and the average distance between each locus was from 1.8 cM to 11.9 cM. The 13A-genome groups span 2,215.2 cM containing 590 makers with an average distanceof 3.8 cM, the 13 D-genome groups span 2,203 cM with 490 markers with an averagedistance of 4.1 cM. In this research, 11 of 13 pairs of homoeologous chromosomeswere bridged with a total of 45 SSR duplicated loci, except for c2-c14 and c3-c17.200 distorted segregation loci (116 SSRs, 42 TRAPs, 18 SRAPs, 22 AFLPs and 2morphological markers) were mapped in the 26 groups of allotetroploid cotton. At thepresent map, skewed markers were clustered in different degrees, which were usuallyobserved at the end or in the middle of the group. And maybe, some of them wereSegregation Distortion Regions(SDR).4. This is the first time that the novel molecular marker, TRAP (Target RegionAmplification polymorphism), was used to construct genetic map in cotton. A total of57 fixed primers were designed on EST sequences using Primer Premier 5.0.Combined with the random primers of SRAP, 198 polymorphic loci were observedby using 93 primer pairs. Every primer combination could generate 1-7 polymorphicloci, with an average 2.1 polymorphic loci per primer pair. 19 of the 198 loci wereco-dominant loci, and 45 were distorted segregation loci. Totally, 171 loci weremapped on 26 linkage groups. Except for three short linkage groups (NL6, NL7, NL8), it could be found in the remained groups, and most distributed on the c2, c4, c5,c6, c9, c10, c14, c20, A02, A03.5. The fiber yield, fiber quality, and some traits related to short-season of F₂ plants andcorresponding F_2:3 families were investigated; but the fiber quality trait of F_2:3 was notobtained because not enough fiber was harvest. QTLs were scanned by the method ofcomposite interval mapping (CIM) in program QTL Cartographer V2.0. When the logodds-ration threshold of QTL detection was 3.0, 79 QTLs could be detected,including 25 QTLs related to fiber quality traits explained from 8.69% (qFU-c6-1)to 23.19% (qFL-c1-2) of phenotypic variation (PV); 36 QTLs related to fiber yield(16 QTLs in F₂ plants, 20 QTLs in F₃ plants); and 18 QTLs related to short-season.6. 8 TRAP markers linked to the QTLs of fiber length, fiber uniformity ratio andmacronaire value, were detected. For example, T16E2c was linked to a QTL(qFL-c1-2) in chromosome 1 (within 0.01cM), and a QTL (qFU-c17-1) related tofiber uniformity ratio was positioned at the interval of T9E10b-JESP195. And thesetwo primers were designed from the genes related to fiber extension and fiberformation respectively. So, TRAP marker is not only benefiting for increasing thegenetic map density, but also it is easy to link with the related QTLs.