| Cotton is one of the world’s most important cash crops. Improvement of yield and fiber quality is the focus of cotton breeding. To develop elite allelic variation and functional markers of important agronomic character genes are helpful for marker-assisted selection in crop. It was reported that sucrose synthase gene Gh Su SA1 and actin depolymerization factor gene Gh ADF1 could improve cotton fiber quality including fiber length and fiber strength when over-expressed Gh Su SA1 and anti-sensed Gh ADF1 were transformed into cotton, respectively. In this study, functional markers were developed based on sucrose synthase gene Su SA1 and actin depolymerization factor gene ADF1. Gossypium hirsutum CCRI8 and G. barbadense Pima90-53 were used to amplify their genomic sequence. Based on the genomic sequence, the primers were designed to amplify the polymorphic marker which was present between CCRI8 and Pima90-53. Combined the polymorphic, marker linkage map and QTL mapping of fiber quality published by our lab, linkage analysis of the new marker and QTL mapping were done. These will provide the new marker for genetic improvement and marker-assisted breeding of fiber quality in cotton. The main results were as follows:1. BLAST analysis was done between ORF sequence of Su SA1 and the genome database including diploid ancestors, G. arboreum and G. raimondii. A- genome and Dgenome sequences of Su SA1 were obtained and located at Ca7 and Cd8, respectively. According to D genome sequence of Su SA1, the primers were designed to amplify genomic sequence in CCRI8 and Pima90-53. Two kinds of genotypes, g Gh Su SA1-1, g Gh Su SA1-2 were obtained from CCRI8, g Gh Su SA1-1 originated from A genome and g Gh Su SA1-2 originated from D genome. Two kinds of genotypes, g Gb Su SA1-1, g Gb Su SA1-2 were obtained from Pima90-53, g Gb Su SA1-1 originated from A genome and g Gb Su SA1-2 originated from D genome. According to the SNP sequence variation between CCRI8 and Pima90-53 of Su SA1-1, primer S1-1-11 were designed, and 214 bp band was obtained in the Pima90-53 using this primer, but no band in the CCRI8. Primer S1-2-1 was designed based on the In Del sequence differences between CCRI8 and Pima90-53, and the 260 bp marker band was amplified in the CCRI8 and 248 bp in the Pima90-53.2. BLAST analysis was conducted between ORF sequence of ADF1 and the genome database including diploid ancestors, G. arboreum and G. raimondii. A- and D- genome sequences of ADF1 were obtained and located at Ca5 and Cd13, respectively. According to D genome sequence of ADF1, the primers were designed to amplify genomic sequence in CCRI8 and Pima90-53, Two kinds of genotypes, g Gh ADF1-1, g Gh ADF1-2 were obtained from CCRI8, g Gh ADF1-1 originated from A genome and g Gh ADF1-2 originated from D genome. Two kinds of genotypes, g Gb ADF1-1, g Gb ADF1-2 were obtained from Pima90-53, g Gb ADF1-1 originated from A genome and g Gb ADF1-2 originated from D genome. According to the SNP sequence variation between CCRI8 and Pima90-53 of ADF1-1, primer A11-1 were designed, which could amplify about 200 bp band in the CCRI8 and 229 bp band in the Pima90-53. Primer A12-1 was designed based on the SNP differences between CCRI8 and Pima90-53, and a 143 bp marker band was obtained using this primer in the Pima90-53, but no band in the CCRI8.3. Using Mapmaker3.0 software, linkage analysis was conducted between the markers developed in the study and the markers obtained from the genetic linkage map in the BC1 population of(CCRI8×Pima90-53)×CCRI8. The results showed that the markers including S1-1-11, S1-2-1, A11-1, A12-1 which were closely linked with Su SA1 and ADF1 were mapped at A8(c8), D8(c24), A5(c5) and D13(c18), respectively. Based on the newly genetic map and fiber quality data provided by our lab, QTL mapping for fiber quality traits were performed. With LOD value of 5.0, QTL related to microniare were mapped at A8 S1-1-11, this QTL could explain 11.1% of phenotypic variations; With LOD value of 3.0, the linkage group D8 S1-2-1 contained QTL related to microniare, and this QTL explained 9.7% of phenotypic variations. With LOD value of 3.0, QTL related to fiber length was located at D13 A12-1, and this QTL explained 4.7% of their phenotypic variations. |
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