| As a leading global fiber crop, cotton provides most of the natural fiber for the textile industry.The genus Gossypium comprises approximately 50 species. Among them, four speciesare cultivated, including two diploid species, G. arboreum and G. herbaceum, and two allotetraploid species, G. barbadense and G. hirsutum. G. hirsutum(upland cotton) is most widely grown worldwide, accounting for 95% of both acreage and fiber production.With the continuous improvement of textile technology and the improvement of people’s living standard, cotton breeders have attached greater importance to create a new cultivar with high yield and quality. The traditional breeding techniques have made great contributions to improve fiber quality. Because the fiber quality traits are controlled by multiple genes, and they are negativelt correlated with the yield, the traditional breeding method is time-consuming and does not yet entirely meet the requirements of modern breeding.The development of molecular biology and biotechnology provides an effective strategy for the genetic study of complex traits and the molecular breeding. Up to now, many QTL for fiber yield and quality traits have been identified,but a few cultivars with high fiber yield and fiber quality are breeded by moelcualr breeding. The main causes are(1) the QTL identified for fiber yield and quality traits are far from the linked markers,(2) a few genes or QTL for fiber yield and quality traits are cloned. Therefore, it needs to construct high-density linkage map, fine-map the QTL for fiber yield and quality traits and identify the QTL candidate genes.In our previous studies, one major QTL controlling multiple fiber quality traits was identified at T1 region on chromosome 6 in upland cotton from the(Yumian 1 × T586) segregation populations. Based on the previous work on the the genetic map of recombinant inbred population(Yumian 1×T586), this study firstly update the genetic map using the new SSR and then fine-map the QTL controlling fiber quality traits on chromosome 6. For fine mapping the major QTL controlling fiber quality traits, a large poulation was established from a cross between Yumian 1 and a recombinant inbred line RIL118. RIL118 are characterized with trichomes and short and coarse fiber and are seleted from recombinant inbred population(Yumian 1×T586). The digital gene expression profiling was used to identify the candidate genes for the QTL controlling fiber quality traits. The main results are following. 1. The update genetic mapA total of 2,449 new SSR primer pairs and 5,583 SSR public markers mapped on the genetic map by other studies were used to screen Yumian 1 and T586, and 475 primers showed polymorphism. When the polymorphic primers were used to genotype the recombinant inbred line population(Yumian 1×T586), 489 loci were produced.A total of 1801 loci, including 1303 SSR loci obtained in our previous studies and nine morphological marker loci, were applied to construct the genetic map. The genetic included 1684 loci(1675 SSR and nine morphological marker loci), and covered 3338.2 c M with an average of 1.98 c M between adjacent markers. 2. Genetic analysis of trichomeIn the(Yumian 1×RIL118) F2 population with 6975 individuals, 1796 plants were featured with thick trichomes like RIL118, 1770 plants were featured with sparse/normal hairy like Yumian1 and 3409 plants were the middle type. The ratio of segregation fits to 1:2:1(χ2=3.72<χ20.05, 2=5.99), the result confirmed that T1 was controlled by a single dominant gene. 3. Phenotypic analysis of fiber quality traitsThe two parents remarkably differed in fiber length(FL), uniformity(FU), micronaire(FM), enlongation(FE) and strength(FS). The frequency distributions of five fiber quality traits displayed continuous variation. The fiber quality traits of T1T1 genotype were almost exactly the same with RIL118, and the fiber quality traits of t1t1 genotype were similar with Yumian 1. All five fiber quality traits had significantly correlation with each other. Fiber Micronaire and elongation had positive correlation with each other, which significantly negative correlations with other fiber quality traits. There had significantly positive correlation among fiber uniformity, length and strength. 4. Coarse map QTL of fiber quality traitsBased on the RFLP probles on chromosome 6 and chromosome 25 from the public interspecific genetic map, 132 SSR primer pairs were designed. According the genome sequence of chromosome 10(corresponding to chromosome 6 and chromosome 25 of tetraploid cotton) from G. raimondii, 386 SSR primer pairs were developmented. The newly desighed SSR primers were used to screen the two mapping parents Yuanlian 1 and RIL118, 5(from RFLP probe) and 13(from G. raimondii genome sequnce) primer pairs showed polymorphism. The newly identified SSR markers and the markers on chromosome 6 from the updated genetic were used to genotype 386 individual plants randomly selected from(Yumian 1×RIL118) F2 population in 2011, and a total of 115 loci were mapped on chromosome 6. The genetic map covered 133.1 c M. Based the fiber quality trait data and the genetic map, the QTL controng FL, FM, FU and FS were identified between MUCS114 to MUSS099. The LOD score was 62.6, 42.5, 31.6 and 52.43 for FL, FM, FU and FS, respectively. The QTL explained the phenotypic variation 59.3%, 45.7%, 36.4% and 53.8%, and the additive effect was 2.78,-0.43, 1.90 and 2.92 for FL, FM, FU and FS, respectively. 5. Fine mapping QTL for fiber quality traitsTwenty-four markers within the QTL region were employed to genotype the other 1074 plants in 2011, and the contructed QTL region genetic map covered 0.35 c M. Based on the genetic map and the fiber quality traits from 1434 individuals, the QTL controlling five fiber quality traits were mapped within a 0.28-c M interval between HAU2119 and SWU2302. The QTL explained 54.7%(LOD=222.3), 40.5%(LOD=145.0), 30.1%(LOD=100.4), and 50.0%(LOD=194.3) of phenotypic variation, and the additive effects were 2.65,-0.41,-1.6 and 2.91 for FL, FM, FU and FS, respectively.To further confirm the location of the QTL, the individual number of(Yumian 1×RIL118) F2 population was enlarged to 6975 plants in 2012. However, new recombinant events did not be found between HAU2119 and SWU2302. The QTL controlling fiber quality traits was further mapped in the interval between HAU2119 and SWU2302 using 51 recombinants in the QTL from the 6975 plants. 6. Physical mapping for the QTL controlling fiber quality traitsTo assess and facilitate genetic map, all SSR markers on the genetic map were used to do Blastn searches against the available G. raimondiiand G. hirsutum genome sequences. All the markers could be aligned to the reference genomes. The 0.28-c M genetic interval corresponded to a 2.7-Mb physical distance on the chromosome 10 in G. raimondii genome and a 4.4-Mb physical distance on chromosome A06 in G. hirsutum genome. 7. Identification of QTL candidate genesTo examine fiber cell development of Yumian 1 and RIL118, scanning electron microscopy was used to observe the development of fiber cell initials in the ovular surface on 1 DPA and anatomy microscope was used to observe the development of fiber cell elongation from 3 DPA, 5 DPA and 7 DPA. Fiber length of Yumian 1 was much longer than that of RIL118 on 3DPA and later. RNA-sequencing showed that 1262 and 4436 significantly differentially expressed genes exist on 0 DPA of ovule and 5 DPA of fiber between the two parents, respectively. Four genes in the QTL region corresponding G. raimondii genome extremely differentially expressed, and q RT-PCR analysis showed that three genes in the QTL region corresponding G. hirsutum genome behaved similarly. |
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