| Cotton from the genus Gossypium is the world’s most important fiber crop plant. For nearly 100 years, systematists have been interested in the classification of the genus Gossypium. A wide variety of data, including morphologic, meiotic, karyotypic, genetic and molecular have been generated to address relationships among members of the genus. Currently, the most widely accepted classification for Gossypium follows Fryxell (1992), who divided Gossypium into four subgenera, eight sections, nine subsections and approximately 50 species. Forty-five of the species are diploid and differentiated cytogenetically into eight genome groups (A-G and K), and five are tetraploid. The five tetraploid species are of allopolyploid origins, originated from interspecific hybridization between diploid A- and D-genome species, two of them, G. hirsutum and G. barbadense, have been independently domesticated for their fiber. G. hirsutum has broad adaptation, moderate fiber quality and high yield. Because of its yield potential and adaptation to diverse environmental conditions and production systems, about 97% of the world’s cotton fiber derives from G. hirsutum (NCCoA,2006). On the other hand, G. barbadense is characterized by superior fiber quality, indicated G. barbadense contains novel alleles for superior fibre quality, but the narrow range of adaptation and low yield limited its planted regions. The two species are sexually compatible, although partial sterility, longer maturity, and hybrid breakdown are often observed in later generation hybrids.Now, the best extant model of the ancestral A-genome parent is G. herbaceum, while the D-subgenome donor in tetraploid cotton species remained elusive. Though G. hirsutum and G. barbadense are cultivated cotton species, they have very different agronomic and fiber quality characters. So, in this study, based on the EST-SSR sequence and the structures and expression partterns of fiber development genes, which had been cloned, we revealed the D-genome donor of tetraploid species, and put a solid foundation to further understand the genetic basis of cotton fiber development. In a previous study, we used EST-SSR to screen for polymorphisms to enhance our backbone geneticmap of allotetraploid cotton. Using G. raimondii derived-eSSR, a high polymorphismrate (47.9%) between G. hirsutum and G. barbadense was observed, which was much higher than that observed by G. arboreum and G. hirsutum derived-eSSR (Guo et al.,2007a). We questioned the role of the D-genome cotton species in the evolution of tetraploid cotton. In this study, we used EST-SSR sequences to reveale the relationship of D-genome in diploid in Gossypium and the D-subgenome donor in tetraploid species.14 EST-SSR primer pairs from G. raimondii were used to amplify 23 species in Gossypium. In total,438 amplicons were cloned, sequenced and analyzed. From the analysis of SSR motifs and the rates of base substitutions in the flanking region based on the combined data set, the D-genome and D-subgenome exhibited higher levels of polymorphism than the A-genome and A-subgenome, both in the microsatellite domains and the flanking regions. Suggest that in the process of evolution, the A-genome and A-subgenome have experienced lower divergence rates and are therefore more conserved than D-genome and D-subgenome. The phylogenetic trees of 13 D-genome diploid species,8 AD-genome tetraploid species and all the 23 species were constructed based on the combined SSR flanking sequence data, respectively. The results showed that 13 D-genome species were congruent with Fryxel’s subsection taxonomy. The relationship between D-subgenome tetraploid species and D-genome diploid species indicated that G. raimondii is the sole D-genome donor of all tetraploid species.To understand the genetic basis of cotton fiber development, further to reveal the essence of fiber quality difference between upland cotton and sea-island cotton, we selected 19 fiber development genes, including 18 accessioned to NCBI and a new sucrose synthase gene (SusA1) cloned by our lab, to study their structure and expression difference in the two cultivated tetraploid cotton. First, we cloned these genes in the genome DNA of G. hirsutum ace. TM-1, G barbadense cv. Hai7124 and their two putative diploid progenitor cottons, G. herbaceum and G. raimondii, to investigate their frame and sequence divergence. Then, the chromosomal locations of each homeolog of several studied genes, having effective SNP or amplification polymorphism loci between TM-1 and Hai7124, were carried out using our [(TM-1×Hai7124)×TM-1] inter-specific BC1 mapping population in allotetraploid cotton. Genes’distribution on chromosomes and their distance from QTLs, which were located by privous studies, were analysis. Further, expression patterns of each gene and each homeolog (duplicate genes) were explored to evaluate the expression difference on fiber development between G. hirsutum and G. barbadense. Synthesizing the analysis of genes frames, expression patterns and chromosomal location results, the interspecific divergence of fiber development genes in cultivated tetraploid cotton species was further elucidated. The results will also put a solid foundation for mining the key genes with important fiber quality contribution, further utilizing them to improve the fiber quality in cotton molecular breeding.In this study, in the orthologous and homoelogous loci of 19 studied genes, the sequence and structure of 68.42% were conservative and 31.58%were diverse. Gene tree topologies showed that 16 genes were independent evolution between A- and D-subgenome in the allopolyploid after polyploid formation, while 3 evolved different degrees of colonization. The evolution rates between A (D)-genome and A (D)-subgenome revealed that D-subgenome of allotetraploid had rapid differentiation in the evolution history, and compared with TM-1, Hai7124 may have a closer relationship with their primogenitor. Based on the sequence divergence between TM-1 and Hai7124,26 duplicate genes were located on our backbone genetic map, in which at least one fiber quality QTL reported previously was detected in the interval. The genes expression profiles showed that at fiber initiation and early elongation period, most genes had higher transcripts in Hai7124 than in TM-1, however, at fiber elongation period, most genes transcripts, except for CelA3 and HOX3, were the same or higher in TM-1 than in Hai7124 with an exception at 8DPA, and at primary-secondary transition period, expression peak of transcripts in most genes was earlier in TM-1 than in Hai7124. The genome-specific expression profiles showed that the same A- or D-biased or equal expression profile in the two cultivated cotton species were related with functional partitioning of genomic contributions during cellular development after the allopolyploid formation, however, significant alternation of homoelog A/D ratio at the same fiber developmental time points between G. hirsutum and G. barbadense indicated that domestication for fiber qualities may play an important role in fiber quality divergence of G. hirsutum and G. barbadense. The combined analysis of the structure and expression patterns of these studied genes further indicated that agronomic selection play important role in altering the molecular evolutionary patterns of genes related with fiber development between G. hirsutum and G. barbadense. |
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