Construction And Application Of Inter And Intra-Specific Saturated Genetic Map In Tetraploid Cotton

A high-density molecular map is the basement of genome research in plant. A saturated genetic map shares new light to our understanding of structural genomics, and is useful in the novel gene discovery, economically important QTLs analysis, et al. In this paper, we were mining DNA molecular markers and constructing high density genetic mapping in cotton.Total 3592 primer pairs were developed, including eSSRs from G. raimondii, G. hirsutum, G. barbadense-derived ESTs, gSSRs from 70 BAC clones of G. hirsutum cv. Maxxa and RT primers, REMAP maker, STV, Gh primers. They were used to screen polymorphisms in order to enhance our backbone genetic map in allotetraploid cotton. After integrating these new loci, our enhanced genetic map consists of 2577 loci covering 3591.0 cM, at 1.39 cM intervals in 26 linkage groups. This microsatellite-based, gene-rich linkage map contains 57.04% functional marker loci, of which 78.44% are eSSR loci. There were 208 duplicated loci, bridging 13 homoeologous At/Dt chromosome pairs. Two reciprocal translocations after polyploidization were further confirmed between A2 and A3, and between A4 and A5 chromosomes. Four big distorted intervals were found in the A2, A3, A7 and D7 chromosome. All distorted loci in the same chromosome were skewed towards the heterozygotes or homozygotes. This high-density cultivated cotton species genetic map will be used for QTL tagging and agronomic traits analysis.At the same time, relationship was observed between the level of polymorphism, motif type of the randomly developed eSSRs and gSSR from BAC clones of G. hirsutum cv. Maxxa. Among the eSSRs, trinucleotide are the most abundant motif, tetranucleotide are the least abundant motif. For the gSSRs, hexanucleotide are the most abundant motif, tetranucleotide are the least abundant motif. Their eSSRs polymorphic rates were higher for compound motif, tetranucleotide, hexanucleotide repeats. We also observed the polymorphic rate which the most abundant motif type was not high. AC/TG was the higher polymorphic rate in dinucleotide repeat, ATAC/TATG was the higher polymorphic rate in tetranucleotide repeat.A comparison of the eSSRs tagging information derived different genome showed that eSSR derived from G. arboretum were tagged At:Dt=1.5:1, derived from G raimondii were tagged At:Dt=1:1.5, derived from G. hirsutum and G. barbadense were tagged At:Dt =1:1. The tagging results showed that eSSRs derived from A genome species were preferentially tagged in the A-subgenome, and eSSRs from D genome species were preferentially tagged in the D-subgenome in the tetraploid linkage map. However, eSSRs derived from AD genome species were equally tagged in the A-and D-subgenomes of the tetraploid linkage map.By comprehensive analyses of the amplified product molecular size among tetraploid G. hirsutum cv. Maxxa, acc. TM-1, and G. barbadense cv. Hai7124, and diploid G. herbaceum var. africanum and G. raimondii,37 BACs were further anchored to their corresponding subgenome chromosomes, showing 12 BACs from the A-and 25 from the D-subgenome.14 primers were developed from 344 LTRs of 97 BAC clones in G hirsutum cv. Maxxa.60 gSSRs developed from 70 BAC clones were randomly assembled with 14 primers. Their REMAP maker produced 188 polymorphic loci, evenly distributing in the whole genome. REMAP technique was preliminarily constituted in cotton.Using SSR as bridge markers, a saturated intraspecific genetic linkage joinmap was constructed from 18 different mapping populations of Upland cotton (Gossypium hirsutum L.). The new integrated Upland cotton intraspecific genetic linkage joinmap comparises 694 loci, that mapped to 67 linkage groups assigned perfectly to their corresponding 26 chromosomes with the average distance between markers of 5.12 cM, covering 3553 cM or nearly 100% of the total recombinational length of the tetraploid cotton genome. Further, elite fiber QTL from five super fiber quality donors,7235, HS427, PD6992, Yumian 1 and J415, were aligned on the joinmap and showed that more elite QTL were biased non-randomly on Dt subgenome than on At subgenome, even if At progenitor produces spinnable fiber but Dt progenitor does not. The result suggested that the Dt subgenome from the non-fiber-production ancestor plays an important role in the genetic control of fiber growth and development in polyploidy cotton. So far, this is the most saturated genetic linkage joinmap assembled from different genetic backgrounds of cotton populations in G hirsutum. The research is ongoing for the identification of QTL allele and homoelogous relationship for breeding target traits, such as yield, fiber quality and resistance etc, and further provides the foundation for molecular breeding by design in G hirsutum.