Marker Increase Of Genetic Map And Collinearity Analysis Of Interspecific Gossypium Hirsutum With Gossypium Barbadense, Gossypium Tomentosum And Gossypium Darwinii

Cotton is the world leading natural fiber producing crop,and also an important oil-seed crop.Cotton?Gossypium spp?is extensively grown species across the globe,and found in both tropical and subtropical regions.So cotton genome mapping will provide the requisite foundation for advanced research.Cotton has a large genome,hence high density genetic mapping is needed in order to have a progress towards the whole genome assembly.A genetic map do estimates the relative position of the molecular markers along the chromosome which corresponds to the genes based on recombination events.Genetic maps will not only pave the way in understanding genome organization and structure,but also will offer the opportunity for tagging superior traits for crop improvement through marker-assisted selection?MAS?.Genetic maps developed by PCR-based markers will be more efficient in marker-assisted selection because these markers are environmentally neutral and abundant across the genomes thus makes it possible to observe the genetic variations at DNA level.It has been proven that upland cotton germplasm has narrow genetic base,hence it needs to be enriched by introducing superior genes from wild relatives through introgression.Therefore,it is imperative to have a better understanding of genome organization of wild relatives.There are five tetraploid cottons including G.barbadense,G.tomentosum and G.darwinii which have many useful genes such as high fibre quality,biotic and abiotic stress tolerance.These genes need to be introgressed into the G.hirsutum in order to broaden its genetic diversity,resulting to higher selection with improved agronomic traits.Currently,researchers mostly use G.barbadense as one of the parent to generate interspecific cross to get high levels of polymorphism for the construction of high density genetic maps.Based on genome-wide simple sequence repeat?SSR?markers,three linkage maps of allotetraploid cotton have been constructed using BC₁ or F2 population derived from interspecific crosses of G.hirsutum ×G.barbadense,G.hirsutum × G.tomentosum and G.hirsutum × G.darwinii,respectively.Collinearity Analysis of allotetraploid interspecific genetic map with Gossypium hirsutum physical map was done to help in understanding,the following concepts on the Gossypium in relation its origin,evolution,classification,and also molecular marker assistant breeding technique.The following results were obtained successively.1.Developing of genome SSR markers from G.ramondii genome sequencesA total of 12560 pairs of genome SSR markers were detected on 13 chromosomes of both Gossypium arboretum L.and Gossypium raimondii Ulbrich.Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the 26 chromosomes.The average was 966 pairs per chromosome with the least markers on chromsome 13 with 852 pairs and the most markers on chromosome 9 with 1323 pairs.The TM value were changed from 55? to 61? and amplified fragment length changed from 100 bp to 200 bp with avarage of 171 bp.Redundancy detection showed that a total of 217 pairs of SSRs had the same sequence to previous findings.The chromosome-specific SSRs and previously-reported chromosome markers were grouped together,none of the markers mapped on to another homologous chromosome,which provided that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton.The SSRs on each chromosome were sorted by motif type and repeat length for convenient selection.The sequences of all the chromosomes-specific SSRs primers,are available within this desertation.2.Marker increase of Gossypium hirsutium ×Gossypium barbadense genetic mapA high density genetic map was constructed using BC₁ population derived from an interspecific cross of Gossypium hirsutium × Gossypium barbadense?Zhongmiansuo35 × Pima s7?.The map was exclusively based on survey of genome wide simple sequence repeat?SSR?.The map consisted of 3,433 markers loci distributed across all the 26 chromosomes and covered 4,059.3 c M of cotton genome,with an average inter-marker distance of 1.29 c M.Marker number anchored on the chromosomes varied from 53 to 242 with an average of 132.04 on each chromosome.The maximum length of chromosome was 252.2 c M and the minimum was 94.4 c M with an average length of 107.15 c M.A sub-genome covered less genetic distance?1,958.6 c M?with an average distance of 1.59 c M than D sub-genome which covered a length of 2,100.7 c M with an average distance of 0.98 c M.The smallest homologous chromosome pair was Chr.04 and Chr.22,and the largest was Chr.05 and Chr.19 as far as mapped loci are concerned.3.Marker increase of Gossypium hirsutium × Gossypium tomentosum genetic mapA high density genetic map was constructed using F2 population derived from an interspecific cross of G.hirsutum?the cultivar name as CRI-12?x G.tomentosum.The map was exclusively based on survey of genome wide SSR.The map consisted of 1917 markers loci distributed across all the 26 chromosomes and covered 3345.4 c M of cotton genome,with an average inter-marker distance of 1.80 c M.Marker number anchored on the chromosomes varied from 44 to 112 with an average of 73.73 on each chromosome.The maximum length of chromosome was 219.6 c M and the minimum was 73.9 c M with an average length of 128.67 c M.A sub-genome covered less genetic distance?1588.7 c M?with an average distance of 1.87 c M than D sub-genome which covered a length of 1756.7 c M with an average distance of 1.68 c M.The smallest homologous chromosome pair was Chr.04 and Chr.22,and the largest was Chr.05 and Chr.19 as far as mapped loci are concerned.4.Marker increase of Gossypium hirsutium × Gossypium darwinii genetic mapA high density genetic map was constructed using F2 population derived from an interspecific cross of G.hirsutum?the cultivar name as CRI-12?× G.darwinii.The map was exclusively based on survey of genome wide SSR.The map consisted of 1964 markers loci distributed across all the 26 chromosomes and covered 3615.3 c M of cotton genome,with an average inter-marker distance of 1.84 c M.Marker number anchored on the chromosomes varied from 21 to 129 with an average of 75.54 on each chromosome.The maximum length of chromosome was 238.7 c M and the minimum was 34.5 c M with an average length of 121.74 c M.A sub-genome covered less genetic distance?1658.9 c M?with an average distance of 2.03 c M than D sub-genome which covered a length of 1956.4 c M with an average distance of 1.71 c M.The smallest homologous chromosome pair was Chr.04 and Chr.22,and the largest was Chr.05 and Chr.19 as far as mapped loci are concerned.5.Collinearity Analysis of Gossypium hirsutum × Gossypium barbadense genetic map and Gossypium hirsutum physical mapCollinearity analysis of G.hirsutum × G.barbadense genetic linkage maps with Gossypium hirsutum physical map was analysed.The results showed that overall loci order on the genetic map of G.hirsutum × G.barbadense was in agreement with the order of corresponding sequences on the At and Dt sub-genomes of G.hirsutum.In the At sub-genome?c1–c13?of G.hirsutum,1.156 GB corresponded to 1958.6 c M of G.hirsutum ×G.barbadense,whereas in the Dt sub-genome?c14–c26?772 Mb was equivalent to 2100.7 c M.The genetic map of G.hirsutum × G.barbadense covers a total of 1.928 Gb genome,which accounts for 83.84% size of total chromosome for G.hirsutum.6.Collinearity Analysis of Gossypium hirsutum ×Gossypium tomentosum genetic map and Gossypium hirsutum physical mapCollinearity analysis of G.hirsutum × G.tomentosum genetic linkage maps with Gossypium hirsutum physical map was analysed.The results showed that overall loci order on the genetic map of G.hirsutum × G.tomentosum was in agreement with the order of corresponding sequences on the At and Dt sub-genomes of G.hirsutum.In the At sub-genome?c1–c13?of G.hirsutum,1.111 GB corresponded to 1588.7 c M of G.hirsutum × G.tomentosum,whereas in the Dt sub-genome?c14–c26?750 Mb was equivalent to1756.7 c M.The genetic map of G.hirsutum × G.tomentosum covered a total of 1.861 Gb genome,which accountsfor 80.93% size of total chromosome for G.hirsutum.7.Collinearity Analysis of Gossypium hirsutum × Gossypium darwinii genetic map and Gossypium hirsutum physical mapCollinearity analysis of G.hirsutum × G.darwinii genetic linkage maps with Gossypium hirsutum physical map was analysed.The results showed that,the overall loci order on the genetic map of G.hirsutum × G.darwinii was in agreement with the order of the corresponding sequences on the At and Dt sub-genomes of G.hirsutum.In the At sub-genome?c1–c13?of G.hirsutum,1.091 GB corresponded to 1658.9c M of G.hirsutum × G.darwinii,whereas in the Dt sub-genome?c14–c26?757 Mb was equivalent to 1956.4 c M.The genetic map of G.hirsutum × G.darwinii covered a total of 1.847 Gb genome,which accounts for 80.32% size of total chromosome for G.hirsutum.8.Collinearity Analysis of Allotetraploid Gossypium tomentosum and Gossypium darwiniiComparing the two genetic linkage maps,we found that most SSR markers present collinearity between the two genetic linkage maps.Meanwhile,part of the non linear relationship appeared on the individual chromosomes between the genetic linkage maps of G.hirsutum × G.tomentosum and G.hirsutum × G.darwinii,which include 7 inversion fragments on Chr.02,Chr.05,Chr.08,Chr.12,Chr.14,Chr.16 and Chr.25,3 translocation fragments on chr05,chr14 and chr26.Further comparing the inversion and translocation fragments,we noticed four of seven markers orientation of G.tomentosum consistent with G.hirsutum or G.raimondii,one of the seven inversion markers orientation of G.darwinii was similar with G.hirsutum;meanwhile one of three translocation marker orientation of G.tomentosum similar with G.raimondii.This result indicates that G.darwinii and G.tomemtosum,are genetically closer to G.hirsutum,and thus,share a similar origin,but diverse due to evolution and selection process.