Update Of Genetic Map From G.hirsutum×G.barbadense And Analysis Of Chromosome Structural Variation

Cotton is the most important natural fiber crop and the important oil crop.There are approximately 52 species for the Gossypium genus,including 45 diploids and 7 allotetraploids.Four of these species become cultivated cotton after people's domestication.Both G.hirsutum and G.barbadense are widely cultivated all over the world.Upland cotton(G.hirsutum L.)is the most widely grown worldwide,accounting for over 95% of fiber production,but the fiber quality of upland cotton is poor.In contrast,the fiber quality of sea-island(G.barbadense L.)is better than upland cotton and has stronger resistance to verticillium wilt.The purpose of cotton breeding is not only the increase of yield but also the improvement of fiber quality.In the past few years,it is an important approach that translate the gene controlling fiber quality from sea island into upland cotton to improve fiber quality of upland cotton.Traditional breeding is time-consuming and low efficiency.The rapid development of molecular marker technology and high-throughput sequencing technology provides the important technical guarantee for cotton breeding.Genetic maps developed will be more efficient to study structural variation of genome,identify QTL,map-based cloning and marker-assisted select.Chromosomal structure variation is a widespread phenomenon in the process of evolution.These chromosome structure variations may be related to plant disease resistance,yield and quality traits.For cotton,these chromosome rearrangements may be associated with the cotton fiber development,which has always been a important subject for cotton research workers.So,analyzing these genome structure variations will facilitate our understanding of the molecular mechanism of cotton fiber.Based on the previous work in our lab,the new SSR markers designed from the G.arboreum genome sequence were used to update the genetic map from(CCRI35 × Pima S-7)BC1 population.In addition,the collinearity analysis was conducted between the genetic map and four sequenced genomes.The present study will help in understanding the origin,evolution,and classification of cotton,and identifying favorable alleles in cotton.The main results were as follows.1.Marker increase of genetic mapA total 13007 primers designed form G.arboreum genome were used to identify the polymorphism between CIR35 and Pima S-7 and 1762 pairs of primers showed good polymorphism.Then,these polymorphic primers were used to genotype the(CCRI35×Pima S-7)BC1 population,and 1961 loci were produced with a polymorphism ratio of 13.55%.Together with 4052 loci obtained in our previous studies,a genetic map with 6009 loci was constructed,which covered 3863.97 cM with an average of 0.64 cM between adjacent markers.2.Collinearity analysis of genetic map and physical mapPhysical maps were constructed by blasting the sequence of polymorphic loci to genome of G.hirsutum,G.barbadense,G.raimondii and G.arboreum.Comparative genomic analysis showed that genetic map has a good collinearity when compared with two tetraploid cotton genomes and G.raimondii genome,but poor collinearity between the genetic map and the G.arboreum genome.Two large reciprocal translocations between A02 and A03 and between A04 and A05 were identified when comparing genetic map with either G.arboreum or G.raimondii genomes.Then we found 17 inversions and 7 simple translocations between genetic map and G.raimondii.3.Comparison between two physical maps of tetraploid cottonsSixteen inversions were identified after comparison analysis between two physical maps constructed based on G.hirsutum and G.barbadense.