Construction Of Genetic Linkage Map And QTL Analysis For Main Ornamental Traits In Chrysanthemum Morifolium Ramat.

Chrysanthemums（Chrysanthemum morifolium Ramat.）are famous ornamental crops that possess substantial aesthetic value and industrial value.However,genetic analysis and marker-assisted selection（MAS）breeding in chrysanthemum have been hampered due to the huge genome,high heterozygosity,as well as controversial inheritance mode.MAS breeding shows great potential to increase the effectiveness of plant breeding,which is an effective tool in modern chrysanthemum breeding.In order to facilitate MAS,the dataset of EST（Expressed sequence tag）sequences of‘Jinbudiao’was used to develop EST-SSR（EST-simple sequence repeat）markers for chrysanthemum,and the mapping population of chrysanthemum was constructed.The obtained EST-SSR markers and mapping population were used to classify the inheritance mode of chrysanthemums,develop genetic linkge map,perform genetic analysis and QTL（Quantitative trait locus）analyses for important ornamental traits in chrysanthemum.The main results were as follows:1.In total,4,661 SSR loci were identified from 3,823 SSR-containing unigenes in‘Jinbudiao’transcriptome with an average of one SSR per 6.98 kb.Of these SSR sequences,tri-nucleotide repeats（30.0%）predominated,followed by di-nucleotide repeats（17.9%）.A total of 1,584 primer pairs were subsequently synthesized,831 valid EST-SSR markers were identified,of which 361 were polymorphic.Twenty-five polymorphic EST-SSR markers were randomly selected to assess cross-species transferability and polymorphism within 59 genotypes.The polymorphism information content values ranged from 0.29 to 0.86,with a mean of 0.67.And 16（64%）markers were amplified in all 12 species of Chrysanthemum and Ajania.Neighbor-joining analysis among the 59 samples revealed by SSRs were highly consistent with the traditional taxonomic classification,which was confirmed by population structure analysis and principal component analysis（PCA）.This research provides a large number of new EST-SSR markers for further genetic mapping and MAS breeding in chrysanthemum.2.The results of major gene and polygene mixed inheritance analyses showed that the inheritance of number of disc florets（NDF）,number of florets（NF）,ray floret length（RFL）,leaf length（LL）,leaf width（LW）and leaf length/width（LL/W）was in line with the 0MG model.The inheritance of inflorescence diameter（ID）,ray floret width（RFW）and ray floret length/width（RFL/W）was controlled by two pairs of additive-dominant-epistasis major genes（2MG-ADI）.And the major gene heritability for these traits was 21.76%,33.73%and 30.28%,respectively.The inheritance of central disc flower diameter（CDFD）was controlled by two pairs of equally additive-dominant major genes（2MG-EAD）and the major gene heritability is 53.87%.The number of whorls of ray florets（NWRF）and was controlled by one pair of additive-dominant major genes（1MG-AD）and the major gene heritability is 56.36%.The inheritance of number of ray florets（NRF）was controlled by two pairs of additive-dominant major genes（2MG-AD）and the major gene heritability is 76.26%.3.Chrysanthemum is a complete or near-complete hexasome.Firstly,204 marker alleles fit hexasomic inheritance and 150 marker alleles fit disomic inheritance,showing that marker alleles were inherited predominantly in a hexasomic manner.Secondly,the observed proportion of non-simplex to simplex EST-SSR marker alleles gave an appropriate match to the expected 1:3 ratio for hexasomic inheritance.Thirdly,the ratio of simplex marker alleles linked in coupling to repulsion was 1:0,further supporting hexasomic inheritance.Finally,the results of the analysis of allele configuration and segregation behavior of five EST-SSR markers also suggested random pairing of chromosomes.4.A genetic map was constructed with EST-SSR markers.The preliminary maternal and paternal maps consisted of 268 marker alleles arranged into 49 and 53 linkage groups（LGs）,respectively.Those LGs had a mean chromosome length of 36.8 and 38.4 c M in the maternal and paternal parent,respectively.The recombined parental maps covered 906.3 c M and 970.1 c M of the genome with an average genetic distance of 6.4 c M and 7.5 c M between two neighbouring loci,respectively.Finally,264 polymorphic loci were allocated to 9 LGs.The integrated map spanned 954.5 c M in length with an average genetic distance of 3.6 c M between two neighbouring loci.5.Phenotypic data of the F₁ progeny were collected during three consecutive flowering seasons.Quantitative trait loci（QTLs）analysis was performed for 12 inflorescence and leaf traits.Overall,36（21 major）QTLs were identified.For ID,CDFD,NWRF,NRF,NDF,NF,RFL,RFW and RFL/W,seven,two,two,one,three,four,four,four and five QTLs were detected,respectively.A total of two,one and one QTLs were detected to influence LL,LW and LL/W,respectively.Three,one and one clusters were found on LG 3,LG 4 and LG 8,respectively.That can facilitate MAS and lead to maximum genetic gain in chrysanthemum breeding programs.In summary,evidence for hexasomic inheritance was provided based on analysis of EST-SSR markers in an F₁ progeny of chrysanthemum.And a genetic map was constructed with EST-SSR markers in chrysanthemum,laying an important foundation for QTL fine mapping.