Association Analysis Of Ornamental Traits In Lotus(Nelumbo Nucifera Gaertn.)and Fine Mapping Of Plant Architecture Traits

Lotus?Nelumbo nucifera Gaertn.?is a famous traditional Chinese flower.It has great ornamental,edible and medicinal value,as well as special cultural and religious significance.China is the world distribution and cultivation center of lotus,and has abundant lotus germplasm resources.With the promotion and application of ornamental lotus,innovative utilization of germplasm resources and new varieties breeding become important directions for the development of lotus industry.Taking advantage of the genes and molecular markers associated with the target traits,molecular breeding is an effective method to change the target traits or screen the superior germplasms.Therefore,the identification of molecular markers which significantly associated with ornamental traits and the analysis of genetic mechanisms play important roles in improving breeding efficiency and promoting the breeding process.In this study,the main ornamental lotus germplasms in China and SSR markers were used to carried out the association analysis for the ornamental traits of lotus,and the SSR markers significantly associated with the ornamental traits were obtained.In addition,the genome wide re-sequencing technology and candidate region association analysis were used to fine mapping the plant architecture related traits.The main results in this study were as follows:?1?In total,12 ornamental traits were investigated in 293 lotus germplasms for four consecutive years.Statistical analysis showed that the coefficient variation of each trait varied from 4.24%to 78.45%.Petal number showed the largest coefficient variation?70.00%-78.45%?and leaf shape was the smallest?4.24%-5.51%?.There were no significant differences in the phynotype variation of petiole length,peduncle length,flower diameter and petal number among the four years,while carpel number showed significant difference and leaf length,leaf width,petal length,petal width and petal shape showed extremely significant difference.Except petal number,all traits showed normal distribution in the population.The petiole length,peduncle length,leaf length,leaf width,flower diameter,petal length and petal width showed extreme significant positive correlation in four-year observation.?2?We genotyped the 293 lotus germplasms with 93 genomic SSR markers.Population structure and kinship relationship were analyzed based on the genotype data.The results showed that the association population could be divided into two subgroups?K=2?,and about 80.08%kinship were less than 0.1.Linkage disequilibrium analysis showed that the level of linkage disequilibrium among the SSR markers was relatively low,and most of the markers were under significant linkage equilibrium?r²<0.1,P<0.01?.?3?Using mixed linear model,37 significant associations were identified which involved 11 ornamental traits with 19 SSR markers.The phenotypic contribution rates ranged from 3.94%to 15.09%with mean 9.14%.It is worth noting that 12 significant associations were identified repeated in different years which involved 7 ornamental traits with 5 SSR markers.?4?Based on three-year phenotypic observation of petiole length and peduncle length in lotus association population,21 large and 22 small architecture lotuses which showed extreme plant architecture were screened.Cytological observations of 10 large and 10small architecture lotus germplasms showed that the vertical cell number and cell length were the main factors affecting the plant architecture variation.Vertical cell number had a greater effect on plant architecture than the cell length did.?5?Based on whole genome re-sequencing data of 10 large architecture and 10 small architecture lotuses,F_ST genome scan identified 11.02 Mb of genomic regions that were highly differentiated between the two lotus groups.Chi-square test revealed that 17,154SNPs and 1,554 InDels showed distinct allelic distribution between the two lotus groups within these regions.In total,51 InDel markers were developed based on the information of InDel loci in the highly differentiated regions,and applied to genotype association population.Candidate region association analysis was carried out for the plant architecture related traits.29 InDel markers were significantly associated with petiole length,and the phenotypic contribution rate ranged from 2.84%to 9.72%.25 InDel markers were significantly associated with peduncle length and the phenotypic contribution rate ranged from 2.62%to 10.04%.In total,17 InDel markers were significantly associated with both peduncle length and petiole length and were identified repeated in different years.?6?According to the chromosome distribution of the significantly associated markers,one plant architecture QTL locus was identified.One candidate gene was verified by expression pattern analysis.In addition,two candidate plant architecture QTL loci and several candidate genes were also identified,but these results need further confirmation and validation.