High-density Genetic Map And QTL Mapping Of Genes Controlling Petal Number In Lotus

The scared lotus?Nelumbo nucifera L.?is widely cultivated in China more than seven thousand years ago as one of food resources,medicinal,ornamental and the religious symbol.Crossbreeding was still the most commonly used method in lotus breeding,but a time-consuming approach.It is important for the development of ornamental lotus industry to breed new cultivars gathering multiple prominent traits.Combing with markerassisted breeding methods,modern molecular breeding technologies can be used to to improve the breeding efficiency,Constructing high-density genetic maps between lotus with extreme phenotype difference is an effective way to obtain such information.The development of the next generation sequencing technology and bioinformatics tools made it possible to develop SNPs markers accurately and efficiently.In this research,we constructed a high-density F2 genetic map benefited from whole genome resequencing technology.In order to locate the gene?s?controlling petal count,we made a cross between the bloom lotus cultivar “Jinqiu” and seed lotus cultivar “Baihuajianlian”.Then a F2 population of 121 individuals with excellent quantitative character separation in petals count were obtained.After that we constructed a high-density genetic map with SNPs markers and mapped some candidate genes linked with petals count.The main result of this study were summarized as following:?1?The whole genome of 121 lotus individuals were re-sequenced on Illumina Nova-seq platform.In total,704 Gb of raw data and 636 Gb of clean data were generated.10,145,108 raw SNPs were identified using GATK haplotyper algorithm.After removing low-quality SNPs,79,596 valid SNP markers were used for genetic mapping.Finally,1,939 bin markers were sorted into 8 linkage groups that spanned 772.921 cM,with an average marker interval of 0.485 cM.LG5 had the least bin marker number while LG3 contained the most.?2?With genetic map,we mapped a major QTL that related with the gene controlling petal count,which spanned from 90.7cM to 101.3cM on LG5.According to lotus genome annotation,we found 237 genes in this region.After SNPs annotation,35 missense mutated genes were obtained.The peak of LOD score,with marker 000072.1₇3888887 most closely linked.Therefore,three major candidate genes?LOC104593900,LOC104593882 and LOC1045-93872?that are located nearby marker 000072.1₇3888887 were selected as major candidate genes.In summary,a high-density genetic maps of lotus was constructed,and a major QTL that related with petals count were detected.Finally we got 35 candidate genes and 3 of them might play majors roles in petal counts.Our research is of great significance for marker-assisted breeding of lotus petal improvement.