| Cassava,a typical tropical crop,has many excellent characteristics such as high photosynthesis efficiency,high storage root yield,drought tolerance and low soil fertility tolerance.Besides,it is a very important food crop and biomass energy crop.The cassava genome is highly heterozygous and diverse in genetic diversity,which provides abundant materials for variety improvement.However,the conventional breeding time cycle is long and breeding efficiency is low.Many agronomic traits of cassava,such as starch content,dry matter content,storage roots yield and post-harvest physiological deterioration(PPD),are all quantitative traits controlled by multiple genes,and their genetic studies are still very limited.Therefore,excavating the superior allelic variation and its markers of the important characters of cassava,and developing the genomic selection breeding technology have important guiding significance for the improvement of cassava varieties.In this study,23 traits including leaf types,plant types,yield and quality related traits as well as postharvest physiological deterioration of 158 cassava germplasm from various places(including China,South America,Southeast Asia and so on)were tested in 3 years and 4 locations under 12 environments through the analysis of phenotypic diversity.The SNPs,indels and methylation markers were obtained using the amplified fragment polymorphism and methylation(AFSM)sequencing method.Then the genetic diversity,population structure and genome wide association study were analyzed for the population.The main results were as below:1.Under different environments,there was abundant phenotypic variation among cassava accessions in 23 traits including leaf type,stem type,root yield and quality.In 11 quantitative traits,the generalized heritability variation ranged from 0.38 to 0.92 in which leaf length-to-width ratio was the highest(0.92),with the lowest dry matter content(0.38).In the postharvest physiological deterioration study,we had selected ten PPD resistant accessions including Nuomimushu,Hainanxiye,Guire4,Royang5,ZM8625,ZM8641,SC205,G16,BRA258 and E407.Then we comprehensively evaluated these germplasm resources and selected ten excellent accessions(Guire6,CH16,BRA274,CM7595-1,SC124,SC205,10 J,16P,17 Q and 2B)based on the comprehensive index.2.A total of 34.98 million polymorphic markers(SNPs and Indels)were obtained using AFSM resequencing method.These markers were evenly covered 18 chromosomes with the average density of 1.48 Kb/SNV.Genetic diversity of cassava population was evaluated using 25,989 SNPs and indels,and its genetic diversity index(?)was found to be 1.21 × 10-4.Population structure analysis showed that these cassava materials could be divided into three subgroups.Principal component analysis and phylogenetic tree analysis showed that the subpopulation of cassava was mainly affected by its origin and there was no obvious differentiation relationship with the collected land.Geographic differentiation is related to its short history of introduction,therefore there is no obvious geographical differentiation in China.The FST value between subgroups ranged from 0.034 to 0.07 showing low or moderate level of genetic differentiation among subgroups.3.A total of 115 significant sites were obtained under a variety of environments using genome-wide association analysis in 158 cassava accessions.Among them,there were 4 significant loci detected for quality traits.Twenty-two significant loci were detected for stem type traits,of which 5 loci were simultaneously detected in multiple environments,with the contribution rate between 0.12 and 0.21.Thirty-five significant loci were detected for leaf-type related traits,and seven significant loci were replicated in multiple environments(contribution rate: 0.12-0.25).Fifty-four significant loci were detected in root yield components and quality traits,of which 2 loci simultaneously detected in multiple environments.Four,10,9,9,8 locis were found significant associated with starch content,dry matter content,root number,root yield,dry matter yield,with the contribution rate 0.12-0.18,0.13-0.19,0.12-0.16,0.13-0.18,0.13-0.18,respectively.4.An integrated analysis of the significant loci revealed that 14 significant loci were found to be associated within different trait pairs.Among them,root yield and dry matter yield had 5 identical sites on chromosomes 2,4 and 18(3 for chromosome 2,1 for chromosome 4,1 for chromosome 18),respectively.Starch content and dry matter content had 2 identical sites on chromosomes 13 and 9,respectively.Another trait pair,the number of storage root and storage root weight,had 1 identical sites on chromosomes 9.Besides,leaf length-to-width ratio and intermediate lobular length had 4 identical sites on chromosomes 1,2,5 and 6;and intermediate lobular width and leaf length-to-width ratio had 2 identical sites on chromosomes 3,10.Correlation analysis showed that there were significant correlations between these trait pairs.5.Candidate gene analysis was performed on all significant sites and 195 candidate genes were identified.Of these,131 genes were used for differential expression analysis.We found 68 candidate genes related to stem type and leaf type.Forty-eight genes were highly expressed in root and leaf tissues,with the rest were low expressed.Out of sixty-three candidate genes for root yield and quality,10,37 and 16 were found highly,medium and low expressed,respectively.The GO annotation of 165 candidate genes revealed that most of them were genes of cellular components,catalytic activity,and biological processes involved in cell metabolism. |
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