| As an important C4 crop for sucrose and bioethanol production,sugarcane(Saccharum spp.)is grown in over 100 tropical and subtropical countries.Sucrose is accounting for about 78%of the total sugar production in the world,while it's more than 90%for China.Globally,approximately 60%of bio-ethanol production is contributed by sugarcane.However,the production of sugarcane can be impacted by many plant pathogens,which seriously affect sugarcane yield.Therefore,identification of genetic components conveying disease resistance is urgent and desirable for sugarcane disease control.Due to a complex genome structure of modern sugarcane cultivars,there are many challenges for genetic and genomic studies in sugarcane.Moreover,the complex nature of sugarcane genetic inheritance and genome lead to the widespread segregation of the traits in hybrids.Thus the probability of the combination of good genes is extremely low and sugarcane breeding has to rely on large populations.In China,the number of seedlings planted is as high as 0.8?1 million per year.The use of array technology is undoubtedly an efficient method for identifying quantitative trait locus(QTL)and markers associated with traits of interest,which provides a tool for marker-assisted selection in sugarcane.Key findings from current study are listed as below:1.The design and development of the Axiom Sugarcane 100K SNP array.Screening of target enrichment sequencing(TES)data from 12 and 288 sugarcane accessions identified 1.2 million(Data set 1)and 3.4 million(Data set 2)SNPs,from which 1)a total of 31,449 single dose(SD)and 68,648 low dosage(33,277 SD and 35,371 double dose or DD)SNPs were selected respectively and finally tiled on the array.2)According to the annotation of the 100K SNPs using sorghum genome annotation,most of them(91,860,91.77%)were located within gene regions(12,935 genes),with an average of 7.1 SNPs/gene.3)According to the sorghum gene annotation file,the comparison results showed that the 100K SNP array contains a total of 551 genes related with sugar metabolism,disease resistance,and biomass(cell wall),covering 5,055 non-redundant SNPs.4)At the same time,the comparison with 12,387 non-redundant sugarcane species-specific SNPs between S.officinarum and S.spontaneum and with 207,761 genus-specific SNPs between Saccharum and non-Saccharum showed that the 100K SNP array contained 305 sugarcane species-specific SNPs and 6,856 genus-specific SNPs.2.The polymorphic rate validation of the Axiom Sugarcane 100K SNP array.To evaluate the quality and utilization of the Axiom Sugarcane 100K SNP array,a total of 469 sugarcane clones were genotyped,including one interspecific crossing population(Green German × IND81-146),one selfing population(CP80-1827),and 11 diverse sugarcane accessions.The data analysis revealed a high polymorphic rate(77,113 SNPs,77.04%)among the 469 samples.The results demonstrated that the Axiom Sugarcane 100K SNP array is an efficient genotyping tool for sugarcane germplasms.3.Construction of high-density genetic maps using the Axiom Sugarcane 100K SNP array.Further,high-density linkage maps were constructed using SD SNPs that passed the Chi-squared test(P>0.01)in the segregating populations,including 1)3,514 SNPs(95.91%)spanning 3,336 cM in 150 linkage groups(LGs)for Green German(0.95 cM/marker),currently the highest density linkage map with the largest number of markers in sugarcane;2)1,518 SNPs spanning 2,615 cM in 92 LGs for IND81-146(1.72 cM/marker),currently the highest density linkage map with the largest number of markers in S.spontaneum;and 3)562 SNPs spanning 3,651 cM in 111 LGs for CP80-1827(6.5 cM/marker).The results of linkage map construction using different sugarcane germplasms proved the wide applicability and high efficiency of the SNP array,indicating that it has good application and promotion value.4.Identification of QTLs related with SCYLV resistance.Based on above constructed linkage maps,QTL analysis identified 1)a total of 17 QTLs controlling SCYLV resistance from Green German × IND81-146 population,including 10 major QTLs explaining 10.16?31.83%of the phenotypic variance;2)two QTLs from CP80-1827 population,including one major QTL explaining 11.2%of the phenotypic variance and one minor QTL explaining 7.84%of the phenotypic variance;and finally 3)identified 27 disease resistance genes in these 19 QTL regions associated with SCYLV resistance.In conlusion,to accelerate genetic and genomic research and facilitate development of markers associated with trait of interest in sugarcane,an Axiom Sugarcane100K single nucleotide polymorphism(SNP)array,which is high-throughput,high efficient,and easy-to-operate,has been designed and developed.This array was further utilized for construction of high-density genetic maps by analyzing an interspecific crossing population with two parental lines resistant and susceptible to Sugarcane yellow leaf virus(SCYLV),and a selfing population from a main cultivar in the United States,CP80-1827.This not only validated the quality and utility of the developed array,but also led to the genotyping of diverse sugarcane germplasms with different genetic backgrounds and identification of QTLs related with SCYLV resistance.This study demonstrated the successful development and utilization of a SNP array for highly polyploid sugarcane.It provides an efficient genotyping tool with high-density markers for sugarcane community.Its implementation will further facilitate genetic breeding in sugarcane. |
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