| Grape is one of the oldest cultivated crop and most important commercial crops in the world.With the long-term cultivation and domestication,grape owns a high level genetic heterozygozity and there exist significant differences between different species and varieties of Vitis,and even within different cultivars.Understanding the genetic construct and characterizing the loci governing important agronomic traits of grapevine are of theoretical significance and practical value for genetic improvement and regulation of growth and development of grape.Genome wide association study(GWAS)was a most effective tool used to identify gene structure and the genetic loci controling quantitative traits,and now reduced representation sequencing makes the GWAS more widely used.In this study,290 grape germplasms were selected to the reduced representation sequencing,and the sequenced data was then processed for genetic evolution and GWAS analysis.The results are as follows:After DNA qualification,RsaⅠ+HaeⅢ enzyme digestion was performed to generate SLAF labels with the length in a range of 314-464bp,more analysis indicated that these labels were distributed evenly on the genome.The rice Control which was used to evaluate the accuracy of the sequencing libraries,sequencing was acquired 0.14M reads.The Control data of paired-end mapped reads was 87.99%,though aligning sequences with the reference of rice(Oryza sativa L.ssp.japonica)genome revealed that the efficiency of enzyme was 92.87%.These results can prove that the sequencing libraries was normal.A total of 636.82M reads data was obtained,average Q30 was 90.98%,the GC content was 39.08%according to the reduced representation sequencing in 290 grape varieties.A total of 435,905 high quality SLAF label was acquired in this study,and the sequencing depth was 8.09-fold for each sample.Polymorphism SLAF label was 337,849 and 4,240,892 SNPs were dentified from these SLAF-seq tags,then 506,336 SNPs were obtained according to the minor allele frequencies(MAF)>0.05.The average r2 for all chromosomes was estimated at 6.75 Kb.The phylogenetic tree showed that even different degrees of introgression were detected in V.vinifera L.and hybrids of V.vinifera L.×V.Labrusca L.,they were clearly distinguished.PCA showed that the vast majority of the V.vinifera L.and hybrids of V.vinifera L.× V.Labrusca L.can cluster together,respectively.The 290 genotypes were classified into approximately 15 divergent groups.Based on MLM model:the loci of flower’s sex was spanning from 4.8 to 5.0 Mb on Chr2;loci of seed numbers was spanning from 2.58 to 2.74 Mb on Chr18;loci of seed length was spanning between 1.59-1.63Mb and 2.58-29.3Mb on Chr18;in loci of veraison time,5,1,50,80,9,46,6,14,19,13,7,74,102,78,129,63,13,8,26 SNPs were located on chromosomes 1 to 19;in loci of berry ripenning data,13,10,16,80,6,38,10,11,2,15,9,14,9,15,3,1,10,15 SNPs were located on chromosomes 1 to 7 and 9 to 19;and loci of prostrate hairs density on the tip was in the physical interval positions between 0.61Mb-1.06Mb and 2.6Mb-2.78Mb on Chr5.Based on GLM model:the loci of the berry shape was spanning from 6.66 to 8.28 Mb on Chrl6;the loci of berry weight was spanning from 2.31 to 5.84 Mb on Chr11;loci of berry length was located on chromosomes 2,4,5,10,12,13,17,19;the loci of berry width were located on chromosomes 11,15,17,the loci of berry size were located on chromosomes 2,3,4,5,9,11,12,13,14,15,16,17,19;and the loci of scan for thickness of bloom were spanning from 14.06 to 16.10 Mb on Chr2. |
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