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ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa).
3 Biotech ( IF 2.8 ) Pub Date : 2020-07-27 , DOI: 10.1007/s13205-020-02291-5
Sathishkumar Natarajan 1 , Mohammad Rashed Hossain 1 , Hoy-Taek Kim 1 , Michael Immanuel Jesse Denison 1 , Mostari Jahan Ferdous 1 , Hee-Jeong Jung 1 , Jong-In Park 1 , Ill-Sup Nou 1
Affiliation  

Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F1 population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1723G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F1 plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.



中文翻译:

ddRAD-seq衍生了全基因组SNP,高密度连锁图谱和草莓(Fragaria x ananassa)果实品质性状的QTL。

了解遗传决定因素对于改善草莓的果实品质特性至关重要。在这项研究中,我们重点研究了通过使用全基因组范围内的单核苷酸多态性(SNP)鉴定出的果实长度(FL),-直径(FD),-重量(FW)和-可溶性固形物(SSC)的基因座。从Maehyang (♀)X Festival(♂)提出的F 1群体的ddRAD测序。共鉴定出12,698个高质量SNP,其中1554个SNP具有明显的孟德尔偏析(p <0.05)被映射到53个连锁组(LG),跨度总计2937.93 cM,平均标记密度为2.14 cM /基因座。确定了六个FL的QTL和FD,FW和SSC的四个QTL,分别解释了总表型变异的24–35%,21–42%,24–54%和23–50%。提取并彻底讨论了位于这些QTL区域内的基因。另外,基于UDP-葡萄糖4-表异构酶GEPI48样基因FAN_iscf00021287的SNP A1 723 G设计了高分辨率解链标记(MF154)。标记物检测到高糖含量和低糖含量的F 1植物和商业品种的检测准确度分别为81.39%和86.95%。这些SNP,连锁图谱,QTL和候选基因将有助于理解和改善草莓的果实品质性状。

更新日期:2020-07-27
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